View source for FP curator comments for St.Louis and Sanger structure correction data type

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| align="center" style="background:#f0f0f0;"|'''WBPaperID'''
| align="center" style="background:#f0f0f0;"|'''Firstpass curator comment'''
| align="center" style="background:#f0f0f0;"|'''timestamp'''
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| 1951||sqt-1 and rol-6 untilizes different modes of splicing, see primer extension experiments in the article. ||2/2/02 21:01
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| 2050||cdNA for unc-51 was isolated and sequenced but accession number was not given. ||2/2/02 21:01
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| 2237||cDNA sequence for tmy-1. The accession number of the tmy-1 sequence in the GSDB, DDBJ, EMBL and NCBI is D38539. Those of cDNA clones are as follows; CeTMI, D38540; CeTMII, D38541; CeTMIII, D38542. ||2/2/02 21:01
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| 2619||MRP-1 cDNA: EMBL466260. EMBL MRP-2: 466261 ||2/2/02 21:01
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| 2779||probably since nhr-2 cDNA was isolated and sequenced, however the accession number for the cDNA was not found in the article. ||2/2/02 21:01
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| 2793||fft-1 has multiple transcripts. cDNA for fft-1, fft-2 were isolated and sequenced. Accession number not found in the article. ||2/2/02 21:01
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| 2800||pag-3 cDNA was sequenced, see GenBank #U63996. ||2/2/02 21:01
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| 2848||Probably, klp-3 cDNA was sequenced, however GenBank accession number was not found. ||2/2/02 21:01
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| pmid10753959 ||Check mPals-1 versus worm genomic DNA, and compare to C01B7.4 vs. worm genome: no grossly obvious discrepancies. ||2/2/02 21:01
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| med21154835 ||E04F6.11 ~ AF173172 ||2/2/02 21:01
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| 1812||cDNA of ost-1 was sequenced. GenBank: L21758 ||2/2/02 21:01
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| 2284||cDNA sequence for ubq-2 was mentioned but accession number was not found in the article. ||2/2/02 21:01
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| 2306||unc-119 cDNA: GenBank U32854 ||2/2/02 21:01
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| 2436||Probably, partial lin-7 cDNA was isolated and full-length cDNA was assembled, no accession number. ||2/2/02 21:01
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| 2462||Very possible, since vab-7 cDNA was sequenced, however the accession number was not found in the article. ||2/2/02 21:01
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| 2864||gsa-1 cDNA was sequenced. DDBJ accession number AB003486. Genomic sequenced of gsa-1 is AB003487 ||2/2/02 21:01
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| 3060||cDNA of pak-1 was isolated and sequenced, see GenBank accession number D83215 ||2/2/02 21:01
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| 3164||cDNA clones corresponding to cdc-25.1 = K06A5.7a cdc-25.2 = F16B4.8 cdc-25.3 = ZK637.11 have been sequenced. ||2/2/02 21:01
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| 3190||The cDNA sequence of mdl-1: GenBank U82968, mxl-1: GenBank U82967 ||2/2/02 21:01
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| 3205||Probably, however, details are not revealed in the article. Please check Genbank for the sequeneces, the accession number is not listed by the author either. Sequences can be found by searching for the gene names : cehd-3,4,5,7,8,9,13,15,17,20,22,28,39. ||2/2/02 21:01
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| 3292||Possible changes, since they isolated a cuc-1 cDNA, however, no Genbank accession number was found, neither did they map the gene to cosmids. ||2/2/02 21:01
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| 3338||deg-3 and des-2 are encoded in a singel C.elegans operon. cDNA of des-2 and deg-3 are isolated and sequenced, however, Genbank accession number was not found from this article.. ||2/2/02 21:01
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| 3361||The unc-97(su110) molecular lesion was identified by PCR amp lification of the F14D12.2 gene from unc-97(su110) mutant animals and subsequent DNA sequencing. BLAST searches identified unc-97 cDNAs in Y. Kohara\'sThe unc-97(su110) molecular lesion was identified by PCR amplification of the F14D12.2 gene from unc-97(su110) mutant an imals and subsequent DNA sequencing. BLAST searches identified unc-97 cDNAs in Y. Kohara\'s (Mishima, Japan) cDNA collection (yk460d6, yk457c11, yk455g5, yk457c10, yk403d5, yk267h9, yk114h11, yk184e5). yk184e5 was completely sequenced and found to encode a full-length cl one. The nucleotide and protein coding sequence have been submitted to GenBank/EMBL/ DDBJ under accession number AF035583. UNC-97 homolo gous proteins were identified using the BLAST search algorithm. The cDNA representing the Drosophila expressed sequence tag (EST) sequen ce was obtained from Genome Systems. The complete nucleotide and protein coding sequence for d-pinch have been submitted to GenBank/EMBL /DDBJ under accession number AF078907. Sequence alignments and dendograms were constructed using the pileup algorithm in the GCG softwar e package. ||2/2/02 21:01
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| 3382||Sequencing of the pos-1 cDNA yk61h1 (accession number AB006208) showed that the pos-1 mRNA is 1138 bases in length excluding the poly(A) tail. ||2/2/02 21:01
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| 3401||Sequenced cDNA for dbl-1. cDNA Genbank accession number: AF004395 ||2/2/02 21:01
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| 3510||wee-1.1 cDNA was sequenced and found to be identical to the Genefinder prediction. ||2/2/02 21:01
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| 3549||Result: the predicted gene lacks residues 509-590 of the actual CDS as determined from cDNA sequencing. ---------------------------------------------------------------------------- SWALL:Q9Y048 ID Q9Y048 PRELIMINARY; PRT; 590 AA. AC Q9Y048; DT 01-NOV-1999 (TrEMBLrel. 12, Created) DT 01-NOV-1999 (TrEMBLrel. 12, Last sequence update) DT 01-JUN-2000 (TrEMBLrel. 14, Last annotation update) DE MRNA FOR DYSTROBREVIN. OS Caenorhabditis elegans. OC Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; OC Rhabditidae; Peloderinae; Caenorhabditis. OX NCBI_TaxID=6239; RN [1] RP SEQUENCE FROM N.A. RA Gieseler K., Bessou C., Segalat L.; RT Dystrobrevin- and dystrophin-like mutants display similar phenotypes RT in the nematode C. elegans.; RL Submitted (DEC-1998) to the EMBL/GenBank/DDBJ databases. DR EMBL; AJ131742; CAA10498.1; -. DR InterPro; IPR000433; -. DR Pfam; PF00569; ZZ; 1. FT VARIANT 38 38 Q - *. SQ SEQUENCE 590 AA; 65426 MW; CA0ACD6D54AEBB2A CRC64; MLWSNGGGGP REPSSAPSPD HHRAMHSVPP IVASEMQQLI DEMRLQDFDS IRFATYRAAC KLRFIQQKTK VHLVDIWNMI EAFRENGLNA LPLHTVIKTS RAELLLTTVF HNLNKRLVAS QHVDTDVSIS LLLAFLLGAY DKQNTGRLTV FSIKVALATL CAGKLVDKLR YIFSQIADSN GLMDHIKFTD FLQQILSLTT AVFEAPTFGF SENAVNQCFH KDEKVSLNVF LDTFLSDPCP PCIMWLPLLH RMASVSNVYH PVVCDACQVR SFTGFRYKCQ RCANYQLCQS CFWRGRTSQN HSNEHEMKEY SSYKSPTKQL VHSIHKSLQC IPATSTVGDA NIDIFNAKIG GPVSSKPARP LNLNNIVPAT PTTIRRQHAA TSSADWPTSP VLLPGQASHG GVIDDEHKLI ARYAAKLSGR ADYPLSNGRS MNSSMVGDER TLIAQLEEEN SMMVREMARL ESQTTSDDGL AGLRDRKMEL EEKMFEMQQR RRELMMQLEH LMAQLNTGPQ PSGGVSSASL SQLPFTASDQ QLTGVNSTVA NAFRAGSLPA TSLQGDLLHA ADQITTNMSD LVRQLDLAQS DENGVTINGF // -------------------------------------------------------------------------------- Blast Server Results Low complexity filtering disabled Repeatmasker disabled BLASTP 2.0a13MP-WashU [10-Jun-1997] [Build 23:08:12 Jun 10 1997] Reference: Gish, Warren (1994-1997). unpublished. Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990). Basic local alignment search tool. J. Mol. Biol. 215:403-10. Query= AJ131742 (590 letters) Database: wormpub/wormpep_current 19,730 sequences; 8,603,921 total letters. Searching....10....20....30....40....50....60....70....80....90....100% done Smallest Sum High Probability Sequences producing High-scoring Segment Pairs: Score P(N) N F47G6.1 CE17838 locus:dyb-1 (ST.LOUIS) TR:Q9TZI6 prot... 2644 2.6e-276 1 F47G6.1 [Full Sequence] [AceBrowser] CE17838 locus:dyb-1 (ST.LOUIS) TR:Q9TZ I6 protein_id:AAC67445.1 Length = 513 Score = 2644 (930.7 bits), Expect = 2.6e-276, P = 2.6e-276 Identities = 507/508 (99%), Positives = 507/508 (99%) Query: 1 MLWSNGGGGPREPSSAPSPDHHRAMHSVPPIVASEMQQLIDEMRLQDFDSIRFATYRAAC 60 MLWSNGGGGPREPSSAPSPDHHRAMHSVPPIVASEMQQLIDEMRLQDFDSIRFATYRAAC Sbjct: 1 MLWSNGGGGPREPSSAPSPDHHRAMHSVPPIVASEMQQLIDEMRLQDFDSIRFATYRAAC 60 Query: 61 KLRFIQQKTKVHLVDIWNMIEAFRENGLNALPLHTVIKTSRAELLLTTVFHNLNKRLVAS 120 KLRFIQQKTKVHLVDIWNMIEAFRENGLNALPLHTVIKTSRAELLLTTVFHNLNKRLVAS Sbjct: 61 KLRFIQQKTKVHLVDIWNMIEAFRENGLNALPLHTVIKTSRAELLLTTVFHNLNKRLVAS 120 Query: 121 QHVDTDVSISLLLAFLLGAYDKQNTGRLTVFSIKVALATLCAGKLVDKLRYIFSQIADSN 180 QHVDTDVSISLLLAFLLGAYDKQNTGRLTVFSIKVALATLCAGKLVDKLRYIFSQIADSN Sbjct: 121 QHVDTDVSISLLLAFLLGAYDKQNTGRLTVFSIKVALATLCAGKLVDKLRYIFSQIADSN 180 Query: 181 GLMDHIKFTDFLQQILSLTTAVFEAPTFGFSENAVNQCFHKDEKVSLNVFLDTFLSDPCP 240 GLMDHIKFTDFLQQILSLTTAVFEAPTFGFSENAVNQCFHKDEKVSLNVFLDTFLSDPCP Sbjct: 181 GLMDHIKFTDFLQQILSLTTAVFEAPTFGFSENAVNQCFHKDEKVSLNVFLDTFLSDPCP 240 Query: 241 PCIMWLPLLHRMASVSNVYHPVVCDACQVRSFTGFRYKCQRCANYQLCQSCFWRGRTSQN 300 PCIMWLPLLHRMASVSNVYHPVVCDACQVRSFTGFRYKCQRCANYQLCQSCFWRGRTSQN Sbjct: 241 PCIMWLPLLHRMASVSNVYHPVVCDACQVRSFTGFRYKCQRCANYQLCQSCFWRGRTSQN 300 Query: 301 HSNEHEMKEYSSYKSPTKQLVHSIHKSLQCIPATSTVGDANIDIFNAKIGGPVSSKPARP 360 HSNEHEMKEYSSYKSPTKQLVHSIHKSLQCIPATSTVGDANIDIFNAKIGGPVSSKPARP Sbjct: 301 HSNEHEMKEYSSYKSPTKQLVHSIHKSLQCIPATSTVGDANIDIFNAKIGGPVSSKPARP 360 Query: 361 LNLNNIVPATPTTIRRQHAATSSADWPTSPVLLPGQASHGGVIDDEHKLIARYAAKLSGR 420 LNLNNIVPATPTTIRRQHAATSSADWPTSPVLLPGQASHGGVIDDEHKLIARYAAKLSGR Sbjct: 361 LNLNNIVPATPTTIRRQHAATSSADWPTSPVLLPGQASHGGVIDDEHKLIARYAAKLSGR 420 Query: 421 ADYPLSNGRSMNSSMVGDERTLIAQLEEENSMMVREMARLESQTTSDDGLAGLRDRKMEL 480 ADYPLSNGRSMNSSMVGDERTLIAQLEEENSMMVREMARLESQTTSDDGLAGLRDRKMEL Sbjct: 421 ADYPLSNGRSMNSSMVGDERTLIAQLEEENSMMVREMARLESQTTSDDGLAGLRDRKMEL 480 Query: 481 EEKMFEMQQRRRELMMQLEHLMAQLNTG 508 EEKMFEMQQRRRELMMQLEHLMAQLN G Sbjct: 481 EEKMFEMQQRRRELMMQLEHLMAQLNVG 508 -------------------------------------------------------------------------------- - ||2/2/02 21:01
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| 3578||Sequenced cDNA of egl-27. See the material and methods in the article. The start and stop positions of the egl-27 exons in cosmid C04A2 are as follows: exon 1 (2318-2462), exon 2 (2752-2870), exon 3 (3924-4064), exon 4 (5149-5274), exon 5 (5324-5388), exon 6 (7490-7652), exon 7 (7748-7927), exon 8 (7980 or 7989-8207), exon 9 (8782-9010), exon 10 (9707-9902), exon 11 (12659-13784), exon 12 (13828-14337) and exon 13 (14388-15203). multiple transcripts. ||2/2/02 21:01
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| 3717||The methionine codon that used for the grd-2 (F46B3.5) construct was very likely not the aythentic initiation codon. The new grd-2 gene product has an extra 78 amino acids in front of the methionine residue that we used for Met fusion construct. ||2/2/02 21:01
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| 3729||TR-PCR and sequencing proved Gene-Finder prediction of lin-42 was correct. ||2/2/02 21:01
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| 3938||cDNA of lin-49 (Genbank: AF163018) and lin-59 (Genbank: AF163019) were isolated. ||2/2/02 21:01
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| 4213||sos-1, T28F12.3, St. Louis sequence, paper shows 17 exons. ||17:58.3
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| 4215||PLK-1 cDNA is sequenced and published, accession number GenBank AF080581. ||2/2/02 21:01
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| 4381||Sequence correction K08A8.1 St. Louis, see fig.2; Wormbase shows eight exons, paper shows five. ||48:45.7
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| 4396||C40H1.1 (cpb-1) Sanger sequence, Wormbase shows six exons, paper shows seven. ||45:13.1
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| 4433||ida-1 structure, determined from cDNA, demonstrates the predicted B0244.2 structure to be incorrect. ------------------------------------------------------------------------ BLASTP 2.1.2 [Oct-19-2000] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= gi|5701822|emb|CAB52188.1| IDA-1 protein [Caenorhabditis elegans] note: this is the experimental CDS from Zahn et al. (767 letters) Database: wormpep41 19,742 sequences; 8,614,883 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B0244.2 CE20447 locus:ida-1 protein tyrosine phosphatase (S... 1446 0.0 C09D8.1 CE24794 locus:ptp-1 protein-tyrosine phosphatase wi... 115 1e-25 ... B0244.2 CE20447 locus:ida-1 protein tyrosine phosphatase (ST.LOUIS) Length = 721 Score = 1446 bits (3701), Expect = 0.0 Identities = 721/767 (94%), Positives = 721/767 (94%), Gaps = 46/767 (5%) Query: 1 MRFFHSIIVLLFSISTGSAFLLYGCNLSENLCDNDESCYPDGVFGQCYSSESGSPEPTVL 60 MRFFHSIIVLLFSISTGSAFLLYGCNLSENLCDNDESCYPDGVFGQCYSSESGSPEPTVL Sbjct: 1 MRFFHSIIVLLFSISTGSAFLLYGCNLSENLCDNDESCYPDGVFGQCYSSESGSPEPTVL 60 Query: 61 DNLDDTQLELLKLELTRLAAKDKDWGDEETQCVLAYFKMSMFYQLQYDPDFCQVRKPANV 120 DNLDDTQLELLKLELTRLAAKDKDWGDEETQCVLAYFKMSMFYQLQYDPDFCQVRKPANV Sbjct: 61 DNLDDTQLELLKLELTRLAAKDKDWGDEETQCVLAYFKMSMFYQLQYDPDFCQVRKPANV 120 Query: 121 WALIQLIDTGLTEDPTILDEDVNPENVTDEDMAQIIEQLKEPSLPTEEDIEEALNAQNED 180 WALIQLIDTGLTEDPTILDEDVNPENVTDEDMAQIIEQLKEPSLPTEEDIEEALNAQNED Sbjct: 121 WALIQLIDTGLTEDPTILDEDVNPENVTDEDMAQIIEQLKEPSLPTEEDIEEALNAQNED 180 Query: 181 VDDEILDQYVQAVVNNENPDFSELSDGQLNILIGRLVDLKKNVENEEAQLLTGDGEQEMA 240 VDDEILDQYVQAVVNNENPDFSELSD Sbjct: 181 VDDEILDQYVQAVVNNENPDFSELSD---------------------------------- 206 Query: 241 VPLDDLEERGEQAILKKDIEQVGEINQGLDNTEHKIVKGRKDQVVTRVDANRVYLKVHLK 300 AILKKDIEQVGEINQGLDNTEHKIVKGRKDQVVTRVDANRVYLKVHLK Sbjct: 207 ------------AILKKDIEQVGEINQGLDNTEHKIVKGRKDQVVTRVDANRVYLKVHLK 254 Query: 301 NEDQLMPLIEFLQNTIAIPNNLYFDDFQFENGQLSMRISRFEGAKPKADKRIDSVEGVAS 360 NEDQLMPLIEFLQNTIAIPNNLYFDDFQFENGQLSMRISRFEGAKPKADKRIDSVEGVAS Sbjct: 255 NEDQLMPLIEFLQNTIAIPNNLYFDDFQFENGQLSMRISRFEGAKPKADKRIDSVEGVAS 314 Query: 361 AVYKRRKDIARLSGADVRETGIGSGEDGSLPVESSERDWLLMPVLFVCAFTVTALGLVAA 420 AVYKRRKDIARLSGADVRETGIGSGEDGSLPVESSERDWLLMPVLFVCAFTVTALGLVAA Sbjct: 315 AVYKRRKDIARLSGADVRETGIGSGEDGSLPVESSERDWLLMPVLFVCAFTVTALGLVAA 374 Query: 421 VQIARSRRHYKDNIQQIAEQLDGKNSFAYQDLCRQRADGGRASKSSSTSSWCEETAVPTI 480 VQIARSRRHYKDNIQQIAEQLDGKNSFAYQDLCRQRADGGRASKSSSTSSWCEETAVPTI Sbjct: 375 VQIARSRRHYKDNIQQIAEQLDGKNSFAYQDLCRQRADGGRASKSSSTSSWCEETAVPTI 434 Query: 481 DISTGHVVLNFLQEYLSEPTKIEAQWNGIKDYRNEERTKTKAEKFASQNRTILPFDDNIV 540 DISTGHVVLNFLQEYLSEPTKIEAQWNGIKDYRNEERTKTKAEKFASQNRTILPFDDNIV Sbjct: 435 DISTGHVVLNFLQEYLSEPTKIEAQWNGIKDYRNEERTKTKAEKFASQNRTILPFDDNIV 494 Query: 541 DIDGKTAENEDFYLNASFIYDDDPRQAVYIAAQTPASSQIAAFWQTIWQHGVCLVVNLST 600 DIDGKTAENEDFYLNASFIYDDDPRQAVYIAAQTPASSQIAAFWQTIWQHGVCLVVNLST Sbjct: 495 DIDGKTAENEDFYLNASFIYDDDPRQAVYIAAQTPASSQIAAFWQTIWQHGVCLVVNLST 554 Query: 601 PEECKQEKNYWPDTGSEVHGAFEIHLVSEHIWSDDYLVRSFYLKNLQNSQTRTITQFHYL 660 PEECKQEKNYWPDTGSEVHGAFEIHLVSEHIWSDDYLVRSFYLKNLQNSQTRTITQFHYL Sbjct: 555 PEECKQEKNYWPDTGSEVHGAFEIHLVSEHIWSDDYLVRSFYLKNLQNSQTRTITQFHYL 614 Query: 661 SWQKESTPTSAKSILEFRRKVNKSYRGRSSAVLVHSWDGSGRTGVYCAVDVLCARLLRGI 720 SWQKESTPTSAKSILEFRRKVNKSYRGRSSAVLVHSWDGSGRTGVYCAVDVLCARLLRGI Sbjct: 615 SWQKESTPTSAKSILEFRRKVNKSYRGRSSAVLVHSWDGSGRTGVYCAVDVLCARLLRGI 674 Query: 721 RQIDVVATVEHLRDQRDGMVATGDQFKLVYGCVAQEVNHLLKSIATK 767 RQIDVVATVEHLRDQRDGMVATGDQFKLVYGCVAQEVNHLLKSIATK Sbjct: 675 RQIDVVATVEHLRDQRDGMVATGDQFKLVYGCVAQEVNHLLKSIATK 721 ------------------------------------------------------------------------ ||2/2/02 21:01
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| 4472||ceTFIIEalpha/ZK550.4 is OK as is. ceTFIIEbeta/F54D5.11 has a misprediction in Wormpep41. ------------------------------------------------------------------------------- BLASTP 2.1.2 [Oct-19-2000] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= gi|4584399|emb|CAA70050.2| TFIIE-alpha protein [Caenorhabditis elegans] (433 letters) Database: wormpep41 19,742 sequences; 8,614,883 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ZK550.4 CE16735 (HINXTON) TR:O62513 protein_id:CAB05314.1 871 0.0 W02D9.3 CE14458 high mobility group protein like (HINXTON)... 38 0.015 ... ZK550.4 CE16735 (HINXTON) TR:O62513 protein_id:CAB05314.1 Length = 433 Score = 871 bits (2226), Expect = 0.0 Identities = 433/433 (100%), Positives = 433/433 (100%) Query: 1 MSSGPATSGSSSAHTETQVVDEIPEALNTILLMVVKNFFSSEHFIIVYHIMRAQCIREEN 60 MSSGPATSGSSSAHTETQVVDEIPEALNTILLMVVKNFFSSEHFIIVYHIMRAQCIREEN Sbjct: 1 MSSGPATSGSSSAHTETQVVDEIPEALNTILLMVVKNFFSSEHFIIVYHIMRAQCIREEN 60 Query: 61 LKARIQFDQKMLRQLLASLKAEKLVKERTITQKNENNRTVSIIFYYINYRAVLNVVRYKI 120 LKARIQFDQKMLRQLLASLKAEKLVKERTITQKNENNRTVSIIFYYINYRAVLNVVRYKI Sbjct: 61 LKARIQFDQKMLRQLLASLKAEKLVKERTITQKNENNRTVSIIFYYINYRAVLNVVRYKI 120 Query: 121 DHMRQKLESREQMDTNRAHYRCGACQSSYDMLEINRILDAESGRLICWRCHGDVLADETV 180 DHMRQKLESREQMDTNRAHYRCGACQSSYDMLEINRILDAESGRLICWRCHGDVLADETV Sbjct: 121 DHMRQKLESREQMDTNRAHYRCGACQSSYDMLEINRILDAESGRLICWRCHGDVLADETV 180 Query: 181 VPSRTTRTAVARFNEQMTPLFSHICALNGIQLAPHLLEPDITKYLEDDKELQLQQQQMDF 240 VPSRTTRTAVARFNEQMTPLFSHICALNGIQLAPHLLEPDITKYLEDDKELQLQQQQMDF Sbjct: 181 VPSRTTRTAVARFNEQMTPLFSHICALNGIQLAPHLLEPDITKYLEDDKELQLQQQQMDF 240 Query: 241 TSGGGGGGRIQLGGVAHSYQNIASINYQNGDAVFVDLNADINKGPVEEAKIMPEWLKDNA 300 TSGGGGGGRIQLGGVAHSYQNIASINYQNGDAVFVDLNADINKGPVEEAKIMPEWLKDNA Sbjct: 241 TSGGGGGGRIQLGGVAHSYQNIASINYQNGDAVFVDLNADINKGPVEEAKIMPEWLKDNA 300 Query: 301 IGGGEASHNEHVLDQAKTEEEETSTKQRRYGPSLDYLKEIECSSEESAPNVKIEEPPAKQ 360 IGGGEASHNEHVLDQAKTEEEETSTKQRRYGPSLDYLKEIECSSEESAPNVKIEEPPAKQ Sbjct: 301 IGGGEASHNEHVLDQAKTEEEETSTKQRRYGPSLDYLKEIECSSEESAPNVKIEEPPAKQ 360 Query: 361 IKMEVDEEAIKMEVDNDESEEEDLIHVAGRALPLSQITPRMVENEMSELEKESYCSVVQD 420 IKMEVDEEAIKMEVDNDESEEEDLIHVAGRALPLSQITPRMVENEMSELEKESYCSVVQD Sbjct: 361 IKMEVDEEAIKMEVDNDESEEEDLIHVAGRALPLSQITPRMVENEMSELEKESYCSVVQD 420 Query: 421 LFAMFFSQQIAIH 433 LFAMFFSQQIAIH Sbjct: 421 LFAMFFSQQIAIH 433 ------------------------------------------------------------------------------- BLASTP 2.1.2 [Oct-19-2000] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= gi|1638825|emb|CAA70049.1| TFIIE-beta protein [Caenorhabditis elegans] (289 letters) Database: wormpep41 19,742 sequences; 8,614,883 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value F54D5.11 CE03415 transcription intiation factor TFIIE-BETA... 570 e-163 F59G1.5 CE02705 locus:ptp-2 PROTEIN-TYROSINE PHOSPHATASE (S... 34 0.079 ... F54D5.11 CE03415 transcription intiation factor TFIIE-BETA (HINXTON) TR:Q20776 protein_id:CAA91336.1 Length = 306 Score = 570 bits (1454), Expect = e-163 Identities = 289/306 (94%), Positives = 289/306 (94%), Gaps = 17/306 (5%) Query: 1 MDPELLRQRTAFQKHAATTMAVQNKPTTAPNSHTTYSSEAAKAKKKKSSGPAQNLSKLPD 60 MDPELLRQRTAFQKHAATTMAVQNKPTTAPNSHTTYSSEAAKAKKKKSSGPAQNLSKLPD Sbjct: 1 MDPELLRQRTAFQKHAATTMAVQNKPTTAPNSHTTYSSEAAKAKKKKSSGPAQNLSKLPD 60 Query: 61 FNNSVSNANALSNATNFSTMAKIVDYMKKRHLNNQQWPLTLQEILDELQIFDLSKRSLAF 120 FNNSVSNANALSNATNFSTMAKIVDYMKKRHLNNQQWPLTLQEILDELQIFDLSKRSLAF Sbjct: 61 FNNSVSNANALSNATNFSTMAKIVDYMKKRHLNNQQWPLTLQEILDELQIFDLSKRSLAF 120 Query: 121 LQEALPNNPRLIMESEKFAFRPPYKIKGKTSLVAVARKHYQDGKGGILVSDLAECVANYD 180 LQEALPNNPRLIMESEKFAFRPPYKIKGKTSLVAVARKHYQDGKGGILVSDLAECVANYD Sbjct: 121 LQEALPNNPRLIMESEKFAFRPPYKIKGKTSLVAVARKHYQDGKGGILVSDLAECVANYD 180 Query: 181 ALLQ-----------------QVSSEVIVVPTQVNKKKDRVVFYNDKEFTFPELEDDFKA 223 ALLQ QVSSEVIVVPTQVNKKKDRVVFYNDKEFTFPELEDDFKA Sbjct: 181 ALLQLKISKIDFKIISGLFFVQVSSEVIVVPTQVNKKKDRVVFYNDKEFTFPELEDDFKA 240 Query: 224 LWRHVSVDHLDEKKIEEYLQKKGLDAMKDLTPKVRMQAPLKRKAAKRRFNQKVQNEHMDG 283 LWRHVSVDHLDEKKIEEYLQKKGLDAMKDLTPKVRMQAPLKRKAAKRRFNQKVQNEHMDG Sbjct: 241 LWRHVSVDHLDEKKIEEYLQKKGLDAMKDLTPKVRMQAPLKRKAAKRRFNQKVQNEHMDG 300 Query: 284 VLEDYE 289 VLEDYE Sbjct: 301 VLEDYE 306 ------------------------------------------------------------------------------- ||2/2/02 21:01
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| 4498||Y48B6A.9: AF324059 (hot-7) prediction was altered from the previously predicted gene in the last exon ||2/2/02 21:01
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| 4508||See Table 1 in the article. There are corrections to the gene finder predictions. ||2/2/02 21:01
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| 4514||CeCNT3 peptide sequence is different from prediction by Gene Finder. The old CDS is stored at GenBank AF016413, the new CDS is stored at GenBank AF162674. ||2/2/02 21:01
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| 4527||Y54E10A.4 cf fog-1 transcripts EMBL database (Accession Nos. AJ2978469) ||2/2/02 21:01
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| 4536||Complete search for pseudogenes from Wormpep18. Contain large scale dataset for 2168 pseudogenes. see http://bioinfo.mbb.yale.edu/genome/worm/pseudogene ||2/2/02 21:01
|-
| 4567||(gene names not yet in acedb) GLR-4 (AF318608) ~ C06A8.9 NMR-2 (AF318614) ~ T01C3.10 ||2/2/02 21:01
|-
| 5230||Sanger sequence: f27e5.1 is mispredicted, figure 1 ||07:04.2
|-
| 4601||unc-32 has multiple splicing patterns. See the article for details. FIG. 3. The unc-32 gene encodes several isoforms of V-ATPase a sub-unit. The different unc-32 transcripts were determined by sequencing different cDNA clones and RT-PCR products, and the respective proteins are named as follows: UNC-32 AF contain, respectively, exons 4a/7b, 4b/7a, 4c/7b, 4a/7a, 4c/7a, and 4b/7b. Their GenBank accession numbers are, respectively, AF320899, AF320900, AF320901, AF320902, AF320903, and AF320904. Their predicted molecular masses, in kilodaltons, are, respectively, 103.4, 100.7, 102, 102.8, 101.3, and 101.1. Note that the different UNC-32 proteins differ from both predicted ZK637.8a and 8b proteins. A, UNC-32 A, F, and E protein sequences. Apart from the alternative exons (of variable size, hence marked with dashes), the sequences are identical and are not shown for the sake of clarity. Although the fourth exons are not similar, exons 7b and 7a in the variants F and E, respectively, are highly similar. Residues that are identical are black; those that are similar are gray. The vertical lines above the sequences mark the corresponding exon-intron boundaries. B, exon-intron structure of the six different alternative splice variants. The primers used for the RT-PCR presented in C are also shown. Alternative exons are gray. The relative abundances of different transcripts were evaluated after digestion of RT-PCR products made from mRNA from mixed stage wild-type worms and are shown as percentages. C, different patterns of mRNA splicing are revealed by RT-PCR in the unc-32 mutants, and their sequences are presented. Top panel, analysis of the e189 mutation. On the left, the amplicon containing the fourth exon was amplified with the primers 8.11 and 8.2 and digested with HaeIII. Transcripts containing exon 4a (970 bp) or 4c (937 bp) are not cut, whereas transcripts containing exon 4b are cut in three fragments (466, 407, and 49 bp; the 49-bp band is not visible in this image). The e189 mutation removes a HaeIII site, which is normally formed by the splicing of exon 3 to 4b, and results in the appearance of a larger band (arrow) and the loss of the 49-bp band (not shown). The band at 2375 bp results from direct PCR amplification of genomic DNA, shown in lane gwt. On the right are presented the sequences of both wild-type and e189 transcripts. The e189 mutation removes the exon 4b acceptor splicing site; a new acceptor splicing site, located 22 bp upstream of the normal one, is used, introducing a stop codon. Bottom panel, analysis of the f131 mutation. On the left, the amplicon including the seventh exon was amplified with primers 8.5 and 8.6. Transcripts containing exon 7a (983 bp) or 7b (1001 bp) are not resolved. The f131 mutation in the splice donor site of exon 6 provokes the apparition of a larger band (arrow). The band at 2465 bp results from direct PCR amplification of genomic DNA, shown in lane gwt. On the right are presented the sequences of both wild-type and f131 transcripts. The f131 mutation removes the exon 6 donor splicing site; therefore, intron 6 is not spliced out and fuses to exon 7a, resulting in the introduction of stop codons. The bottom band is a mixture of various transcripts using cryptic splice sites.pyrophosphokinase (24). The latter encodes a putative mito- chondrial thioredoxin reductase. ||2/2/02 21:01
|-
| 4603||probably, osm-5 cDNA was isolated and sequenced, but accession number not found in the article. ||2/2/02 21:01
|-
| 4607||cDNA for glc-3 was sequenced. EMBL AJ243914 ||2/2/02 21:01
|-
| 4608||cDNA of unc-78 is sequenced and ORF confirmed. GenBank AF324437 ||2/2/02 21:01
|-
| 4612||cDNA of atx-2 was isolated ans sequenced from yk63e6, yk460c11, however, accession numbers were not found from the article. ||2/2/02 21:01
|-
| 4615||The cle-1 gene structure was determined by analysis of cDNAs generated by the genome project and sequencing of reverse transcription (RT)PCR products generated from total C. elegans RNA. The cle-1 isoforms were first reported as three genes (C36B1.2, C36B1.1, and F39H11.4, in 5 to 3 order) available from GenBank/EMBL/DDBJ under accession numbers Z80215 and Z81079. The following cDNAs were examined: cm11a3 (Z14325), cm10e6 (M88890), yk96a11 (D75069, D72240), yk297a9 (C26933, C53322), yk12b4 (D27520), and yk238e4 (C61305, C52129). Se- quence analysis shows that yk238e4 is a full-length cle-1B cDNA and that cm11a3 is a full-length cle-1C cDNA containing an SL1 splice leader. All nucleotide numbering is based on cosmid F39H11 sequences annotated with cle-1 information (AF164959). ||2/2/02 21:01
|-
| 4616||sop-3(RNAi) suppressedThe predicted sop-3 ||2/2/02 21:01
|-
| 4617||Standard molecular techniques were used for cloning and sequencing (Ausubel et al., 1987; Sambrook et al., 1989). The cloning and sequencing of genomic ceh-6 has been described previously (Brglin et al., 1989). A cDNA for ceh-6 was generated using PCR with the primers PCR6-1 (CCCGGGATCCTCCATGGCCACCAGCTT, containing a BamHI site) and PCR6-2 (TTCGAAGCTTCTAT- TGTTGTCTCGGGCTCT, containing a HindIII site) from first strand cDNA. Several clones from an embryonic gt11 library were isolated with this cDNA probe. The sequence of the longest combined cDNA has been submitted to GenBank under Accession Number AF286377. ||2/2/02 21:01
|-
| 4619||based on this sequence. A sqv-7 cDNA 990 bases long that consists of only the sqv-7 predicted ORF was obtained by reverse transcriptasePCR using RNA isolated from a mixed- stage C. elegans population. To determine the 5 and 3 ends of the transcript, we performed 5 and 3 rapid amplification of cDNA ends (RACE) as described by the manufacturer (GIBCO BRL) using mixed-stage RNA as the template. The 5 RACE product contains a variant SL2 splice leader sequence, GGTTTTAACCCAGTTAACCAAG (29) and lacks a 5 untranslated region. The 3 RACE product contains 304 bases of 3 untranslated region. We used the 990 bases corresponding to the sqv-7 ORF to probe a Northern blot containing mixed-stage RNA and detected a single transcript of approximately 1,700 nt (data not shown). Accession number not found. ||2/2/02 21:01
|-
| 4620||cDNA of fat-1 was mentioned but accession number not found ||2/2/02 21:01
|-
| 4624||egl-44 and egl-46 cdna were isolated and sequenced, however,accession number were not found. ||2/2/02 21:01
|-
| 4627||The Caenorhabditis genome consortium had previously identified potential coding sequences in this region for two large protein fragments with tandem immunoglobulin repeats. By RT-PCR, we confirmed that these fragments come from a single mRNA, comprising 62 exons, 15,811 nucleotides in length plus a 22 nucleotide trans- spliced SL1 leader and a polyA tail. As predicted, a 43 kb SacI- SpeI fragment spanning this transcription unit, constructed by bacterial recombination, rescues him-4 mutants. ||2/2/02 21:01
|-
| 4630||For H1.1-H1.5, H1.Q and H1.X, a representative cDNA was sequenced to confirm the protein primary structures (GenBank Accession Numbers: AF017810, AF017811, AF012253, AF005371, AF005372, AF216291, AF002679 ||2/2/02 21:01
|-
| 4634||efl-1 predicted protein seq. was confirmed by cDNA sequencing, however, no accession number. ||2/2/02 21:01
|-
| 4635||cDNA for dpl-1, efl-1, efl-2 were isolated, however not given accession number.. ||2/2/02 21:01
|-
| 4638||While CKA-1 is identical to T03D8.1A in wormpep42, CKA-1S is identical to residues 45-593 of T03D8.1A. Note: cka-1 generates two proteins, CKA-1 and CKA-1S, through use of alternative initiation (methionine) codons in a single mRNA: CKA-1 initiates at Met-1 of the T03D8.1A CDS, while CKA-1S initiates at Met-45 of the T03D8.1A CDS. ||2/2/02 21:01
|-
| 4641||cDNA of aip-1 was cloned, but accession number not found in the article. ||2/2/02 21:01
|-
| 4647||figure 3 ||2/2/02 21:01
|-
| 4655||af338583 ||2/2/02 21:01
|-
| 4659||The authors write: ...a sequence of 63 bp is wrongly assigned by the Genefinder program to the putative exon 8 (303 bp). We found this sequence to be absent from both cDNA clones ... and hence the actual protein should correspondingly be 21 amino acids shorter. Actually, I find not one but two corrections, by doing BlastP with their PMR-1 CDS versus wormpep42. In addition to the excess exon seen by the authors (in wormpep42\'s ZK256.1A CDS), I also observe that the CDS ZK256.1B is seriously aberrant (since it is heavily truncated by comparison with the observed, highly conserved PMR-1 CDS). ************************************************************************ BLASTP 2.1.2 [Oct-19-2000] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= PMR-1 [from Medline 11134055] (901 letters) Database: wormpep42 19,746 sequences; 8,613,489 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ZK256.1A CE20425 E1-E2 ATPases (HINXTON) TR:Q9XTG4 protein... 1762 0.0 ZK256.1B CE20426 CALCIUM-TRANSPORTING ATPASE 1 (EC 3.6.1.3... 1369 0.0 ... ZK256.1A CE20425 E1-E2 ATPases (HINXTON) TR:Q9XTG4 protein_id:CAB04015.1 Length = 922 Score = 1762 bits (4514), Expect = 0.0 Identities = 900/922 (97%), Positives = 901/922 (97%), Gaps = 21/922 (2%) Query: 1 MIETLTSEQAASHEVVPCTHQLRTNLEEGLTTAEATRRRQYHGYNEFDVGEEEPIYKKYL 60 MIETLTSEQAASHEVVPCTHQLRTNLEEGLTTAEATRRRQYHGYNEFDVGEEEPIYKKYL Sbjct: 1 MIETLTSEQAASHEVVPCTHQLRTNLEEGLTTAEATRRRQYHGYNEFDVGEEEPIYKKYL 60 Query: 61 EQFQNPLILLLLASAFVSIVMKQYDDAISITVAVVIVVTVGFVQEYRSEKTLEQLTKLVP 120 EQFQNPLILLLLASAFVSIVMKQYDDAISITVAVVIVVTVGFVQEYRSEKTLEQLTKLVP Sbjct: 61 EQFQNPLILLLLASAFVSIVMKQYDDAISITVAVVIVVTVGFVQEYRSEKTLEQLTKLVP 120 Query: 121 PTCHVLRDGKEAMMLARELVPGDIVLLNTGDRIPSDLRIAESFSLQIDESSLTGETEPKH 180 PTCHVLRDGKEAMMLARELVPGDIVLLNTGDRIPSDLRIAESFSLQIDESSLTGETEPKH Sbjct: 121 PTCHVLRDGKEAMMLARELVPGDIVLLNTGDRIPSDLRIAESFSLQIDESSLTGETEPKH 180 Query: 181 KETRSVPAASATGSDVEHLTCIAFMGTLVCAGRGRGIVISTAANSQFGEVVKMMMGEESP 240 KETRSVPAASATGSDVEHLTCIAFMGTLVCAGRGRGIVISTAANSQFGEVVKMMMGEESP Sbjct: 181 KETRSVPAASATGSDVEHLTCIAFMGTLVCAGRGRGIVISTAANSQFGEVVKMMMGEESP 240 Query: 241 KTPLQKSMDDLGKQLSIYSFGVIAVIFLIGMFQGRNVVDMFTIGVSLAVAAIPEGLPIVV 300 KTPLQKSMDDLGKQLSIYSFGVIAVIFLIGMFQGRNVVDMFTIGVSLAVAAIPEGLPIVV Sbjct: 241 KTPLQKSMDDLGKQLSIYSFGVIAVIFLIGMFQGRNVVDMFTIGVSLAVAAIPEGLPIVV 300 Query: 301 AVTLAIGVMRMAKRRAVVKKMPAVETLGCVTVICSDKTGTLTKNEMTAQAIATPEGKLAE 360 AVTLAIGVMRMAKRRAVVKKMPAVETLGCVTVICSDKTGTLTKNEMTAQAIATPEGKLAE Sbjct: 301 AVTLAIGVMRMAKRRAVVKKMPAVETLGCVTVICSDKTGTLTKNEMTAQAIATPEGKLAE 360 Query: 361 ITGIGYSAEGGVVQYQGEQVHQWTHPEFARIIEAGLVCNNATIEADKLIGQPTEGAIVVL 420 ITGIGYSAEGGVVQYQGEQVHQWTHPEFARIIEAGLVCNNATIEADKLIGQPTEGAIVVL Sbjct: 361 ITGIGYSAEGGVVQYQGEQVHQWTHPEFARIIEAGLVCNNATIEADKLIGQPTEGAIVVL 420 Query: 421 AKKAQLEGVRSEYKRLREMPFSSDTKWMGVQCADAHGQNVYFIKGALDRVLDQCGTYYSS 480 AKKAQLEGVRSEYKRLREMPFSSDTKWMGVQCADAHGQNVYFIKGALDRVLDQCGTYYSS Sbjct: 421 AKKAQLEGVRSEYKRLREMPFSSDTKWMGVQCADAHGQNVYFIKGALDRVLDQCGTYYSS 480 Query: 481 DNQRKQCDQYSRQHILEIGKELGQKGLRVLGLARGESMQSLMFLGMIGMMDPPRPGAADA 540 DNQRKQCDQYSRQHILEIGKELGQKGLRVLGLARGESMQSLMFLGMIGMMDPPRPGAADA Sbjct: 481 DNQRKQCDQYSRQHILEIGKELGQKGLRVLGLARGESMQSLMFLGMIGMMDPPRPGAADA 540 Query: 541 ISIVKASGVDVKLITGDAMETAQSIGQSLGILSSSDSCLSGQQVDQMSDHDLELVIRQVT 600 ISIVKASGVDVKLITGDAMETAQSIGQSLGILSSSDSCLSGQQVDQMSDHDLELVIRQVT Sbjct: 541 ISIVKASGVDVKLITGDAMETAQSIGQSLGILSSSDSCLSGQQVDQMSDHDLELVIRQVT 600 Query: 601 VFYRASPRHKLKIVKALQALGEVVAMTGDGVNDAVALKKADIGVAMGVCGTDVCKEAADM 660 VFYRASPRHKLKIVKALQALGEVVAMTGDGVNDAVALKKADIGVAMGVCGTDVCKEAADM Sbjct: 601 VFYRASPRHKLKIVKALQALGEVVAMTGDGVNDAVALKKADIGVAMGVCGTDVCKEAADM 660 Query: 661 ILCDDDFSTMTAAIEEGKAIYHNITNFVRFQLSTSVAALSLIAASTMFKFDNPLNAMQIL 720 ILCDDDFSTMTAAIEEGKAIYHNITNFVRFQLSTSVAALSLIAASTMFKFDNPLNAMQIL Sbjct: 661 ILCDDDFSTMTAAIEEGKAIYHNITNFVRFQLSTSVAALSLIAASTMFKFDNPLNAMQIL 720 Query: 721 WINIIMDGPPAQSLGVEPVDDDIIRQRPRNTKQPMLTGKLIADILASAAIIVVGTLSVFY 780 WINIIMDGPPAQSLGVEPVDDDIIRQRPRNTKQPMLTGKLIADILASAAIIVVGTLSVFY Sbjct: 721 WINIIMDGPPAQSLGVEPVDDDIIRQRPRNTKQPMLTGKLIADILASAAIIVVGTLSVFY 780 Query: 781 KEMSADNKVTPRDTTMTFTCFVLFDMWNALSCRSSRKMIWQIGLRRNRMFSLAVSASLIC 840 KEMSADNKVTPRDTTMTFTCFVLFDMWNALSCRSSRKMIWQIGLRRNRMFSLAVSASLIC Sbjct: 781 KEMSADNKVTPRDTTMTFTCFVLFDMWNALSCRSSRKMIWQIGLRRNRMFSLAVSASLIC 840 Query: 841 QLLVIYWAPLQHIFQTEALSLF---------------------DLIFLTTITSSVFIFNE 879 QLLVIYWAPLQHIFQTEALSLF +LIFLTTITSSVFIFNE Sbjct: 841 QLLVIYWAPLQHIFQTEALSLFGTEIVENALIFELNLKKVLNSNLIFLTTITSSVFIFNE 900 Query: 880 TRKYFSLRSKSLNHDPLSVSGI 901 TRKYFSLRSKSLNHDPLSVSGI Sbjct: 901 TRKYFSLRSKSLNHDPLSVSGI 922 ZK256.1B CE20426 CALCIUM-TRANSPORTING ATPASE 1 (EC 3.6.1.38) (GOLGI CA2+-ATPASE) (HINXTON) TR:Q9XTG4 protein_id:CAB04016.1 Length = 705 Score = 1369 bits (3505), Expect = 0.0 Identities = 694/696 (99%), Positives = 695/696 (99%) Query: 1 MIETLTSEQAASHEVVPCTHQLRTNLEEGLTTAEATRRRQYHGYNEFDVGEEEPIYKKYL 60 MIETLTSEQAASHEVVPCTHQLRTNLEEGLTTAEATRRRQYHGYNEFDVGEEEPIYKKYL Sbjct: 1 MIETLTSEQAASHEVVPCTHQLRTNLEEGLTTAEATRRRQYHGYNEFDVGEEEPIYKKYL 60 Query: 61 EQFQNPLILLLLASAFVSIVMKQYDDAISITVAVVIVVTVGFVQEYRSEKTLEQLTKLVP 120 EQFQNPLILLLLASAFVSIVMKQYDDAISITVAVVIVVTVGFVQEYRSEKTLEQLTKLVP Sbjct: 61 EQFQNPLILLLLASAFVSIVMKQYDDAISITVAVVIVVTVGFVQEYRSEKTLEQLTKLVP 120 Query: 121 PTCHVLRDGKEAMMLARELVPGDIVLLNTGDRIPSDLRIAESFSLQIDESSLTGETEPKH 180 PTCHVLRDGKEAMMLARELVPGDIVLLNTGDRIPSDLRIAESFSLQIDESSLTGETEPKH Sbjct: 121 PTCHVLRDGKEAMMLARELVPGDIVLLNTGDRIPSDLRIAESFSLQIDESSLTGETEPKH 180 Query: 181 KETRSVPAASATGSDVEHLTCIAFMGTLVCAGRGRGIVISTAANSQFGEVVKMMMGEESP 240 KETRSVPAASATGSDVEHLTCIAFMGTLVCAGRGRGIVISTAANSQFGEVVKMMMGEESP Sbjct: 181 KETRSVPAASATGSDVEHLTCIAFMGTLVCAGRGRGIVISTAANSQFGEVVKMMMGEESP 240 Query: 241 KTPLQKSMDDLGKQLSIYSFGVIAVIFLIGMFQGRNVVDMFTIGVSLAVAAIPEGLPIVV 300 KTPLQKSMDDLGKQLSIYSFGVIAVIFLIGMFQGRNVVDMFTIGVSLAVAAIPEGLPIVV Sbjct: 241 KTPLQKSMDDLGKQLSIYSFGVIAVIFLIGMFQGRNVVDMFTIGVSLAVAAIPEGLPIVV 300 Query: 301 AVTLAIGVMRMAKRRAVVKKMPAVETLGCVTVICSDKTGTLTKNEMTAQAIATPEGKLAE 360 AVTLAIGVMRMAKRRAVVKKMPAVETLGCVTVICSDKTGTLTKNEMTAQAIATPEGKLAE Sbjct: 301 AVTLAIGVMRMAKRRAVVKKMPAVETLGCVTVICSDKTGTLTKNEMTAQAIATPEGKLAE 360 Query: 361 ITGIGYSAEGGVVQYQGEQVHQWTHPEFARIIEAGLVCNNATIEADKLIGQPTEGAIVVL 420 ITGIGYSAEGGVVQYQGEQVHQWTHPEFARIIEAGLVCNNATIEADKLIGQPTEGAIVVL Sbjct: 361 ITGIGYSAEGGVVQYQGEQVHQWTHPEFARIIEAGLVCNNATIEADKLIGQPTEGAIVVL 420 Query: 421 AKKAQLEGVRSEYKRLREMPFSSDTKWMGVQCADAHGQNVYFIKGALDRVLDQCGTYYSS 480 AKKAQLEGVRSEYKRLREMPFSSDTKWMGVQCADAHGQNVYFIKGALDRVLDQCGTYYSS Sbjct: 421 AKKAQLEGVRSEYKRLREMPFSSDTKWMGVQCADAHGQNVYFIKGALDRVLDQCGTYYSS 480 Query: 481 DNQRKQCDQYSRQHILEIGKELGQKGLRVLGLARGESMQSLMFLGMIGMMDPPRPGAADA 540 DNQRKQCDQYSRQHILEIGKELGQKGLRVLGLARGESMQSLMFLGMIGMMDPPRPGAADA Sbjct: 481 DNQRKQCDQYSRQHILEIGKELGQKGLRVLGLARGESMQSLMFLGMIGMMDPPRPGAADA 540 Query: 541 ISIVKASGVDVKLITGDAMETAQSIGQSLGILSSSDSCLSGQQVDQMSDHDLELVIRQVT 600 ISIVKASGVDVKLITGDAMETAQSIGQSLGILSSSDSCLSGQQVDQMSDHDLELVIRQVT Sbjct: 541 ISIVKASGVDVKLITGDAMETAQSIGQSLGILSSSDSCLSGQQVDQMSDHDLELVIRQVT 600 Query: 601 VFYRASPRHKLKIVKALQALGEVVAMTGDGVNDAVALKKADIGVAMGVCGTDVCKEAADM 660 VFYRASPRHKLKIVKALQALGEVVAMTGDGVNDAVALKKADIGVAMGVCGTDVCKEAADM Sbjct: 601 VFYRASPRHKLKIVKALQALGEVVAMTGDGVNDAVALKKADIGVAMGVCGTDVCKEAADM 660 Query: 661 ILCDDDFSTMTAAIEEGKAIYHNITNFVRFQLSTSV 696 ILCDDDFSTMTAAIEEGKAIYHNITNFVRFQLST + Sbjct: 661 ILCDDDFSTMTAAIEEGKAIYHNITNFVRFQLSTKL 696 ************************************************************************ ||2/2/02 21:01
|-
| 4692||tol-1 (AF348166) ~= C07F11.1 + W05D2.1 pik-1 (AF348167) ~= K0911.1 one exon missing trf-1 (AF348168) ~= F45G2.6 one extra exon ||2/2/02 21:01
|-
| 4711||importin alpha 3 ima-3 ~= F32E10.4 first 146 aa in prediction has no supporting data ||2/2/02 21:01
|-
| 4743||cps-6 (AF390558) ~= C41D11.8 (the first 3 predicted exons are erroneous)\" ||2/2/02 21:01
|-
| 4762||AF364604 ~ F37A6.3(a,b) AF370362 ~ T01D3.2 AF370361 ~ C15C8.2\" ||2/2/02 21:01
|-
| 4805||F09E10.11a is shown as a gene encoding 8 aa. should be shown as a non-coding gene named tts-1 as speculated in the paper ||2/2/02 21:01
|-
| 4808||R01H10.3 is gives rise to 5 alternatively spliced transcripts ||2/2/02 21:01
|-
| 4810||as reported rme-8 contains 23 exons (the alternative form contains 24), while f18c12.2a and 2b contain 24 and 25 exons respectively ||2/2/02 21:01
|-
| 4813||atp-2 ~C34E10.6 (first exon is not found in sequenced transcript, or in any known EST) ||2/2/02 21:01
|-
| 4833||Sequence analysis of elt-5 and -6 cDNAs and determination of the 5 end of elt-6 cDNA The elt-5 and -6 cDNA sequences were determined by sequencing EST clones yk474 and yk113, respectively. (yk clones were generous gifts from Y. Kohara.) These sequences differ in several respects from the Worm Genome Consortium\'s predictions for the corresponding open reading frames (ORFs) F55A8.1 and F52C12.5 (C. elegans Sequencing Consortium, 1998). Most notably, the predicted ORF F55A8.1 does not include the last intron (3) and exon (4) of the elt- 5 cDNA, and the predicted ORF F52C12.1 does not include exons 1 and 2, and introns 1 and 2 of the elt-6 cDNA. The elt-5 and -6 cDNA sequences have been reported to GenBank (Accession Numbers AF353302 and AF353303, respectively). ||2/2/02 21:01
|-
| 4835||genbank ab054992 ||2/2/02 21:01
|-
| 4836||quote from the paper: The cDNA sequence differs from that predicted by GENEFINDER analysis of F07F6 (Wilson et al., 1994). This refers to the gene structure of nmr-1. Genomic organization of nmr-1 is shown in fig. 3. as there is no genbank entry for full-length nmr-1 it is hard to tell what are the differences and if they had been fixed by now. ||2/2/02 21:01
|-
| 4840||alternative transcript for lad-1, c18f3.2 (figure 1) ||2/2/02 21:01
|-
| 4858||size discrepancy between the wtp and the reported transcript (genbank X59589) ||2/2/02 21:01
|-
| 4884||AY052773, AY052771 ||2/2/02 21:01
|-
| 4889||two alternative transcripts for jnk-1 (figure 1) ||2/2/02 21:01
|-
| 4891||AF257062 ||2/2/02 21:01
|-
| 4915||The B0412.5 coding sequence is complement(join(975..1226,4487..4579)) on cosmid B0412 (gi|1750400, Genbank accession number U80953.1). But Craxton detects a synaptotagmin homology in nucleotides complement(584..706) of the same cosmid -- just downstream of B0412.5. This suggests that a gene model correction may be necessary? ||2/2/02 21:01
|-
| 4944||alternative transcripts CeTM I through IV from figure 2 are not shown in acedb ||2/2/02 21:01
|-
| 4961||c25a11.4 has five splicing variants (figure 1) ||2/2/02 21:01
|-
| 5000||three splice variants for gar-2 shown in figure 1. FIG. 1. (Top) Exon/intron arrangement of the three gar-2 splice variants. Boxes represent exons and lines represent introns. Exons involved in alternative splicing are indicated by gray boxes. The positions of putative transmembrane domains (IVII) are indicated. The first and fifth introns are unusually long (;4.6 and ;2.3 kb, respectively). SL1, spliced leader 1; ATG, translation initiation codon; TGA, translation termination codon. (Bottom) The sequences of the alternatively spliced exons and their flanking regions. The uppercase and lowercase letters denote exon and intron sequences of gar-2a, respectively. The 59 splice donor and 39 splice acceptor sequences are underlined, while the alternatively used 59 splice donor and 39 splice acceptor sequences within the 10th exon of gar-2a are shaded. The primers (AF4 and AR3) used for the RT-PCR analysis of the gar-2 splice variants (see Fig. 2) are indicated by arrows. The nucleotide sequences of gar-2a, gar-2b, and gar-2c have been submitted to GenBank under Accession Nos. AY053364, AY053365, and AF272738, respectively. ||5/4/02 16:22
|-
| 5015||From_Laboratory HX. alternative splicing AF431893, AF431892, AF431891 ||26/2/02 19:48
|-
| 5031||hmr-1b transcript is derived from three predicted genes ZK39.1, Y52B11B.2, and W02B9.1 ||21/2/02 17:44
|-
| 5032||C33D9.1 should contain 16 exons and is ulternatively spliced (AF339059, AF326352)) ||45:19.0
|-
| 5054||RW clone. t13c5.1 is alternatively spliced ||25/2/02 14:56
|-
| 5097||three splice variants. The cDNA sequences of the cloned receptors were roughly identical to the predicted sequence, but some differences were observed and the first exon and some exonintron junctions were not predicted correctly. An extra exon was inserted in CeDOP1L and alternative splicing to generate a shorter exon 8 was observed in CeDOP1S as compared with CeDOP1M (Fig. 1A). ||14/2/02 17:52
|-
| 5148||SAanger seq. C02F4.2 (figure 2b) alternative transcript ||30:27.6
|-
| 5169||St. Louis Sequence The feh-1 gene structure derived from our analysis differs slightly from the predicted coding sequence Y54F10AM.2, which is available through WormBase (genetic map position: III:-14.02). In fact, both by sequence analysis of yk423e6 cDNA clone and by RT-PCR analysis (data not shown), we have not been able to detect in the feh-1 transcript any sequence corresponding to that of the exon V, predicted in the Y54F10AM.2 sequence. In addition, the small predicted exon X is contained in a larger exon (IX in the actual gene), which is the last exon of the gene, as it contains the translation stop codon (Fig. 3A). ||26:19.0
|}


[[Category:Curation]]