LOCUS       NM_153631               3026 bp    mRNA    linear   PRI 05-OCT-2024
DEFINITION  Homo sapiens homeobox A3 (HOXA3), transcript variant 2, mRNA.
ACCESSION   NM_153631 XM_005249730
VERSION     NM_153631.3
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3026)
  AUTHORS   Allen,B., Savoy,L., Ryabinin,P., Bottomly,D., Chen,R., Goff,B.,
            Wang,A., McWeeney,S.K. and Zhang,H.
  TITLE     Upregulation of HOXA3 by isoform-specific Wilms tumour 1 drives
            chemotherapy resistance in acute myeloid leukaemia
  JOURNAL   Br J Haematol 205 (1), 207-219 (2024)
   PUBMED   38867543
  REMARK    GeneRIF: Upregulation of HOXA3 by isoform-specific Wilms tumour 1
            drives chemotherapy resistance in acute myeloid leukaemia.
REFERENCE   2  (bases 1 to 3026)
  AUTHORS   Fu,Y., Zhang,X., Wu,H., Zhang,P., Liu,S., Guo,T., Shan,H.,
            Liang,Y., Chen,H., Xie,J. and Duan,Y.
  TITLE     HOXA3 functions as the on-off switch to regulate the development of
            hESC-derived third pharyngeal pouch endoderm through EPHB2-mediated
            Wnt pathway
  JOURNAL   Front Immunol 14, 1258074 (2024)
   PUBMED   38259452
  REMARK    GeneRIF: HOXA3 functions as the on-off switch to regulate the
            development of hESC-derived third pharyngeal pouch endoderm through
            EPHB2-mediated Wnt pathway.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3026)
  AUTHORS   Yang,R., Zhang,G., Dong,Z., Wang,S., Li,Y., Lian,F., Liu,X., Li,H.,
            Wei,X. and Cui,H.
  TITLE     Homeobox A3 and KDM6A cooperate in transcriptional control of
            aerobic glycolysis and glioblastoma progression
  JOURNAL   Neuro Oncol 25 (4), 635-647 (2023)
   PUBMED   36215227
  REMARK    GeneRIF: Homeobox A3 and KDM6A cooperate in transcriptional control
            of aerobic glycolysis and glioblastoma progression.
REFERENCE   4  (bases 1 to 3026)
  AUTHORS   Liu,G., Liu,B., Liu,X., Xie,L., He,J., Zhang,J., Dong,R., Ma,D.,
            Dong,K. and Ye,M.
  TITLE     ARID1B/SUB1-activated lncRNA HOXA-AS2 drives the malignant
            behaviour of hepatoblastoma through regulation of HOXA3
  JOURNAL   J Cell Mol Med 25 (7), 3524-3536 (2021)
   PUBMED   33683826
  REMARK    GeneRIF: ARID1B/SUB1-activated lncRNA HOXA-AS2 drives the malignant
            behaviour of hepatoblastoma through regulation of HOXA3.
REFERENCE   5  (bases 1 to 3026)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   6  (bases 1 to 3026)
  AUTHORS   Mulder,G.B., Manley,N. and Maggio-Price,L.
  TITLE     Retinoic acid-induced thymic abnormalities in the mouse are
            associated with altered pharyngeal morphology, thymocyte maturation
            defects, and altered expression of Hoxa3 and Pax1
  JOURNAL   Teratology 58 (6), 263-275 (1998)
   PUBMED   9894676
REFERENCE   7  (bases 1 to 3026)
  AUTHORS   Manley,N.R. and Capecchi,M.R.
  TITLE     Hox group 3 paralogs regulate the development and migration of the
            thymus, thyroid, and parathyroid glands
  JOURNAL   Dev Biol 195 (1), 1-15 (1998)
   PUBMED   9520319
REFERENCE   8  (bases 1 to 3026)
  AUTHORS   Apiou,F., Flagiello,D., Cillo,C., Malfoy,B., Poupon,M.F. and
            Dutrillaux,B.
  TITLE     Fine mapping of human HOX gene clusters
  JOURNAL   Cytogenet Cell Genet 73 (1-2), 114-115 (1996)
   PUBMED   8646877
REFERENCE   9  (bases 1 to 3026)
  AUTHORS   Scott,M.P.
  TITLE     Vertebrate homeobox gene nomenclature
  JOURNAL   Cell 71 (4), 551-553 (1992)
   PUBMED   1358459
REFERENCE   10 (bases 1 to 3026)
  AUTHORS   McAlpine,P.J. and Shows,T.B.
  TITLE     Nomenclature for human homeobox genes
  JOURNAL   Genomics 7 (3), 460 (1990)
   PUBMED   1973146
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC004080.2, AC010990.3 and
            AC004079.1.
            
            On or before Jun 16, 2020 this sequence version replaced
            XM_005249730.2, NM_153631.2.
            
            Summary: In vertebrates, the genes encoding the class of
            transcription factors called homeobox genes are found in clusters
            named A, B, C, and D on four separate chromosomes. Expression of
            these proteins is spatially and temporally regulated during
            embryonic development. This gene is part of the A cluster on
            chromosome 7 and encodes a DNA-binding transcription factor which
            may regulate gene expression, morphogenesis, and differentiation.
            Three transcript variants encoding two different isoforms have been
            found for this gene. [provided by RefSeq, Jul 2008].
            
            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 :: SRR14038194.3556626.1,
                                           SRR14038191.1194432.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968540, SAMEA2142348
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000612286.5/ ENSP00000484411.1
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-296               AC004080.2         25658-25953         c
            297-400             AC004080.2         13453-13556         c
            401-585             AC004080.2         256-440             c
            586-669             AC010990.3         2437-2520           c
            670-1315            AC004079.1         92510-93155         c
            1316-3026           AC004079.1         89405-91115         c
FEATURES             Location/Qualifiers
     source          1..3026
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="7"
                     /map="7p15.2"
     gene            1..3026
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E"
                     /note="homeobox A3"
                     /db_xref="GeneID:3200"
                     /db_xref="HGNC:HGNC:5104"
                     /db_xref="MIM:142954"
     exon            1..296
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E"
                     /inference="alignment:Splign:2.1.0"
     exon            297..400
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E"
                     /inference="alignment:Splign:2.1.0"
     exon            401..585
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E"
                     /inference="alignment:Splign:2.1.0"
     exon            586..669
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E"
                     /inference="alignment:Splign:2.1.0"
     exon            670..1315
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E"
                     /inference="alignment:Splign:2.1.0"
     CDS             790..2121
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E"
                     /note="homeo box A3; homeo box 1E; Hox-1.5-like protein;
                     homeobox protein Hox-1E"
                     /codon_start=1
                     /product="homeobox protein Hox-A3"
                     /protein_id="NP_705895.1"
                     /db_xref="CCDS:CCDS5404.1"
                     /db_xref="GeneID:3200"
                     /db_xref="HGNC:HGNC:5104"
                     /db_xref="MIM:142954"
                     /translation="MQKATYYDSSAIYGGYPYQAANGFAYNANQQPYPASAALGADGE
                     YHRPACSLQSPSSAGGHPKAHELSEACLRTLSAPPSQPPSLGEPPLHPPPPQAAPPAP
                     QPPQPAPQPPAPTPAAPPPPSSASPPQNASNNPTPANAAKSPLLNSPTVAKQIFPWMK
                     ESRQNTKQKTSSSSSGESCAGDKSPPGQASSKRARTAYTSAQLVELEKEFHFNRYLCR
                     PRRVEMANLLNLTERQIKIWFQNRRMKYKKDQKGKGMLTSSGGQSPSRSPVPPGAGGY
                     LNSMHSLVNSVPYEPQSPPPFSKPPQGTYGLPPASYPASLPSCAPPPPPQKRYTAAGA
                     GAGGTPDYDPHAHGLQGNGSYGTPHIQGSPVFVGGSYVEPMSNSGPALFGLTHLPHAA
                     SGAMDYGGAGPLGSGHHHGPGPGEPHPTYTDLTGHHPSQGRIQEAPKLTHL"
     exon            1316..3026
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3004..3009
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E"
                     /note="hexamer: AATAAA"
     polyA_site      3026
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E"
                     /note="major polyA site"
ORIGIN      
        1 gcattctttt gctccgctcc gtcctgcctg cttcggagct ctgccttcca gccgggctcg
       61 gctgtgcttt gtccggagat ggcgagcgaa gggaagcccc ggccaggcca ggcctggcgg
      121 ctcccgctgg agattgggcg cgctccgttc ccggcgccgc ggcagcagct ttgcaactcg
      181 caacctggct aatttcctgc gtcctctggc accaggaaag aggacaattc ttctctcggg
      241 ctgcccaagc gacagctgtc agaggggcag gagcttctgg gagccaccgt ctgaaggcta
      301 cgtgtgccgc ctggccattc aaactgtcaa ttttaggtcc agaagtgtcc aaaccacaag
      361 ttctcaaaac tctctgaaaa atggctccct ccgagttaag caattctgaa aggcattctc
      421 tgggaaaagt ctgtggagga gagagggatc ttcttgcaaa taatgtggtc tcaggcaagg
      481 acacagcatc ttggctgtct gctaaaaaaa aaaaatgcct agactctcag tggaaattga
      541 gtgtcaagct gcaaaatctc aaatggcaga ctatcatcat ttaagagcgc ctggacaccg
      601 gaaaaggcga ttccctgagc gcctggagtt ggagacaatt cctggttcag aatttaaaca
      661 tctttctagg tctgcgcggg gcggccattg gcggcggagt gtcacgtgac cgcgggggcg
      721 tgccaatgtg cgccctcacg ggtgtcaaac ccctgtcaga gtgtgcgatc aagatcgtga
      781 aacaacgcga tgcaaaaagc gacctactac gacagctcgg cgatctacgg tggctacccc
      841 taccaggcag ccaacgggtt cgcttataat gccaatcagc agccgtaccc ggcgtccgcc
      901 gctttgggcg ccgacggcga gtaccaccga cccgcctgct ccctccagtc tccctccagc
      961 gccgggggcc accccaaggc acacgaactg agtgaggcgt gcctgcgcac cctgagcgcc
     1021 ccacctagcc agcctccaag cctgggagag ccgcccctgc acccgccgcc gccccaggcc
     1081 gcgccccctg ccccacagcc gcctcagccc gcacctcagc cccctgcacc tacccctgcc
     1141 gcgcccccgc ctccctcttc tgcctcccct cctcagaatg ccagcaacaa ccctacccct
     1201 gccaacgcgg ccaagagccc cctgctcaac tcacccacag tggccaaaca aatcttcccc
     1261 tggatgaaag agtctcgaca aaacacaaag cagaaaacca gcagctccag ctcaggcgaa
     1321 agctgcgctg gcgacaagag cccgccgggg caggcttcgt ccaagcgcgc gcgcacggcc
     1381 tacacgagcg cgcagctggt ggagctggag aaagagttcc acttcaaccg ctacctgtgc
     1441 cggccgcgcc gggtggagat ggccaatctg ctgaacctca ctgagcgcca gatcaagatc
     1501 tggttccaga atcgccgcat gaagtacaaa aaggatcaga agggcaaggg catgctaacg
     1561 tcatcggggg gccagtctcc aagtcgcagc cccgtgcccc ccggagccgg tggctatctg
     1621 aactctatgc attcgctggt caacagcgtc ccgtatgagc cccagtcgcc cccgcccttc
     1681 tccaagcccc cccagggtac ctacgggctg ccccccgcct cctaccctgc gtccctgccc
     1741 agctgcgcac ccccgccacc cccacagaag cgctacacgg cggcaggggc gggcgcaggg
     1801 ggcacccccg actatgaccc gcacgctcat ggcctgcagg gcaacggcag ctatgggacc
     1861 ccacacatac agggaagccc cgtcttcgtg gggggcagct atgtggagcc catgagcaac
     1921 tccgggccag ccctctttgg tctaactcac ctcccccacg ctgcctcggg cgccatggac
     1981 tatgggggtg ccgggccgct gggcagcggc caccaccacg ggccggggcc tggggagccg
     2041 caccccacct acacggacct taccggccac catccttctc agggaagaat tcaggaagca
     2101 cccaagctca cccacctgtg atagtgggct tggggctacg cgccaggaga gtctcccccc
     2161 acccaccttt tttctttggt tgcttttttt tttttttttt tttaggttct tcctgccctt
     2221 tccttccttc cttttctctc ttctccgccc cgcactccgt ttcccggttt cccccctcgt
     2281 tggtaaggcg tttttatagt ttatgtgacg tagcaatctt ggttgctgga atggctgtat
     2341 catagcgata tttatctctt cctgctcctc gataggccac tggccctgca ccctttacct
     2401 tctccactct ttgatcagaa acagggtata tgaacaaatt ttctagtcga gttttcaatg
     2461 tgaatttgtt cttacattat ggctcccgag gggaagcgat tacttttttt aattttaaat
     2521 ttttttttta attgcacttc ttgtaaagag tgagaaaaaa aatcaaaggc gctttgaaac
     2581 aggggctctc tgtgcaagga tgactaagtg tacgtctttc cgtgtgtgta tgctggtgaa
     2641 cagtcagatt tatttatatt tttttgcaag cattgaataa tctaagtttt aaatattatt
     2701 tatccccatc cgttcgtatt tatattaaag aattctgtac cctgatggtt cagaagggtt
     2761 cttgggcctt ttgttcaatt gtgtattggc gtacttagaa ttttttttat ttgaaagaga
     2821 aatataattc ctttaaacgg taacgataca ataaaaccag agaagatcca gcttttgaaa
     2881 acagtgattt aggtttgtaa catccggcaa aactgaaaaa aaaaatctgt aaacgcgaaa
     2941 aatactagat ttgttttgag agttcttcat tccttgctgc tcacattctg agaaacaaaa
     3001 agaaataaag tttttattct gaataa
//
