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cdskit parsegb
Kenji Fukushima edited this page Mar 10, 2023
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4 revisions
cdskit parsegb converts a GenBank-formatted file with the sequence name formatting.
cdskit parsegb -s input.gb -o output.fasta
LOCUS NM_001080339 906 bp mRNA linear MAM 11-OCT-2020
DEFINITION Bos taurus lysozyme (renal amyloidosis) (LYZ1), mRNA.
ACCESSION NM_001080339 XM_001249625
VERSION NM_001080339.1
KEYWORDS RefSeq.
SOURCE Bos taurus (cattle)
ORGANISM Bos taurus
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Ruminantia;
Pecora; Bovidae; Bovinae; Bos.
REFERENCE 1 (bases 1 to 906)
AUTHORS Nonaka Y, Akieda D, Aizawa T, Watanabe N, Kamiya M, Kumaki Y,
Mizuguchi M, Kikukawa T, Demura M and Kawano K.
TITLE X-ray crystallography and structural stability of digestive
lysozyme from cow stomach
JOURNAL FEBS J 276 (8), 2192-2200 (2009)
PUBMED 19348005
REMARK GeneRIF: In this investigation, we obtained the crystallographic
structure of recombinant bovine stomach lysozyme 2 (BSL2).
REFERENCE 2 (bases 1 to 906)
AUTHORS Irwin DM, White RT and Wilson AC.
TITLE Characterization of the cow stomach lysozyme genes: repetitive DNA
and concerted evolution
JOURNAL J Mol Evol 37 (4), 355-366 (1993)
PUBMED 8308905
REFERENCE 3 (bases 1 to 906)
AUTHORS Irwin DM and Wilson AC.
TITLE Multiple cDNA sequences and the evolution of bovine stomach
lysozyme
JOURNAL J Biol Chem 264 (19), 11387-11393 (1989)
PUBMED 2738070
COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final
NCBI review. The reference sequence was derived from M26245.1.
On Jan 16, 2007 this sequence version replaced XM_001249625.1.
##Evidence-Data-START##
Transcript exon combination :: M26245.1, CK975923.1 [ECO:0000332]
RNAseq introns :: single sample supports all introns
SAMN03145435, SAMN03145498
[ECO:0000348]
##Evidence-Data-END##
FEATURES Location/Qualifiers
source 1..906
/organism="Bos taurus"
/mol_type="mRNA"
/db_xref="taxon:9913"
/chromosome="5"
/map="5"
gene 1..906
/gene="LYZ1"
/gene_synonym="LYSOZYME; LYZ"
/note="lysozyme (renal amyloidosis)"
/db_xref="BGD:BT11901"
/db_xref="GeneID:781349"
exon 1..158
/gene="LYZ1"
/gene_synonym="LYSOZYME; LYZ"
/inference="alignment:Splign:2.1.0"
CDS 23..466
/gene="LYZ1"
/gene_synonym="LYSOZYME; LYZ"
/EC_number="3.2.1.17"
/note="1,4-beta-N-acetylmuramidase C; lysozyme C-1"
/codon_start=1
/product="lysozyme C-1 precursor"
/protein_id="NP_001073808.1"
/db_xref="BGD:BT11901"
/db_xref="GeneID:781349"
/translation="MKALIILGFLFLSVAVQGKVFERCELARTLKKLGLDGYKGVSLA
NWLCLTKWESSYNTKATNYNPGSESTDYGIFQINSKWWCNDGKTPNAVDGCHVSCSEL
MENEIAKAVACAKQIVSEQGITAWVAWKSHCRDHDVSSYVEGCTL"
sig_peptide 23..76
/gene="LYZ1"
/gene_synonym="LYSOZYME; LYZ"
/inference="COORDINATES: ab initio prediction:SignalP:4.0"
mat_peptide 77..463
/gene="LYZ1"
/gene_synonym="LYSOZYME; LYZ"
/product="lysozyme C-1"
exon 159..323
/gene="LYZ1"
/gene_synonym="LYSOZYME; LYZ"
/inference="alignment:Splign:2.1.0"
exon 324..399
/gene="LYZ1"
/gene_synonym="LYSOZYME; LYZ"
/inference="alignment:Splign:2.1.0"
exon 400..906
/gene="LYZ1"
/gene_synonym="LYSOZYME; LYZ"
/inference="alignment:Splign:2.1.0"
ORIGIN
1 gacatttgac ttctcagtca acatgaaggc tctcattatt ctggggtttc tcttcctttc
61 tgttgctgtc cagggcaagg tctttgagag atgtgagctt gccagaactc tgaagaaact
121 tggactggat ggctataagg gagtcagtct ggcaaactgg ctgtgtttga ccaaatggga
181 aagcagttat aacacaaaag ctacaaacta caatcctggc agtgaaagca ctgattatgg
241 gatatttcag atcaacagca aatggtggtg taatgatggc aaaaccccca acgcagttga
301 cggctgtcat gtatcctgca gcgaattaat ggaaaatgag atcgcgaaag ctgtagcgtg
361 tgccaagcag attgtcagtg agcaaggcat tacagcatgg gtggcatgga aaagtcactg
421 tcgagaccat gacgtcagca gttatgttga gggttgcacg ctgtaactgt ggagttatca
481 ttcttcagct cattttgtct ctttttcacg ttaaggaagt aatagttgaa tgaaagctta
541 taccaccatt ccttcaagca aacaatggtt ttacagaagc aggagcatat ggtcttctaa
601 gaagcttaat gtttatctaa tgtgttaatt atttgacact aggcctataa tatttttcag
661 tttgctagta aaactaatgc tggtgaatat ttgtctaaat tcttaattat ctaatatatc
721 tccagtatat tcagttctta attaaagcaa gaacatttat gcaccttgct gatcatgaag
781 gaatataaag agggattaga tgaactgttg ctttttctta atttcattag cattatgaca
841 aattcagaga cagatgagtc tgcaactatt gaaattaatt gctggttaac cacagatatg
901 aaatga
//
LOCUS NM_001285711 447 bp mRNA linear MAM 30-JUN-2020
DEFINITION Capra hircus serum lysozyme (S-LZ), mRNA.
ACCESSION NM_001285711 XM_005680194
VERSION NM_001285711.1
KEYWORDS RefSeq.
SOURCE Capra hircus (goat)
ORGANISM Capra hircus
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Ruminantia;
Pecora; Bovidae; Caprinae; Capra.
COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final
NCBI review. The reference sequence was derived from GQ903681.1.
On Oct 22, 2013 this sequence version replaced XM_005680194.1.
##Evidence-Data-START##
Transcript exon combination :: GQ889414.1, GQ903681.1 [ECO:0000332]
RNAseq introns :: single sample supports all introns
SAMN05462052, SAMN05462053
[ECO:0000348]
##Evidence-Data-END##
FEATURES Location/Qualifiers
source 1..447
/organism="Capra hircus"
/mol_type="mRNA"
/db_xref="taxon:9925"
/chromosome="5"
/map="5"
gene 1..447
/gene="S-LZ"
/gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
/note="serum lysozyme"
/db_xref="GeneID:100860864"
CDS 1..447
/gene="S-LZ"
/gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
/codon_start=1
/product="serum lysozyme precursor"
/protein_id="NP_001272640.1"
/db_xref="GeneID:100860864"
/translation="MKALIILGLLLLSVAVQGKVFERCELARTLKRFGMDGFRGISLA
NWMCLARWESSYNTQATNYNSGDRSTDYGIFQINSHWWCNDGKTPGAVNACHIPCSAL
LQDDITQAVACAKRVVSDPQGIRAWVAWRSHCQNQDLTSYIQGCGV"
sig_peptide 1..54
/gene="S-LZ"
/gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
/inference="COORDINATES: ab initio prediction:SignalP:4.0"
exon 1..136
/gene="S-LZ"
/gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
/inference="alignment:Splign:2.0.8"
exon 137..301
/gene="S-LZ"
/gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
/inference="alignment:Splign:2.0.8"
exon 302..380
/gene="S-LZ"
/gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
/inference="alignment:Splign:2.0.8"
exon 381..447
/gene="S-LZ"
/gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
/inference="alignment:Splign:2.0.8"
ORIGIN
1 atgaaggctc tcattattct ggggcttctc ctcctttcgg tcgctgtcca aggcaaggtc
61 tttgagagat gtgagcttgc cagaactctg aaaagatttg gaatggatgg ctttagggga
121 atcagcctgg caaactggat gtgtttggcc agatgggaaa gcagttataa cacacaagct
181 acaaactaca atagtggaga cagaagcact gattatggga tatttcaaat caatagccac
241 tggtggtgta atgatggcaa aaccccagga gcagttaatg cctgtcacat accctgcagc
301 gctttgctgc aagatgacat cactcaagct gtagcatgtg caaagagggt tgtcagtgat
361 ccacaaggca ttagagcatg ggtggcatgg agaagtcatt gtcaaaacca agatctcacc
421 agttacattc agggttgtgg agtgtaa
//
>Bos_taurus_NM_001080339
ATGAAGGCTCTCATTATTCTGGGGTTTCTCTTCCTTTCTGTTGCTGTCCAGGGCAAGGTC
TTTGAGAGATGTGAGCTTGCCAGAACTCTGAAGAAACTTGGACTGGATGGCTATAAGGGA
GTCAGTCTGGCAAACTGGCTGTGTTTGACCAAATGGGAAAGCAGTTATAACACAAAAGCT
ACAAACTACAATCCTGGCAGTGAAAGCACTGATTATGGGATATTTCAGATCAACAGCAAA
TGGTGGTGTAATGATGGCAAAACCCCCAACGCAGTTGACGGCTGTCATGTATCCTGCAGC
GAATTAATGGAAAATGAGATCGCGAAAGCTGTAGCGTGTGCCAAGCAGATTGTCAGTGAG
CAAGGCATTACAGCATGGGTGGCATGGAAAAGTCACTGTCGAGACCATGACGTCAGCAGT
TATGTTGAGGGTTGCACGCTGTAA
>Capra_hircus_NM_001285711
ATGAAGGCTCTCATTATTCTGGGGCTTCTCCTCCTTTCGGTCGCTGTCCAAGGCAAGGTC
TTTGAGAGATGTGAGCTTGCCAGAACTCTGAAAAGATTTGGAATGGATGGCTTTAGGGGA
ATCAGCCTGGCAAACTGGATGTGTTTGGCCAGATGGGAAAGCAGTTATAACACACAAGCT
ACAAACTACAATAGTGGAGACAGAAGCACTGATTATGGGATATTTCAAATCAATAGCCAC
TGGTGGTGTAATGATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCACATACCCTGCAGC
GCTTTGCTGCAAGATGACATCACTCAAGCTGTAGCATGTGCAAAGAGGGTTGTCAGTGAT
CCACAAGGCATTAGAGCATGGGTGGCATGGAGAAGTCATTGTCAAAACCAAGATCTCACC
AGTTACATTCAGGGTTGTGGAGTGTAA