GGRNA | NM_002147.3

LOCUS       NM_002147               1830 bp    mRNA    linear   PRI 07-JUL-2013
DEFINITION  Homo sapiens homeobox B5 (HOXB5), mRNA.
ACCESSION   NM_002147
VERSION     NM_002147.3  GI:85380096
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 1830)
  AUTHORS   Stavnes,H.T., Holth,A., Don,T., Kaern,J., Vaksman,O., Reich,R.,
            Trope',C.G. and Davidson,B.
  TITLE     HOXB8 expression in ovarian serous carcinoma effusions is
            associated with shorter survival
  JOURNAL   Gynecol. Oncol. 129 (2), 358-363 (2013)
   PUBMED   23438671
  REMARK    GeneRIF: HOXB5 and HOXB8 are frequently expressed in ovarian serous
            carcinoma, with anatomic site-related differences for cytoplasmic
            staining. HOXB5 may be affected by chemotherapy in effusions.
REFERENCE   2  (bases 1 to 1830)
  AUTHORS   Carter,T.C., Kay,D.M., Browne,M.L., Liu,A., Romitti,P.A., Kuehn,D.,
            Conley,M.R., Caggana,M., Druschel,C.M., Brody,L.C. and Mills,J.L.
  TITLE     Hirschsprung's disease and variants in genes that regulate enteric
            neural crest cell proliferation, migration and differentiation
  JOURNAL   J. Hum. Genet. 57 (8), 485-493 (2012)
   PUBMED   22648184
  REMARK    GeneRIF: The findings for HOXB5 and PHOX2B provide supportive
            evidence that genes regulating ENCC proliferation, migration and
            differentiation could be risk factors for Hirschsprung's disease
REFERENCE   3  (bases 1 to 1830)
  AUTHORS   di Pietro,M., Lao-Sirieix,P., Boyle,S., Cassidy,A., Castillo,D.,
            Saadi,A., Eskeland,R. and Fitzgerald,R.C.
  TITLE     Evidence for a functional role of epigenetically regulated
            midcluster HOXB genes in the development of Barrett esophagus
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 109 (23), 9077-9082 (2012)
   PUBMED   22603795
  REMARK    GeneRIF: HOXB5, HOXB6, and HOXB7 are activated in Barrett
            esophagus, and the midcluster HOXB gene signature in BE most
            resembled the colon rather than other GI epithelia.
REFERENCE   4  (bases 1 to 1830)
  AUTHORS   Bradfield JP, Taal HR, Timpson NJ, Scherag A, Lecoeur C, Warrington
            NM, Hypponen E, Holst C, Valcarcel B, Thiering E, Salem RM,
            Schumacher FR, Cousminer DL, Sleiman PM, Zhao J, Berkowitz RI,
            Vimaleswaran KS, Jarick I, Pennell CE, Evans DM, St Pourcain B,
            Berry DJ, Mook-Kanamori DO, Hofman A, Rivadeneira F, Uitterlinden
            AG, van Duijn CM, van der Valk RJ, de Jongste JC, Postma DS,
            Boomsma DI, Gauderman WJ, Hassanein MT, Lindgren CM, Magi R,
            Boreham CA, Neville CE, Moreno LA, Elliott P, Pouta A, Hartikainen
            AL, Li M, Raitakari O, Lehtimaki T, Eriksson JG, Palotie A,
            Dallongeville J, Das S, Deloukas P, McMahon G, Ring SM, Kemp JP,
            Buxton JL, Blakemore AI, Bustamante M, Guxens M, Hirschhorn JN,
            Gillman MW, Kreiner-Moller E, Bisgaard H, Gilliland FD, Heinrich J,
            Wheeler E, Barroso I, O'Rahilly S, Meirhaeghe A, Sorensen TI, Power
            C, Palmer LJ, Hinney A, Widen E, Farooqi IS, McCarthy MI, Froguel
            P, Meyre D, Hebebrand J, Jarvelin MR, Jaddoe VW, Smith GD,
            Hakonarson H and Grant SF.
  CONSRTM   Early Growth Genetics Consortium
  TITLE     A genome-wide association meta-analysis identifies new childhood
            obesity loci
  JOURNAL   Nat. Genet. 44 (5), 526-531 (2012)
   PUBMED   22484627
  REMARK    GeneRIF: Single nucleotide polymorphism in HOXB5 gene is associated
            with childhood obesity.
REFERENCE   5  (bases 1 to 1830)
  AUTHORS   Luo,J., Cai,Q., Wang,W., Huang,H., Zeng,H., He,W., Deng,W., Yu,H.,
            Chan,E., Ng,C.F., Huang,J. and Lin,T.
  TITLE     A microRNA-7 binding site polymorphism in HOXB5 leads to
            differential gene expression in bladder cancer
  JOURNAL   PLoS ONE 7 (6), E40127 (2012)
   PUBMED   22768238
  REMARK    GeneRIF: A miRNA 7-binding single nucleotide polymorphism (1010A/G)
            located within 3'-UTR of HOXB5 is associated with gene expression
            and may be a promising prognostic factor for bladder cancer.
REFERENCE   6  (bases 1 to 1830)
  AUTHORS   Galang,C.K. and Hauser,C.A.
  TITLE     Cooperative DNA binding of the highly conserved human Hox 2.1
            homeodomain gene product
  JOURNAL   New Biol. 4 (5), 558-568 (1992)
   PUBMED   1355360
REFERENCE   7  (bases 1 to 1830)
  AUTHORS   Peverali,F.A., D'Esposito,M., Acampora,D., Bunone,G., Negri,M.,
            Faiella,A., Stornaiuolo,A., Pannese,M., Migliaccio,E., Simeone,A.
            et al.
  TITLE     Expression of HOX homeogenes in human neuroblastoma cell culture
            lines
  JOURNAL   Differentiation 45 (1), 61-69 (1990)
   PUBMED   1981366
REFERENCE   8  (bases 1 to 1830)
  AUTHORS   Acampora,D., D'Esposito,M., Faiella,A., Pannese,M., Migliaccio,E.,
            Morelli,F., Stornaiuolo,A., Nigro,V., Simeone,A. and Boncinelli,E.
  TITLE     The human HOX gene family
  JOURNAL   Nucleic Acids Res. 17 (24), 10385-10402 (1989)
   PUBMED   2574852
REFERENCE   9  (bases 1 to 1830)
  AUTHORS   Giampaolo,A., Acampora,D., Zappavigna,V., Pannese,M.,
            D'Esposito,M., Care,A., Faiella,A., Stornaiuolo,A., Russo,G.,
            Simeone,A. et al.
  TITLE     Differential expression of human HOX-2 genes along the
            anterior-posterior axis in embryonic central nervous system
  JOURNAL   Differentiation 40 (3), 191-197 (1989)
   PUBMED   2570724
REFERENCE   10 (bases 1 to 1830)
  AUTHORS   Boncinelli,E., Acampora,D., Pannese,M., D'Esposito,M., Somma,R.,
            Gaudino,G., Stornaiuolo,A., Cafiero,M., Faiella,A. and Simeone,A.
  TITLE     Organization of human class I homeobox genes
  JOURNAL   Genome 31 (2), 745-756 (1989)
   PUBMED   2576652
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from M92299.1, BE621135.1,
            BQ073272.1, M86726.1, BC004454.1 and BQ001097.1.
            On Jan 19, 2006 this sequence version replaced gi:24797132.
            
            Summary: This gene is a member of the Antp homeobox family and
            encodes a nuclear protein with a homeobox DNA-binding domain. It is
            included in a cluster of homeobox B genes located on chromosome 17.
            The encoded protein functions as a sequence-specific transcription
            factor that is involved in lung and gut development. Increased
            expression of this gene is associated with a distinct biologic
            subset of acute myeloid leukemia (AML) and the occurrence of
            bronchopulmonary sequestration (BPS) and congenital cystic
            adenomatoid malformation (CCAM) tissue. [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 :: BI766494.1, M92299.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           ERS025081, ERS025084 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-562               M92299.1           217-778
            563-583             BE621135.1         360-380
            584-584             BQ073272.1         518-518
            585-865             M92299.1           801-1081
            866-937             M86726.1           160-231
            938-1076            M92299.1           1154-1292
            1077-1488           BC004454.1         6-417
            1489-1830           BQ001097.1         9-350               c
FEATURES             Location/Qualifiers
     source          1..1830
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="17"
                     /map="17q21.3"
     gene            1..1830
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /note="homeobox B5"
                     /db_xref="GeneID:3215"
                     /db_xref="HGNC:5116"
                     /db_xref="HPRD:00848"
                     /db_xref="MIM:142960"
     exon            1..621
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /inference="alignment:Splign:1.39.8"
     STS             38..1452
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /db_xref="UniSTS:484893"
     STS             40..1177
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /db_xref="UniSTS:490407"
     CDS             60..869
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /note="homeo box B5; homeo box 2A; homeobox protein Hu-1;
                     homeobox protein Hox-2A; homeobox protein HHO.C10"
                     /codon_start=1
                     /product="homeobox protein Hox-B5"
                     /protein_id="NP_002138.1"
                     /db_xref="GI:4504469"
                     /db_xref="CCDS:CCDS11530.1"
                     /db_xref="GeneID:3215"
                     /db_xref="HGNC:5116"
                     /db_xref="HPRD:00848"
                     /db_xref="MIM:142960"
                     /translation="

MSSYFVNSFSGRYPNGPDYQLLNYGSGSSLSGSYRDPAAMHTGSYGYNYNGMDLSVNRSSASSSHFGAVGESSRAFPAPAQEPRFRQAASSCSLSSPESLPCTNGDSHGAKPSASSPSDQATSASSSANFTEIDEASASSEPEEAASQLSSPSLARAQPEPMATSTAAPEGQTPQIFPWMRKLHISHDMTGPDGKRARTAYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLSERQIKIWFQNRRMKWKKDNKLKSMSLATAGSAFQP

"
     misc_feature    585..602
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="propagated from UniProtKB/Swiss-Prot (P09067.3);
                     Region: Antp-type hexapeptide"
     misc_feature    642..818
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /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(642..656,660..662,711..713,729..731,768..770,
                     774..779,786..791,795..803,807..812)
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:28970"
     misc_feature    order(648..650,657..659,777..779,786..791,798..800)
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:28970"
     exon            622..1821
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /inference="alignment:Splign:1.39.8"
     variation       903
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:11554725"
     STS             1009..1150
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /standard_name="G10507"
                     /db_xref="UniSTS:45825"
     variation       1010
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:9299"
     variation       1077
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:3087996"
     variation       1489
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:872760"
     STS             1566..1801
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
                     /standard_name="RH17800"
                     /db_xref="UniSTS:82172"
     polyA_signal    1800..1805
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
     polyA_site      1821
                     /gene="HOXB5"
                     /gene_synonym="HHO.C10; HOX2; Hox2.1; HOX2A; HU-1"
ORIGIN

gtgaagcacagggttataacgaccacgatccacaaatcaagccctccaaaatcacccaaatgagctcgtactttgtaaactccttctcggggcgttatccaaatggcccggactatcagttgctaaattatggcagtggcagctctctgagcggctcttacagggatcccgctgccatgcacaccggctcttacggctacaattacaatgggatggacctcagcgtcaaccgctcctcggcctcctccagccactttggggcggtgggcgagagctcgcgcgccttccccgcgcccgcccaggagccccgcttcaggcaagcggcttcgagctgctccctgtcctcgcccgagtccctgccctgcaccaacggcgacagccacggcgccaagccctctgcttcgtccccctccgaccaggcgacctcagccagctccagcgccaatttcaccgaaatagacgaggccagcgcgtcctcggagcctgaggaagcggcaagccagctaagcagccccagcctagctcgggcgcagccagagcccatggccacctccacagccgcgcccgaggggcagactccgcaaatattcccctggatgaggaagcttcacatcagccatgatatgaccgggccggacgggaaaagggcccggaccgcgtatacccgctaccagaccctggagctggaaaaggagttccacttcaaccgctacctgacccggcgacggcgcatcgagatcgcccacgcactctgcctgtccgagcgccagatcaagatctggttccagaaccggcgcatgaagtggaagaaggacaacaaattgaaaagtatgagcctggctacagctggcagcgccttccagccctgagcccgcccagaggagcccagcggcccaagagcccgtgccacccccagccctggcccctccaatcctccccgctctgccgccgcccgctggggaccggttcccacaagcctgcctcgccttgtgttacgatatttcgtttggtcttaggtcttcctgtggctccctctctcctggactggttatcttgttattattgttaataataattattattattattttccttccatgctcccaactcccttctgcttgtcccaaatccgccagtgtttctgaatgtttgtgtctgtggttgcagtctttcccccaggaaaaaaaaaaaaagaaattcgcatgtttaatgtgaactctcccctccccatctgtgttctaacttatttataaaaagatgatcgctgtattttgagtttcagctggaaacttctgtaaggggcagcagttgaggtggggtagtgccgcagtggggtcaagctgagctggcttcggagatggagtcccttttcattctcctcctcctccctcctcactccctaggcccaagtctcctaggggcttggtcctagggtgggaaggggctagggaggaccaaagggatggtattgagaagagagaaagaagatagtgagatttaagttcctgctgcctgggtaggccccacaaggcctggtctgggagtatacggaaacaaaaatgatcctcagtgcaaaatgtcttgtgtatttctctgtgaatccatgggtctggctagagggcccaaagcttgtaaatatggggatagtctgggtcagacccatctctcccttacccatcttgcttccaagaccatttgtagtgagcgagtggatgctgtgctacgtgtgaaatctgtctttgcggggcctgtctcagtgattcgcttttggtatttgtttgtagctttcctggaagtcaaataaatgtttcccccactccaaaaaaaaaa

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