2024-04-18 04:40:38, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS NM_001398309 880 bp mRNA linear VRT 23-SEP-2023 DEFINITION Gallus gallus homeobox A6 (HOXA6), transcript variant 2, mRNA. ACCESSION NM_001398309 VERSION NM_001398309.1 KEYWORDS RefSeq. SOURCE Gallus gallus (chicken) ORGANISM Gallus gallus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae; Phasianinae; Gallus. REFERENCE 1 (bases 1 to 880) AUTHORS Tang H, Finn RD and Thomas PD. TITLE TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations JOURNAL Bioinformatics 35 (3), 518-520 (2019) PUBMED 30032202 REFERENCE 2 (bases 1 to 880) AUTHORS Attia L, Yelin R and Schultheiss TM. TITLE Analysis of nephric duct specification in the avian embryo JOURNAL Development 139 (22), 4143-4151 (2012) PUBMED 23034630 REMARK GeneRIF: In the primitive streak, expression of the gene HoxB4 is associated with prospective duct IM, whereas expression of the more posterior Hox gene HoxA6 is associated with more posterior, non-duct-forming IM. REFERENCE 3 (bases 1 to 880) AUTHORS Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C, Mitchell A, Sangrador-Vegas A, Yong SY, Mulder N and Hunter S. TITLE Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation JOURNAL Database (Oxford) 2012, bar068 (2012) PUBMED 22301074 REMARK Publication Status: Online-Only COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from JAENSK010000037.1. ##Evidence-Data-START## Transcript exon combination :: SRR13267647.12816.1, HAEL01011072.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA103992290, SAMEA103992323 [ECO:0000348] ##Evidence-Data-END## COMPLETENESS: full length. PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-328 JAENSK010000037.1 1563382-1563709 c 329-584 JAENSK010000037.1 1559093-1559348 c 585-880 JAENSK010000037.1 1557598-1557893 c FEATURES Location/Qualifiers source 1..880 /organism="Gallus gallus" /mol_type="mRNA" /db_xref="taxon:9031" /chromosome="2" /map="2" gene 1..880 /gene="HOXA6" /gene_synonym="HOX1; HOX1.2; HOX1B" /note="homeobox A6" /db_xref="CGNC:51307" /db_xref="GeneID:420630" exon 1..328 /gene="HOXA6" /gene_synonym="HOX1; HOX1.2; HOX1B" /inference="alignment:Splign:2.1.0" misc_feature 323..325 /gene="HOXA6" /gene_synonym="HOX1; HOX1.2; HOX1B" /note="upstream in-frame stop codon" exon 329..584 /gene="HOXA6" /gene_synonym="HOX1; HOX1.2; HOX1B" /inference="alignment:Splign:2.1.0" CDS 560..844 /gene="HOXA6" /gene_synonym="HOX1; HOX1.2; HOX1B" /note="isoform 2 is encoded by transcript variant 2; homeobox protein Hox-A6; homeo box A6; homeo box 1B; homeobox protein HOXA6; homeobox protein Hox-1B" /codon_start=1 /product="homeobox protein Hox-A6 isoform 2" /protein_id="NP_001385238.1" /db_xref="CGNC:51307" /db_xref="GeneID:420630" /translation="
MQRMNSCAGTVYGAHGRRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIANALCLTERQIKIWFQNRRMKWKKENKFINSTQPGSDETEEKSGE"
misc_feature order(608..622,626..628,677..679,695..697,734..736, 740..745,752..757,761..769,773..778) /gene="HOXA6" /gene_synonym="HOX1; HOX1.2; HOX1B" /note="DNA binding site [nucleotide binding]" /db_xref="CDD:238039" misc_feature order(614..616,623..625,743..745,752..757,764..766) /gene="HOXA6" /gene_synonym="HOX1; HOX1.2; HOX1B" /note="specific DNA base contacts [nucleotide binding]; other site" /db_xref="CDD:238039" misc_feature 617..775 /gene="HOXA6" /gene_synonym="HOX1; HOX1.2; HOX1B" /note="Homeobox domain; Region: Homeobox; pfam00046" /db_xref="CDD:425441" exon 585..880 /gene="HOXA6" /gene_synonym="HOX1; HOX1.2; HOX1B" /inference="alignment:Splign:2.1.0" ORIGIN
attcttttgctgagctctgtcctgcttcggatctctctggctttcaatccccatttcatttgctctttgtaaggctatagtgaacaaagtgtgcggaggttcggcataagcagccgcctagaacacagatccgggatggcaatttccagttcccccgctggaaggtgtggcatattggattcaaagcactggcgtggcagattttcaacttgcaacctggctaatttcctgcttcttctggcaccaaaaggagggcgattcgtctcctgtgcagccaaagcgacagctgtcaaagtcgcaggggctcctgcgagccagaacctaaaagtccaacaccgtcattgcttgcaatcgggcttcctatgagtacggagcctcctgtttctattcagacaaggaaattagtagcgcctctccctccggcagtggcaagcagaggggacaaggggactatctgcacttttctcccgagcaacaatacaaatccaacggcgtgcaaagcaaaatcgtgaatgacgaaggcaccgaccggaagtacacgagccctgtttacccctggatgcagcggatgaactcctgtgccggtacagtatatggagctcatgggagacgagggaggcagacttacacccgctaccaaacgctagagttagagaaggagttccattttaacagatacttaacccgaagacgacgcattgagattgcgaacgctctctgccttaccgagcgccagattaaaatatggtttcaaaacaggcggatgaaatggaaaaaggaaaacaaattcataaattccacccagcccggcagcgacgaaacagaggaaaagtcaggggagtagaaccgtgtttaataaacgctaccaggcccgtcctta
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Creative Commons Attribution 4.0 International License (CC BY 4.0).
If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596.
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