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

//