2024-05-04 16:18:01, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS NM_013075 2219 bp mRNA linear ROD 24-NOV-2023 DEFINITION Rattus norvegicus homeobox A1 (Hoxa1), transcript variant 1, mRNA. ACCESSION NM_013075 XM_008762937 XM_008775736 VERSION NM_013075.3 KEYWORDS RefSeq; RefSeq Select. SOURCE Rattus norvegicus (Norway rat) ORGANISM Rattus norvegicus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus. REFERENCE 1 (bases 1 to 2219) AUTHORS Li M, Gai F and Chen H. TITLE MiR-30b-5p Influences Chronic Exercise Arthritic Injury by Targeting Hoxa1 JOURNAL Int J Sports Med 42 (13), 1199-1208 (2021) PUBMED 33930933 REMARK GeneRIF: MiR-30b-5p Influences Chronic Exercise Arthritic Injury by Targeting Hoxa1. REFERENCE 2 (bases 1 to 2219) AUTHORS Kovacs IA, Luck K, Spirohn K, Wang Y, Pollis C, Schlabach S, Bian W, Kim DK, Kishore N, Hao T, Calderwood MA, Vidal M and Barabasi AL. TITLE Network-based prediction of protein interactions JOURNAL Nat Commun 10 (1), 1240 (2019) PUBMED 30886144 REMARK Publication Status: Online-Only REFERENCE 3 (bases 1 to 2219) AUTHORS Maamar H, Cabili MN, Rinn J and Raj A. TITLE linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis JOURNAL Genes Dev 27 (11), 1260-1271 (2013) PUBMED 23723417 REFERENCE 4 (bases 1 to 2219) AUTHORS Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T and Taipale J. TITLE DNA-binding specificities of human transcription factors JOURNAL Cell 152 (1-2), 327-339 (2013) PUBMED 23332764 REFERENCE 5 (bases 1 to 2219) AUTHORS Yu H, Tardivo L, Tam S, Weiner E, Gebreab F, Fan C, Svrzikapa N, Hirozane-Kishikawa T, Rietman E, Yang X, Sahalie J, Salehi-Ashtiani K, Hao T, Cusick ME, Hill DE, Roth FP, Braun P and Vidal M. TITLE Next-generation sequencing to generate interactome datasets JOURNAL Nat Methods 8 (6), 478-480 (2011) PUBMED 21516116 REFERENCE 6 (bases 1 to 2219) AUTHORS Li J, Tabor HK, Nguyen L, Gleason C, Lotspeich LJ, Spiker D, Risch N and Myers RM. TITLE Lack of association between HoxA1 and HoxB1 gene variants and autism in 110 multiplex families JOURNAL Am J Med Genet 114 (1), 24-30 (2002) PUBMED 11840501 REFERENCE 7 (bases 1 to 2219) AUTHORS Rossel M and Capecchi MR. TITLE Mice mutant for both Hoxa1 and Hoxb1 show extensive remodeling of the hindbrain and defects in craniofacial development JOURNAL Development 126 (22), 5027-5040 (1999) PUBMED 10529420 REFERENCE 8 (bases 1 to 2219) AUTHORS Helmbacher F, Pujades C, Desmarquet C, Frain M, Rijli FM, Chambon P and Charnay P. TITLE Hoxa1 and Krox-20 synergize to control the development of rhombomere 3 JOURNAL Development 125 (23), 4739-4748 (1998) PUBMED 9806922 REFERENCE 9 (bases 1 to 2219) AUTHORS Dolle P, Lufkin T, Krumlauf R, Mark M, Duboule D and Chambon P. TITLE Local alterations of Krox-20 and Hox gene expression in the hindbrain suggest lack of rhombomeres 4 and 5 in homozygote null Hoxa-1 (Hox-1.6) mutant embryos JOURNAL Proc Natl Acad Sci U S A 90 (16), 7666-7670 (1993) PUBMED 8102800 REFERENCE 10 (bases 1 to 2219) AUTHORS Baron A, Featherstone MS, Hill RE, Hall A, Galliot B and Duboule D. TITLE Hox-1.6: a mouse homeo-box-containing gene member of the Hox-1 complex JOURNAL EMBO J 6 (10), 2977-2986 (1987) PUBMED 2891503 COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from JACYVU010000142.1. On Mar 27, 2023 this sequence version replaced NM_013075.2. Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1). Sequence Note:. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: U93092.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA5756307, SAMEA5760476 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END## PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-747 JACYVU010000142.1 4491241-4491987 c 748-2219 JACYVU010000142.1 4489283-4490754 c FEATURES Location/Qualifiers source 1..2219 /organism="Rattus norvegicus" /mol_type="mRNA" /strain="BN" /db_xref="taxon:10116" /chromosome="4" /map="4q24" gene 1..2219 /gene="Hoxa1" /gene_synonym="Hoxa1l" /note="homeobox A1" /db_xref="GeneID:103690132" /db_xref="RGD:11414885" exon 1..747 /gene="Hoxa1" /gene_synonym="Hoxa1l" /inference="alignment:Splign:2.1.0" misc_feature 93..95 /gene="Hoxa1" /gene_synonym="Hoxa1l" /note="upstream in-frame stop codon" CDS 99..1103 /gene="Hoxa1" /gene_synonym="Hoxa1l" /note="isoform 1 is encoded by transcript variant 1; homeobox protein Hox-A1; homeo box A1" /codon_start=1 /product="homeobox protein Hox-A1 isoform 1" /protein_id="NP_037207.2" /db_xref="GeneID:103690132" /db_xref="RGD:11414885" /translation="
MDNARMNSFLEYPILGSGDSGTCSARVYSSDHGITTFQSCAVSANSCGGDDRFLGGRGVQITSPHHHHHHHHHPQPATYQTSGNLGVSYSHSSCGPSYGAQNFSAPYGPYGLNQEADVSGGYPPCAPAVYSGNLSSPMVQHHHHHQGYAGGTVGSPQYIHHSYGQEHQSLALATYNNSLSPLHASHQEACRSPASETSSPAQTFDWMKVKRNPPKTGKVGEYGYVGQPNAVRTNFTTKQLTELEKEFHFNKYLTRARRVEIAASLQLNETQVKIWFQNRRMKQKKREKEGLLPISPATPPGSDEKTEESSEKSSSSPSAPSPASSTSDTLTTSH"
misc_feature 279..344 /gene="Hoxa1" /gene_synonym="Hoxa1l" /note="propagated from UniProtKB/Swiss-Prot (O08656.1); Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite" misc_feature 318..704 /gene="Hoxa1" /gene_synonym="Hoxa1l" /note="propagated from UniProtKB/Swiss-Prot (O08656.1); Region: Interaction with OGT. /evidence=ECO:0000250|UniProtKB:P09022" misc_feature 552..554 /gene="Hoxa1" /gene_synonym="Hoxa1l" /note="O-linked (GlcNAc) threonine. /evidence=ECO:0000250|UniProtKB:P09022; propagated from UniProtKB/Swiss-Prot (O08656.1); glycosylation site" misc_feature 621..>953 /gene="Hoxa1" /gene_synonym="Hoxa1l" /note="Homeodomain-containing transcription factor [Transcription]; Region: COG5576" /db_xref="CDD:227863" misc_feature 705..722 /gene="Hoxa1" /gene_synonym="Hoxa1l" /note="propagated from UniProtKB/Swiss-Prot (O08656.1); Region: Antp-type hexapeptide" misc_feature order(792..797,801..803,852..854,870..872,909..911, 915..920,927..932,936..944,948..953) /gene="Hoxa1" /gene_synonym="Hoxa1l" /note="DNA binding site [nucleotide binding]" /db_xref="CDD:238039" misc_feature 792..950 /gene="Hoxa1" /gene_synonym="Hoxa1l" /note="Homeobox domain; Region: Homeobox; pfam00046" /db_xref="CDD:425441" misc_feature order(798..800,918..920,927..932,939..941) /gene="Hoxa1" /gene_synonym="Hoxa1l" /note="specific DNA base contacts [nucleotide binding]; other site" /db_xref="CDD:238039" misc_feature 936..1100 /gene="Hoxa1" /gene_synonym="Hoxa1l" /note="propagated from UniProtKB/Swiss-Prot (O08656.1); Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite" exon 748..2219 /gene="Hoxa1" /gene_synonym="Hoxa1l" /inference="alignment:Splign:2.1.0" ORIGIN
gtacattcatatcatttttcttctctggtcctatggaggaagtgagaaagttggcacggtcacccagggcttcgcaggacccagtcactcagtgacagatggacaatgcaagaatgaactcctttctggaataccccatccttggcagtggcgattctgggacctgctcggcgcgagtttactcctctgaccatggaattacaactttccaatcctgcgcggtcagtgccaacagctgcggcggcgacgaccgcttcctagggggcaggggggtgcagatcacctcgccccatcaccaccaccaccaccatcaccatccccagccggctacttaccagacttctgggaaccttggggtttcttattcccactcgagttgtggtccaagctatggcgcgcagaacttcagtgcgccttatggcccctatggattaaatcaggaagcagacgtaagtggtgggtaccccccgtgcgctcccgctgtttactctggaaacctctcgtctcccatggtccagcatcaccaccaccaccagggttatgctgggggcacagtgggctcgccccagtacattcaccactcatatggacaagagcaccagagtctggccctggccacgtataataactccttatcccctctccacgccagccaccaagaagcctgtcgttcccctgcttcagagacgtcttctccagcgcagacctttgactggatgaaagttaaaagaaaccctcccaaaacagggaaagttggagagtatggctacgtgggtcaacccaacgcagtgcgcaccaacttcaccaccaagcagctcacagagctggagaaggagttccacttcaacaagtacctaacaagagcccgcagggtggagatagccgcgtccctgcaactcaatgagacccaggtgaagatctggttccagaatcgccgcatgaagcagaagaagcgcgagaaagaggggctcttgcccatttcacccgccacccctcctggaagcgatgagaaaactgaagaatcatctgagaaatccagctcctcgcccagcgccccttctcccgcatcatctacctcagatactctgactacctcccactgaggctgccccagcccaactctgcagcccaggcttctccctgggctgagatttcttacccaaagcacattcttagcttatcttcctttctttccagactctctcttcctttctggtcccatctggggagctcctggctaagataagatatttccagagaattctggagacttggttggaagttaactccttattctataccaggtgcccacatcaatttctgatggtccccaacgccctttctttactgtcttgagatttttttacacaacctatggttcctttactgtccgttggagaacagttccctttgccaacagatatctgcagaagggaggtgtctcgcctttgtatctatgtattgttctgctccacctggcctttaagtaggacatagaggagggagggtgtccaaaggctcatgaggaagagatgctccatgtttacacaattcaccccttgattgctgggtatgaatgctttctcttcagagatttatctttatacacatttcgtagaaatatgtaagtcactaaatcaaacagggtggacaaattctcaaaactggcacaggccatgtgtgattatgggtgaaaggagaaaacctctctcattctgagtcagatacttcagaaggtggccttggttggttctttcagagtttaggcctacaaagcacaaggttcagaacctttcctgtgccgagtcttcccaaactctaaccaattcttcctgcttctctggccaccctgcatttaaaaaagttatgctggactatttgtaacctaaaggaattcttttcaaccaccctttcttttcacagtatcttgtatcttggctggagacaagtgtattttcagctaattgtttgttaatgtgatgtatggcacaacgaatgtatattttgtgtggttcgtgaatagtcttctgcatgtcgcacaatgttttgacctccctgaaatagcacactgagttctatcagttgtcctttgtgagcctaagatagtccccatttcctgtacaatcatgagcagctctgagatcctggagtgacgtggtccagagcagagtttacgggtcttacttaagatgtctgtaataaaatattcaagtttcagg
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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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