LOCUS       NM_016358               2394 bp    mRNA    linear   PRI 06-JUN-2024
DEFINITION  Homo sapiens iroquois homeobox 4 (IRX4), transcript variant 5,
            mRNA.
ACCESSION   NM_016358
VERSION     NM_016358.3
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 2394)
  AUTHORS   Malik,A., Jayarathna,D.K., Fisher,M., Barbhuiya,T.K., Gandhi,N.S.
            and Batra,J.
  TITLE     Dynamics and recognition of homeodomain containing protein-DNA
            complex of IRX4
  JOURNAL   Proteins 92 (2), 282-301 (2024)
   PUBMED   37861198
  REMARK    GeneRIF: Dynamics and recognition of homeodomain containing
            protein-DNA complex of IRX4.
REFERENCE   2  (bases 1 to 2394)
  AUTHORS   Fernando,A., Liyanage,C., Moradi,A., Janaththani,P. and Batra,J.
  TITLE     Identification and Characterization of Alternatively Spliced
            Transcript Isoforms of IRX4 in Prostate Cancer
  JOURNAL   Genes (Basel) 12 (5), 615 (2021)
   PUBMED   33919200
  REMARK    GeneRIF: Identification and Characterization of Alternatively
            Spliced Transcript Isoforms of IRX4 in Prostate Cancer.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2394)
  AUTHORS   Chakma,K., Gu,Z., Abudurexiti,Y., Hata,T., Motoi,F., Unno,M.,
            Horii,A. and Fukushige,S.
  TITLE     Epigenetic inactivation of IRX4 is responsible for acceleration of
            cell growth in human pancreatic cancer
  JOURNAL   Cancer Sci 111 (12), 4594-4604 (2020)
   PUBMED   32894817
  REMARK    GeneRIF: Epigenetic inactivation of IRX4 is responsible for
            acceleration of cell growth in human pancreatic cancer.
REFERENCE   4  (bases 1 to 2394)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   5  (bases 1 to 2394)
  AUTHORS   Xu,X., Hussain,W.M., Vijai,J., Offit,K., Rubin,M.A., Demichelis,F.
            and Klein,R.J.
  TITLE     Variants at IRX4 as prostate cancer expression quantitative trait
            loci
  JOURNAL   Eur J Hum Genet 22 (4), 558-563 (2014)
   PUBMED   24022300
  REMARK    GeneRIF: We independently validated IRX4 as a potential prostate
            cancer risk gene through cis-expression quantitative trait loci
            analysis of prostate cancer risk variants.
REFERENCE   6  (bases 1 to 2394)
  AUTHORS   Vaquerizas,J.M., Kummerfeld,S.K., Teichmann,S.A. and Luscombe,N.M.
  TITLE     A census of human transcription factors: function, expression and
            evolution
  JOURNAL   Nat Rev Genet 10 (4), 252-263 (2009)
   PUBMED   19274049
  REMARK    Review article
REFERENCE   7  (bases 1 to 2394)
  AUTHORS   Bayrak,F., Komurcu-Bayrak,E., Mutlu,B., Kahveci,G. and
            Erginel-Unaltuna,N.
  TITLE     Genetic analysis of the Irx4 gene in hypertrophic cardiomyopathy
  JOURNAL   Turk Kardiyol Dern Ars 36 (2), 90-95 (2008)
   PUBMED   18497553
  REMARK    GeneRIF: Polymorphism A381>G of the Irx4 gene may have a modifier
            effect on septal thickness, resulting in increased corrected QT
            dispersion and higher outflow gradients.
            GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   8  (bases 1 to 2394)
  AUTHORS   Wang,G.F., Nikovits,W. Jr., Bao,Z.Z. and Stockdale,F.E.
  TITLE     Irx4 forms an inhibitory complex with the vitamin D and retinoic X
            receptors to regulate cardiac chamber-specific slow MyHC3
            expression
  JOURNAL   J Biol Chem 276 (31), 28835-28841 (2001)
   PUBMED   11382777
REFERENCE   9  (bases 1 to 2394)
  AUTHORS   Bruneau,B.G., Bao,Z.Z., Tanaka,M., Schott,J.J., Izumo,S.,
            Cepko,C.L., Seidman,J.G. and Seidman,C.E.
  TITLE     Cardiac expression of the ventricle-specific homeobox gene Irx4 is
            modulated by Nkx2-5 and dHand
  JOURNAL   Dev Biol 217 (2), 266-277 (2000)
   PUBMED   10625552
REFERENCE   10 (bases 1 to 2394)
  AUTHORS   Lewis,M.T., Ross,S., Strickland,P.A., Snyder,C.J. and Daniel,C.W.
  TITLE     Regulated expression patterns of IRX-2, an Iroquois-class homeobox
            gene, in the human breast
  JOURNAL   Cell Tissue Res 296 (3), 549-554 (1999)
   PUBMED   10370142
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC025183.5, AF124733.1, BC136505.1, BC110912.1 and AI566193.1.
            
            On Nov 23, 2018 this sequence version replaced NM_016358.2.
            
            Transcript Variant: This variant (5) differs in the 5' UTR and
            lacks an alternate internal exon compared to variant 4. It encodes
            isoform b which is shorter than isoform a.
            
            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 :: AF124733.1, BC110912.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN03267757 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000231357.7/ ENSP00000231357.2
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-159               AC025183.5         17793-17951
            160-367             AF124733.1         1-208
            368-1993            BC136505.1         197-1822
            1994-2367           BC110912.1         1723-2096
            2368-2380           AI566193.1         9-21                c
            2381-2394           AC025183.5         23292-23305
FEATURES             Location/Qualifiers
     source          1..2394
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5p15.33"
     gene            1..2394
                     /gene="IRX4"
                     /gene_synonym="IRXA3"
                     /note="iroquois homeobox 4"
                     /db_xref="GeneID:50805"
                     /db_xref="HGNC:HGNC:6129"
                     /db_xref="MIM:606199"
     exon            1..323
                     /gene="IRX4"
                     /gene_synonym="IRXA3"
                     /inference="alignment:Splign:2.1.0"
     CDS             279..1838
                     /gene="IRX4"
                     /gene_synonym="IRXA3"
                     /note="isoform b is encoded by transcript variant 5;
                     iroquois homeobox protein 4; homeodomain protein IRXA3"
                     /codon_start=1
                     /product="iroquois-class homeodomain protein IRX-4 isoform
                     b"
                     /protein_id="NP_057442.1"
                     /db_xref="CCDS:CCDS3867.1"
                     /db_xref="GeneID:50805"
                     /db_xref="HGNC:HGNC:6129"
                     /db_xref="MIM:606199"
                     /translation="MSYPQFGYPYSSAPQFLMATNSLSTCCESGGRTLADSGPAASAQ
                     APVYCPVYESRLLATARHELNSAAALGVYGGPYGGSQGYGNYVTYGSEASAFYSLNSF
                     DSKDGSGSAHGGLAPAAAAYYPYEPALGQYPYDRYGTMDSGTRRKNATRETTSTLKAW
                     LQEHRKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWPPRNKCADEK
                     RPYAEGEEEEGGEEEAREEPLKSSKNAEPVGKEEKELELSDLDDFDPLEAEPPACELK
                     PPFHSLDGGLERVPAAPDGPVKEASGALRMSLAAGGGAALDEDLERARSCLRSAAAGP
                     EPLPGAEGGPQVCEAKLGFVPAGASAGLEAKPRIWSLAHTATAAAAAATSLSQTEFPS
                     CMLKRQGPAAPAAVSSAPATSPSVALPHSGALDRHQDSPVTSLRNWVDGVFHDPILRH
                     STLNQAWATAKGALLDPGPLGRSLGAGANVLTAPLARAFPPAVPQDAPAAGAARELLA
                     LPKAGGKPFCA"
     exon            324..575
                     /gene="IRX4"
                     /gene_synonym="IRXA3"
                     /inference="alignment:Splign:2.1.0"
     exon            576..685
                     /gene="IRX4"
                     /gene_synonym="IRXA3"
                     /inference="alignment:Splign:2.1.0"
     exon            686..1014
                     /gene="IRX4"
                     /gene_synonym="IRXA3"
                     /inference="alignment:Splign:2.1.0"
     exon            1015..2394
                     /gene="IRX4"
                     /gene_synonym="IRXA3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2347..2352
                     /regulatory_class="polyA_signal_sequence"
                     /gene="IRX4"
                     /gene_synonym="IRXA3"
                     /note="hexamer: AATATA"
     regulatory      2361..2366
                     /regulatory_class="polyA_signal_sequence"
                     /gene="IRX4"
                     /gene_synonym="IRXA3"
                     /note="hexamer: AATAAA"
     polyA_site      2367
                     /gene="IRX4"
                     /gene_synonym="IRXA3"
                     /note="major polyA site"
     polyA_site      2394
                     /gene="IRX4"
                     /gene_synonym="IRXA3"
                     /note="major polyA site"
ORIGIN      
        1 gtaaaatatg tatttctgtc gccgctgcga ggccgctcgg tcccagagcc ccctcgagcc
       61 tccggaatgc gaagttaaag gaatcgcggc ggccaccgct gctcactttg ttacccggtt
      121 agaaaagttt gcggagcgcg gggatggact aaccggctct cctgcttcgc cctcccagcg
      181 cctagaagcc tgcagctccg gagcagtggc cgcgccacgc cggccccagc gcgcagaacc
      241 ctgcaggccc cgcccgtccg ccccgggccg cgcccgccat gtcctacccg cagtttggat
      301 acccctactc ctcggctccc cagttcttga tggccaccaa ctccctgagc acgtgctgcg
      361 agtccggagg ccgcacgctg gcggactccg ggcccgccgc ctcggcccag gcgccggtct
      421 actgcccggt ctacgagagc cggctgctgg ccaccgcgcg ccacgagctc aactcggccg
      481 cggcgctggg cgtctatggg ggtccctatg gcggatcgca gggctatggc aactacgtga
      541 cctacggctc ggaggcgtcc gccttctact cgctgaacag ctttgattcc aaggatggtt
      601 cgggatctgc gcatgggggc ctggcaccag ccgctgccgc ctactaccct tacgagccag
      661 ctctgggcca gtacccctat gacaggtatg gaaccatgga cagcggcacg cggcgcaaga
      721 acgccacgcg cgagaccacc agcacgctca aggcctggct gcaggagcac cgcaagaacc
      781 cctaccccac caagggcgag aagatcatgc tggccatcat caccaagatg accctcacac
      841 aggtctccac ctggttcgcc aacgcgcgcc ggcgcctcaa gaaggagaac aagatgacgt
      901 ggccgccgcg gaacaagtgc gcagacgaga agcggcccta cgcggagggc gaggaggagg
      961 aggggggcga ggaggaggcg cgggaggagc ccctcaagag ctccaagaac gcagagcccg
     1021 tgggcaaaga ggagaaggag ctggagctta gtgacttgga cgacttcgac ccgctggaag
     1081 cagagccgcc ggcgtgcgag ctgaagccgc ccttccactc cctggacggc ggtctggagc
     1141 gcgtccccgc cgcgcccgac ggcccggtca aggaggcctc aggcgcgctc cggatgtctc
     1201 tggccgcggg tggcggagct gctctggacg aggacctgga gagggcccgg agctgtctcc
     1261 gcagcgcggc ggccgggccg gagccactgc cgggcgcaga gggcggccct caggtctgcg
     1321 aggccaagct ggggtttgtg ccggcggggg cgtcggcagg cctggaggct aagccgcgca
     1381 tctggtccct ggcccacaca gccaccgccg ccgccgccgc cgccacctcc ctgagccaga
     1441 ctgagtttcc gtcgtgcatg ctcaagcgcc aaggtcccgc ggcccctgcg gctgtgtcct
     1501 ccgcgcccgc cacgtccccg tctgtggccc ttccccactc tggcgccctg gacaggcacc
     1561 aggactcccc ggtaaccagt ctcagaaact gggtggacgg ggtcttccac gaccccatcc
     1621 tcaggcacag cactttgaac caggcctggg ccaccgccaa gggcgccctc ctggaccccg
     1681 ggcctctggg acgctcgctg ggggcgggcg cgaacgtgct gactgcaccc ctggcccgcg
     1741 cctttccgcc tgccgtgccc caggacgccc cagctgcagg cgccgccagg gagctgctcg
     1801 ccctgcccaa ggccggcggc aaacccttct gcgcctgagg cgggcgggtc ccgagcccag
     1861 gagggaaccc gcgctcaggc ggacggcgcc gactcttttc actgagtttc cagaggaaga
     1921 ctagcgcggc caccgcgaag ccgccaaccc accggagagg gggcttctga acttggactc
     1981 ctgggaacat ggacaagccc ggcgctgcca cgccggggcc tccaccgcct gggcctgagc
     2041 ctgaccgggc cattcccaaa tttgggacgc ggaaggagag gctctcggag cagaagaggc
     2101 cagataccct gaagcataaa gtttacgtca aaagtttaca tggagaaggc ggttccgttc
     2161 tgaagcgtgg tctgctgtcc cctgggcgtg aggcctcctg ggcctgtcgg gcctccgatt
     2221 tcatcctcag cacgtaatgc tcaccaacag cacttgcact gagttgactc ttgcacactc
     2281 ttgactccat aatatgatgc tttttaagat gtatgttcac accaataatt gcctgcttca
     2341 gaggctaata taacaaaacc aataaaaccg agtgatggtg tttgtattgc aaaa
//
