GGRNA | NM_001177478.1

LOCUS       NM_001177478            6188 bp    mRNA    linear   PRI 17-APR-2013
DEFINITION  Homo sapiens highly divergent homeobox (HDX), transcript variant 3,
            mRNA.
ACCESSION   NM_001177478
VERSION     NM_001177478.1  GI:294489215
KEYWORDS    RefSeq.
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 6188)
  AUTHORS   Kimura,K., Wakamatsu,A., Suzuki,Y., Ota,T., Nishikawa,T.,
            Yamashita,R., Yamamoto,J., Sekine,M., Tsuritani,K., Wakaguri,H.,
            Ishii,S., Sugiyama,T., Saito,K., Isono,Y., Irie,R., Kushida,N.,
            Yoneyama,T., Otsuka,R., Kanda,K., Yokoi,T., Kondo,H., Wagatsuma,M.,
            Murakawa,K., Ishida,S., Ishibashi,T., Takahashi-Fujii,A.,
            Tanase,T., Nagai,K., Kikuchi,H., Nakai,K., Isogai,T. and Sugano,S.
  TITLE     Diversification of transcriptional modulation: large-scale
            identification and characterization of putative alternative
            promoters of human genes
  JOURNAL   Genome Res. 16 (1), 55-65 (2006)
   PUBMED   16344560
REFERENCE   2  (bases 1 to 6188)
  AUTHORS   Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G.,
            Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D.,
            Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K.,
            Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F.,
            Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L.,
            Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L.,
            Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S.,
            Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J.,
            Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J.,
            McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S.,
            Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W.,
            Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A.,
            Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S.,
            Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y.,
            Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D.,
            Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M.,
            Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E.,
            Schnerch,A., Schein,J.E., Jones,S.J. and Marra,M.A.
  CONSRTM   Mammalian Gene Collection Program Team
  TITLE     Generation and initial analysis of more than 15,000 full-length
            human and mouse cDNA sequences
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 99 (26), 16899-16903 (2002)
   PUBMED   12477932
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DA719263.1, AK055240.1 and AL035552.9.
            
            Transcript Variant: This variant (3) differs in the 5' UTR, lacks a
            portion of the 5' coding region, and initiates translation at a
            downstream start codon, compared to variant 1. The encoded isoform
            (2) has a shorter N-terminus compared to isoform 1.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK055240.1 [ECO:0000332]
            RNAseq introns              :: mixed/partial sample support
                                           ERS025082, ERS025083 [ECO:0000350]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-26                DA719263.1         3-28
            27-2745             AK055240.1         1-2719
            2746-6188           AL035552.9         85279-88721         c
FEATURES             Location/Qualifiers
     source          1..6188
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xq21.1"
     gene            1..6188
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /note="highly divergent homeobox"
                     /db_xref="GeneID:139324"
                     /db_xref="HGNC:26411"
     exon            1..138
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /inference="alignment:Splign:1.39.8"
     exon            139..247
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    230..232
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /note="upstream in-frame stop codon"
     exon            248..1351
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /inference="alignment:Splign:1.39.8"
     CDS             275..2173
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /note="isoform 2 is encoded by transcript variant 3"
                     /codon_start=1
                     /product="highly divergent homeobox isoform 2"
                     /protein_id="NP_001170949.1"
                     /db_xref="GI:294489216"
                     /db_xref="CCDS:CCDS55456.1"
                     /db_xref="GeneID:139324"
                     /db_xref="HGNC:26411"
                     /translation="

MSSKNSESGTATTGTSLSAPDITVRNVVNIARPSSQQSSWTSANNDVIVTGIYSPASSSSRQGTNKHTDTQITEAHKIPIQKTATKNDTEFQLHIPVQRQVAHCKNASLLLGEKTIILSRQTSVLNAGNSVFNHAKKNYGNSSVQASEMTVPQKPSVCHRPCKIEPVGIQRSYKPEHTGPALHNLCGQKPTIRDPYCRTQNLEIREVFSLAVSDYPQRILGGNAPQKPSSAEGNCLSIAMETGDAEDEYAREEELASMRAQIPSYSRFYESGSSLRAENQSTTLPGPGRNMPNSQMVNIRDMSDNVLYQNRNYHLTPRTSLHTASSTMYSNTNPLRSNFSPHFASSNQLRLSQNQNNYQISGNLTVPWITGCSRKRALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMGIEVPPPRGGPADFSEQPESGSLSALTPGEEAGPEVGEDNDRNDEVSICLSEGSSQEEPNEVVPNDARAHKEEDHHAVTTDNVKIEIIDDEESDMISNSEVEQVNSFLDYKNEEVKFIENELEIQKQKYFKLQTFVRSLILAMKADDKEQQQALLSDLPPELEEMDFNHASLEPDDTSFSVSSLSEKNVSESL

"
     misc_feature    1415..1585
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /note="Homeodomain;  DNA binding domains involved in the
                     transcriptional regulation of key eukaryotic developmental
                     processes; may bind to DNA as monomers or as homo- and/or
                     heterodimers, in a sequence-specific manner; Region:
                     homeodomain; cd00086"
                     /db_xref="CDD:28970"
     misc_feature    order(1415..1420,1424..1426,1475..1477,1505..1507,
                     1544..1546,1550..1555,1562..1567,1571..1579,1583..1585)
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:28970"
     misc_feature    order(1421..1423,1553..1555,1562..1567,1574..1576)
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:28970"
     variation       677
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:35653454"
     variation       811
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:34867209"
     variation       919
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:35928187"
     variation       1290
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:35161124"
     exon            1352..1405
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /inference="alignment:Splign:1.39.8"
     exon            1406..1552
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /inference="alignment:Splign:1.39.8"
     exon            1553..1760
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /inference="alignment:Splign:1.39.8"
     exon            1761..1840
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /inference="alignment:Splign:1.39.8"
     exon            1841..1924
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /inference="alignment:Splign:1.39.8"
     exon            1925..2047
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /inference="alignment:Splign:1.39.8"
     exon            2048..6188
                     /gene="HDX"
                     /gene_synonym="CXorf43; D030011N01Rik"
                     /inference="alignment:Splign:1.39.8"
ORIGIN

aattgatgatcggacacgctgatttcattgtctgaagcggcactggagacccaggaaaaatctcgctgaatccgcctgccccagcagcggcctgatctgggttccgctgattcctttcgtaaccgcaccacacccgagctacaatctctggacaaaattttaagagaaactccctcagaactcctaaaggtaaacaaaagcaggcagattgaggatggcagtcagaatatgaagtgaccatatatggacgtgggttggcaataagagaagaaagatgagtagtaagaactctgaatctggaacagcaacaacaggaacctctttgtcagctccagacatcacagtcagaaatgtggttaatattgctcgaccctcaagccagcagtcttcttggacatctgccaataatgatgtcattgtaactggtatatacagtccagccagttcatcaagtaggcaaggaacaaacaaacatacagacacacaaattacagaagcacataaaatccctattcagaaaacagccactaaaaatgatactgagtttcagttacacattcctgtccaaagacaagtagcacactgtaaaaatgcttccctactcctaggtgaaaaaacaattattttgtcaagacagacaagtgtgctaaatgctggaaactcagtattcaatcacgcaaagaaaaactatggaaactcttcagtacaagcttctgaaatgacagtacctcaaaagccttctgtgtgccaccgaccttgtaaaattgaaccagttgggattcaaaggtcatataagcctgaacacacaggcccagcattacataacttatgtgggcaaaagccaactattagagacccttactgtagaacacaaaacttggaaatccgtgaagtgttttcattggcagttagcgattacccccagagaattctgggaggaaatgccccacagaagcctagctcagcagaaggaaattgtttgtccattgcaatggagactggagatgctgaggatgaatatgccagagaggaagagctggcatcgatgagagcacagataccaagctattcgagattttatgaaagtggcagttcccttcgagctgagaaccaaagtacaaccttgcccggaccaggaagaaatatgccaaattcacaaatggtgaatattagagatatgtcagacaatgtactgtatcaaaacagaaactaccatttgacaccacggacctcattacatacagcatctagtacaatgtacagtaataccaatccattacggagtaatttttctcctcattttgcatcatcaaaccaattgagattatcacaaaaccaaaacaattaccagatttcaggaaaccttactgtgccttggattacagggtgttctagaaaaagagcactacaggaccgcactcagttcagtgaccgagacttagccacccttaagaagtattgggacaatggcatgaccagcctgggctctgtttgtagagagaaaattgaagctgtggcaactgaattaaatgttgactgtgaaatagttcggacttggattgggaatcgaagaaggaaatatcgtttaatggggattgaagttccacctccaagaggaggccctgctgatttctctgagcagcctgagtctggttctttatctgcactcacaccaggagaggaagctgggcctgaagtaggagaggataatgacagaaatgatgaagtatccatctgtttgtctgaaggaagctctcaagaagagcccaatgaagttgttccgaatgatgcaagggctcataaggaagaggaccaccatgcagtaaccacagataatgtgaaaatagaaattattgatgatgaagaaagtgacatgataagtaattctgaagtagaacaagtaaactctttcttggattataagaatgaagaagtcaaattcattgaaaatgagctcgagattcaaaagcaaaaatactttaaacttcagacttttgttagaagcttgatattagcaatgaaagctgatgataaggaacaacagcaggcactgctgtcagatttacctcctgaattagaggaaatggatttcaatcatgcctcactggagcctgatgatacctcattcagtgtatcttctttgtcagagaaaaatgtctcagaaagtttgtgatttcagttggagggaatatatgatacagtcttttggcttcgtaacaggtgtgcatttcaagataactgcattctgttgccctggtattctttagttgggaaaacacattgttgaaacggacgtattctgtgaagaatgtacaagatataatggctacagtgcaacaaaaatgtaggtgaaatttaaaagcattgtttgagagagtatttttttaactgatggaactctggaaaaaaattatatttaagtttcagcagtttaaccctgaaattcattatgtctaatttctaaccagagacaaaataactaaagacatttcagcattgcttatcaagttgctacagcttgattagtcttgtttttgtagccattacatcttctttcttcttctctccttttcctatcatccacttacactttttctcaggaaagtggactgaacatttaaaacaaaactttaaaaaattatttaactcattatttaatgagttctctgatttagtttttaacccctatgaaaatttgacttaaactaatgactgaaaattaaatgattacaggtatgtaattgtaaattgctggtgttcttctattatctaacccaaatatttgtgtgggggtggggaagcacaatggaaaggtaatttaaccaacataacgtcaaataaattacgaagtgtacagaaacaaaatgttgtcaaaattagtcttgatggggattcttcattactacaaatgacaagtattgatacgattgacattccagtagtaaatttgtatacctgggttagatgaagtgttacacaaatattttaaatttatcaccatctttataattcttttttagttcttacatgttatgaaacaggaagtcaaggtaagctgctgagattttttaaaaatttagtcattcagctttgccacaaaatttacctcatttccatatgaggcctgtacagagccatcagccaaggatagtattcaaaaagagttatactactttggttgtaaatcacagtcttctgaattccatgaatactattctatgagtacacacctaaaatgggcaagctacccagttttctattattagtaggtaccagatggcaacacactgtagactgttctttgtagttcttcctttctggagtaccagatggtattaccaagacccatagaagaaaaaatgtcagtttctccctaagcccacagtgtcatatatttgtgacttggcagtgtgcaattgtgttgcatggttaaattactatctatacctaaaagattaatgaagtagctggatggctgtttcagccatcaagtttctgtttccaatttgtttttaatttttgttggtacctagtaggtattcagatatttttaaaaatttgtaattagagccaaatttgatcttgaaatttactagtactaacttatgaacacagaaaggcagtcataaatgtctttacccttgaagtgtcccatcctcccacacacacaaataggtaagctcccactgatagtctttcattttgtcacttatttgtttatattgctgccatactactgatatggtccctttgttagtaggaatatttcagtgttcagatatgcttccttgagccatatggagttttgcaaacaatagttagtttttcttgctgacaagtcaaattccattcagagaaagcagcagagagtaacagagcctcagatattacgattaaatgtaccagtcacaccaactcctccatgagatgaagagtcgcccccatatacaacgaagttagaaaccacttattaagtagcatgaacaaattccaggccttcaagtctctcctagggtctgcttcatagtcattgagtttatctttcaaatataattacttctgcttcaatttaagccccttcttatttggttctcattgcaaattaactataggtatattctctcctacagcttttaacactatagattttatttgtcacgcatcagccattagtcactaaatcgaaaaatacttgttgagctcctgctatagagaagacactgtgctggacattggatttctcagcaagctgtaaacatcacaaataattatttctttttaacatcttctatgatattaataaaccatatttaagtagaatttttaatagatttaaggttctgctaggtgtgattcttagaaggattcctagtccacaattttgagagaaagcatagatgatctttttgtctctgtttaacatttcatcaaaatagaaactatataaatcataacaatacatttagaactccttttgtcttgaaatttgtgtttcagcaccagaatatttttcttcaccatcattggaattaaaacacttctaaaatgaaatgtggctattctgtagcaggaactgaaggaaatacctctatctatagaaaaagaatcataattgccagattgaaattattcatggtagactttgaaaaagatgtcaaggtcaagctttgaaaagttgttatgaagaaagtatattttttacatatgtagataggagttggttttgagatatgttagagcaggaaaaattatcagcttataattactcttgtggacatcttcatggctggggataaaaattaactaactagtgtttctttctttagggctttgagattattaaaacagaccttactatctgaaggctctctcagggagacagaagccaatgtggaaaaaaacaaaaaacaaaaaacaacaacaagaaaaaacttctttttttctttcaactacatttctatgtctgctttaagcttagaacagccaagcagtttttaagccagaaatgtgtatgtaagagcacttaccttccaaaatgtgtacatatgaaaaaaaaaggaaggtattttcttcttttcagccaagctaaacttattcacaagaaaatgagaattgcaattgctctggagaataggaaaattagcacatgcaaagaaaaccttaaaagaaaattggcctcttcatggaaactggggatgttttgtcctaaggtcagttatcaacagcaggatttttgtattgccattgcaagcatgtgatagaaatgtttgttattgttggagaagaaaaggctgagacccaattataccctgtactctttattcgaccaagacctcaaaagatgtcaaagaagccatttctccaaagacagcaacatctattgtgaggcactttcatattcagcagtctgtaagtttgtaggagaaaacataagtggttaatttaaaataattttgggctctaaaatggactttgttgccttttttggtgggggtggtgggaatcggattcagcccatttccaagggatagtttcttcatctcagacaactattttgtgatcctttttaaaagacattctgaaaactttaactcctgcccttcttccgtattacagttgtgttattccagaaatattgtctacttttttaatatattagattttcattcagatcttaaacatgcaaacatgtgataggttagctttttaagggagttatcagtaccactgtatctaaatgttaggtaaatgggtagatttctctttgaagttggtattttccttggcagacagcactgtatcatgctcttcaccaagctatgctctgtaatgctataatcaaggaggctactaacttgtgaacctacagtcaacacaccattgctgaaaacaaactttgattaagaacagatttgctagggggaaaaaagagtaaagtgatattttcaagcaaatataattaaaattgtttcattaaaatatatactgagtgtatattgctccacactgaaattttattttgcattaacttgttaagtaattcattttagcaatcctgcatcccattttactagtactacctctgaaatatactgtcaccttaaaaccacatcagactgtaatgtgaatttttgtagagtttttatttaaacttttatagaggcaataaatgatttccaactaataga

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