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2024-04-18 23:59:05, GGRNA : RefSeq release 60 (20130726)
LOCUS NM_001804 1772 bp mRNA linear PRI 15-JUL-2013 DEFINITION Homo sapiens caudal type homeobox 1 (CDX1), mRNA. ACCESSION NM_001804 VERSION NM_001804.2 GI:121114295 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 1772) AUTHORS Zhang,T., Tang,X.B., Wang,L.L., Bai,Y.Z., Qiu,G.R., Yuan,Z.W. and Wang,W.L. TITLE Mutations and down-regulation of CDX1 in children with anorectal malformations JOURNAL Int J Med Sci 10 (2), 191-197 (2013) PUBMED 23329892 REMARK GeneRIF: The findings represented the relation between CDX1 mutations and CDX1 genotype. Furthermore, it was suggested that the downregulation of CDX1 might be related to the development of Anorectal malformations . REFERENCE 2 (bases 1 to 1772) AUTHORS Fujii,Y., Yoshihashi,K., Suzuki,H., Tsutsumi,S., Mutoh,H., Maeda,S., Yamagata,Y., Seto,Y., Aburatani,H. and Hatakeyama,M. TITLE CDX1 confers intestinal phenotype on gastric epithelial cells via induction of stemness-associated reprogramming factors SALL4 and KLF5 JOURNAL Proc. Natl. Acad. Sci. U.S.A. 109 (50), 20584-20589 (2012) PUBMED 23112162 REMARK GeneRIF: SALL4 and KLF5 were aberrantly expressed in the CDX1(+) intestinal metaplasia of the stomach. Sustained expression of CDX1 gave rise to the induction of early intestinal-stemness markers, followed by the expression of intestinal-differentiation markers. REFERENCE 3 (bases 1 to 1772) AUTHORS Freund,J.N. TITLE [Identity and intestinal pathologies: the Cdx2 homeotic gene] JOURNAL Ann Pathol 32 (5 SUPPL), S24-S27 (2012) PUBMED 23127929 REMARK GeneRIF: The homeotic transcription factor CDX1 is expressed in the intestinal epithelium at all stages of development. Review. Review article REFERENCE 4 (bases 1 to 1772) AUTHORS Rau,T.T., Rogler,A., Frischauf,M., Jung,A., Konturek,P.C., Dimmler,A., Faller,G., Sehnert,B., El-Rifai,W., Hartmann,A., Voll,R.E. and Schneider-Stock,R. TITLE Methylation-dependent activation of CDX1 through NF-kappaB: a link from inflammation to intestinal metaplasia in the human stomach JOURNAL Am. J. Pathol. 181 (2), 487-498 (2012) PUBMED 22749770 REMARK GeneRIF: The epigenetic inactivation of CDX1 by promoter methylation, as well as the functional link of CDX1 promoter methylation to the inflammatory NF-kappaB signaling pathway, were investigated. REFERENCE 5 (bases 1 to 1772) AUTHORS Nyquist,K.B., Panagopoulos,I., Thorsen,J., Haugom,L., Gorunova,L., Bjerkehagen,B., Fossa,A., Guriby,M., Nome,T., Lothe,R.A., Skotheim,R.I., Heim,S. and Micci,F. TITLE Whole-transcriptome sequencing identifies novel IRF2BP2-CDX1 fusion gene brought about by translocation t(1;5)(q42;q32) in mesenchymal chondrosarcoma JOURNAL PLoS ONE 7 (11), E49705 (2012) PUBMED 23185413 REMARK GeneRIF: analysis of an IRF2BP2-CDX1 fusion gene brought about by translocation t(1;5)(q42;q32) in mesenchymal chondrosarcoma REFERENCE 6 (bases 1 to 1772) AUTHORS Domon-Dell,C., Schneider,A., Moucadel,V., Guerin,E., Guenot,D., Aguillon,S., Duluc,I., Martin,E., Iovanna,J., Launay,J.F., Duclos,B., Chenard,M.P., Meyer,C., Oudet,P., Kedinger,M., Gaub,M.P. and Freund,J.N. TITLE Cdx1 homeobox gene during human colon cancer progression JOURNAL Oncogene 22 (39), 7913-7921 (2003) PUBMED 12970739 REMARK GeneRIF: these data show that Cdx1 exhibits a complex pattern during colorectal cancer progression, a high level of expression in polyps, and in one-third of the specimens, suggest that this gene may be a factor in the process toward malignant transformation REFERENCE 7 (bases 1 to 1772) AUTHORS Suh,E.R., Ha,C.S., Rankin,E.B., Toyota,M. and Traber,P.G. TITLE DNA methylation down-regulates CDX1 gene expression in colorectal cancer cell lines JOURNAL J. Biol. Chem. 277 (39), 35795-35800 (2002) PUBMED 12124393 REMARK GeneRIF: CDX1 is downregulated after promoter methylation in colorectal tumor cell lines REFERENCE 8 (bases 1 to 1772) AUTHORS Mizoshita,T., Inada,K., Tsukamoto,T., Kodera,Y., Yamamura,Y., Hirai,T., Kato,T., Joh,T., Itoh,M. and Tatematsu,M. TITLE Expression of Cdx1 and Cdx2 mRNAs and relevance of this expression to differentiation in human gastrointestinal mucosa--with special emphasis on participation in intestinal metaplasia of the human stomach JOURNAL Gastric Cancer 4 (4), 185-191 (2001) PUBMED 11846061 REMARK GeneRIF: Increased CDX1 mRNA expression is associated with chronic atrophic gastritis REFERENCE 9 (bases 1 to 1772) AUTHORS Mallo,G.V., Rechreche,H., Frigerio,J.M., Rocha,D., Zweibaum,A., Lacasa,M., Jordan,B.R., Dusetti,N.J., Dagorn,J.C. and Iovanna,J.L. TITLE Molecular cloning, sequencing and expression of the mRNA encoding human Cdx1 and Cdx2 homeobox. Down-regulation of Cdx1 and Cdx2 mRNA expression during colorectal carcinogenesis JOURNAL Int. J. Cancer 74 (1), 35-44 (1997) PUBMED 9036867 REFERENCE 10 (bases 1 to 1772) AUTHORS Bonner,C.A., Loftus,S.K. and Wasmuth,J.J. TITLE Isolation, characterization, and precise physical localization of human CDX1, a caudal-type homeobox gene JOURNAL Genomics 28 (2), 206-211 (1995) PUBMED 8530027 COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from AC005895.1 and AF239666.1. On Jan 5, 2007 this sequence version replaced gi:4502762. Summary: This gene is a member of the caudal-related homeobox transcription factor gene family. The encoded DNA-binding protein regulates intestine-specific gene expression and enterocyte differentiation. It has been shown to induce expression of the intestinal alkaline phosphatase gene, and inhibit beta-catenin/T-cell factor transcriptional activity. [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 :: U51095.1, U15212.1 [ECO:0000332] RNAseq introns :: single sample supports all introns ERS025094 [ECO:0000348] ##Evidence-Data-END## COMPLETENESS: full length. PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-15 AC005895.1 35181-35195 16-957 AF239666.1 1-942 958-1772 AC005895.1 52144-52958 FEATURES Location/Qualifiers source 1..1772 /organism="Homo sapiens" /mol_type="mRNA" /db_xref="taxon:9606" /chromosome="5" /map="5q32" gene 1..1772 /gene="CDX1" /note="caudal type homeobox 1" /db_xref="GeneID:1044" /db_xref="HGNC:1805" /db_xref="MIM:600746" exon 1..541 /gene="CDX1" /inference="alignment:Splign:1.39.8" misc_feature 1 /gene="CDX1" /note="5'-most transcription initiation site" STS 18..1639 /gene="CDX1" /db_xref="UniSTS:482572" misc_feature 19..21 /gene="CDX1" /note="upstream in-frame stop codon" variation 83 /gene="CDX1" /replace="a" /replace="g" /db_xref="dbSNP:2302274" CDS 97..894 /gene="CDX1" /note="caudal type homeobox transcription factor 1; caudal type homeo box transcription factor 1; caudal-type homeobox protein CDX1; caudal-type homeobox protein 1" /codon_start=1 /product="homeobox protein CDX-1" /protein_id="NP_001795.2" /db_xref="GI:121114296" /db_xref="CCDS:CCDS4304.1" /db_xref="GeneID:1044" /db_xref="HGNC:1805" /db_xref="MIM:600746" /translation="
MYVGYVLDKDSPVYPGPARPASLGLGPQAYGPPAPPPAPPQYPDFSSYSHVEPAPAPPTAWGAPFPAPKDDWAAAYGPGPAAPAASPASLAFGPPPDFSPVPAPPGPGPGLLAQPLGGPGTPSSPGAQRPTPYEWMRRSVAAGGGGGSGKTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKERKVNKKKQQQQQPPQPPMAHDITATPAGPSLGGLCPSNTSLLATSSPMPVKEEFLP
"
misc_feature 562..729
/gene="CDX1"
/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(562..573,577..579,628..630,646..648,685..687,
691..696,703..708,712..720,724..729)
/gene="CDX1"
/note="DNA binding site [nucleotide binding]"
/db_xref="CDD:28970"
misc_feature order(565..567,574..576,694..696,703..708,715..717)
/gene="CDX1"
/note="specific DNA base contacts [nucleotide binding];
other site"
/db_xref="CDD:28970"
variation 117
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:371135665"
variation 336
/gene="CDX1"
/replace="c"
/replace="g"
/db_xref="dbSNP:112755531"
variation 476
/gene="CDX1"
/replace="a"
/replace="c"
/db_xref="dbSNP:370852694"
variation 485
/gene="CDX1"
/replace="c"
/replace="g"
/db_xref="dbSNP:2302275"
exon 542..687
/gene="CDX1"
/inference="alignment:Splign:1.39.8"
variation 556
/gene="CDX1"
/replace="a"
/replace="t"
/db_xref="dbSNP:141296812"
variation 570
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:150404926"
variation 572
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:138123617"
variation 620..621
/gene="CDX1"
/replace=""
/replace="ccc"
/db_xref="dbSNP:373496881"
variation 621
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:143926295"
variation 625
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:201857355"
variation 626
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:200074812"
variation 640
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:146129317"
variation 643
/gene="CDX1"
/replace="a"
/replace="c"
/replace="t"
/db_xref="dbSNP:140956520"
variation 644
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:200155434"
variation 657
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:184290965"
variation 682
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:143202475"
exon 688..1772
/gene="CDX1"
/inference="alignment:Splign:1.39.8"
variation 723
/gene="CDX1"
/replace="g"
/replace="t"
/db_xref="dbSNP:372009949"
variation 734
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:376634181"
variation 735
/gene="CDX1"
/replace="a"
/replace="c"
/db_xref="dbSNP:200299344"
variation 770
/gene="CDX1"
/replace="c"
/replace="g"
/db_xref="dbSNP:370020614"
variation 771
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:148587387"
variation 773
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:371789864"
variation 791
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:374797163"
variation 812
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:142955459"
variation 839
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:372730428"
variation 849
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:200719809"
variation 851
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:151148312"
variation 867
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:201588716"
variation 903
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:369619598"
variation 910
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:201901105"
variation 914
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:145345944"
variation 915
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:187114829"
variation 976
/gene="CDX1"
/replace="a"
/replace="c"
/db_xref="dbSNP:2880319"
variation 1224
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:73796347"
variation 1366
/gene="CDX1"
/replace="c"
/replace="g"
/replace="t"
/db_xref="dbSNP:4705419"
variation 1412
/gene="CDX1"
/replace="a"
/replace="c"
/db_xref="dbSNP:73796348"
variation 1449
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:147235159"
variation 1459
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:139773344"
variation 1460
/gene="CDX1"
/replace="g"
/replace="t"
/db_xref="dbSNP:190378861"
STS 1461..1628
/gene="CDX1"
/standard_name="RH70663"
/db_xref="UniSTS:55638"
variation 1558
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:374395603"
variation 1573
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:374514168"
variation 1574
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:368830723"
variation 1584
/gene="CDX1"
/replace="c"
/replace="g"
/db_xref="dbSNP:372156290"
variation 1620
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:181700725"
variation 1641
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:185664624"
polyA_signal 1690..1695
/gene="CDX1"
variation 1706
/gene="CDX1"
/replace="c"
/replace="t"
/db_xref="dbSNP:189934215"
polyA_site 1716
/gene="CDX1"
variation 1738
/gene="CDX1"
/replace="a"
/replace="g"
/db_xref="dbSNP:376748939"
polyA_signal 1741..1746
/gene="CDX1"
polyA_site 1772
/gene="CDX1"
ORIGIN
aggacagccgagttcaggtgagcggttgctcgtcgtcggggcggccggcagcggcggctccagggcccagcatgcgcgggggaccccgcggccaccatgtatgtgggctatgtgctggacaaggattcgcccgtgtaccccggcccagccaggccagccagcctcggcctgggcccgcaagcctacggccccccggccccgcccccggcgcccccgcagtaccccgacttctccagctactctcacgtggagccggcccccgcgcccccgacggcctggggggcgcccttccctgcgcccaaggacgactgggccgccgcctacggcccgggccccgcggcccctgccgccagcccagcttcgctggcattcgggccccctccagactttagcccggtgccggcgccccctgggcccggcccgggcctcctggcgcagcccctcgggggcccgggcacaccgtcctcgcccggagcgcagaggccgacgccctacgagtggatgcggcgcagcgtggcggccggaggcggcggtggcagcggtaagactcggaccaaggacaagtaccgcgtggtctacaccgaccaccaacgcctggagctggagaaggagtttcattacagccgttacatcacaatccggcggaaatcagagctggctgccaatctggggctcactgaacggcaggtgaagatctggttccaaaaccggcgggcaaaggagcgcaaagtgaacaagaagaaacagcagcagcaacagcccccacagccgccgatggcccacgacatcacggccaccccagccgggccatccctggggggcctgtgtcccagcaacaccagcctcctggccacctcctctccaatgcctgtgaaagaggagtttctgccatagccccatgcccagcctgtgcgccgggggacctggggactcgggtgctgggagtgtggctcctgtgggcccaggaggtctggtccgagtctcagccctgaccttctgggacatggtggacagtcacctatccaccctctgcatccccttggcccatctgtgcagtaagcctgttggataaagaccttccagctcctgtgttctagacctctgggggataagggagtccagggtggatgatctcaatctcccgtgggcatctcaagccccaaatggttgggggaggggcctagacaaggctccaggccccacctcctcctccatacgttcagaggtgcagctggaggctgctgtggggaccacactgatcctggagaaaagggatggagctgaaaaagatggaatgcttgcagagcatgacctgaggagggaggaacgtggtcaactcacacctgcctcttcctgcagcctcacttctacctgcccccatcataagggcactgagcccttcccaggctggatactaagcacaaagcccatagcactgggctctgatggctgctccactgggttacagaatcacagccctcatgatcattctcagtgagggctctggattgagagggaggccctgggaggagagaagggggcagagtcttccctaccaggtttctacacccccgccaggctgcccatcagggcccagggagcccccagaggactttattcggaccaagcagagctcacagctggacaggtgttgtatatagagtggaatctcttggatgcagcttcaagaataaatttttcttctcttttcaaaaatgtataaaaatcattatacatagcattaaagaaacatttttgagaagtacaaatca
//
ANNOTATIONS from NCBI Entrez Gene (20130726):
GeneID:1044 -> Molecular function: GO:0000980 [RNA polymerase II distal enhancer sequence-specific DNA binding] evidence: IDA
GeneID:1044 -> Molecular function: GO:0001205 [RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription] evidence: IDA
GeneID:1044 -> Biological process: GO:0009887 [organ morphogenesis] evidence: TAS
GeneID:1044 -> Biological process: GO:0009952 [anterior/posterior pattern specification] evidence: IEA
GeneID:1044 -> Biological process: GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] evidence: IDA
GeneID:1044 -> Biological process: GO:0060349 [bone morphogenesis] evidence: IEA
GeneID:1044 -> Cellular component: GO:0005634 [nucleus] evidence: IEA
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