GGRNA Home | Help | Advanced search

2024-03-29 20:16:41, GGRNA : RefSeq release 60 (20130726)

LOCUS       NM_006608               3244 bp    mRNA    linear   PRI 15-JUN-2013
DEFINITION  Homo sapiens putative homeodomain transcription factor 1 (PHTF1),
            mRNA.
ACCESSION   NM_006608
VERSION     NM_006608.2  GI:166197665
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 3244)
  AUTHORS   Comuzzie,A.G., Cole,S.A., Laston,S.L., Voruganti,V.S., Haack,K.,
            Gibbs,R.A. and Butte,N.F.
  TITLE     Novel genetic loci identified for the pathophysiology of childhood
            obesity in the Hispanic population
  JOURNAL   PLoS ONE 7 (12), E51954 (2012)
   PUBMED   23251661
REFERENCE   2  (bases 1 to 3244)
  AUTHORS   Eriksson,N., Tung,J.Y., Kiefer,A.K., Hinds,D.A., Francke,U.,
            Mountain,J.L. and Do,C.B.
  TITLE     Novel associations for hypothyroidism include known autoimmune risk
            loci
  JOURNAL   PLoS ONE 7 (4), E34442 (2012)
   PUBMED   22493691
REFERENCE   3  (bases 1 to 3244)
  AUTHORS   Douroudis,K., Kisand,K., Nemvalts,V., Rajasalu,T. and Uibo,R.
  TITLE     Allelic variants in the PHTF1-PTPN22, C12orf30 and CD226 regions as
            candidate susceptibility factors for the type 1 diabetes in the
            Estonian population
  JOURNAL   BMC Med. Genet. 11, 11 (2010)
   PUBMED   20089178
  REMARK    GeneRIF: Results supports the rs6679677 (PHTF1-PTPN22) SNP as a
            susceptibility factor for type 1 diabetes.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3244)
  AUTHORS   Smyth,D.J., Cooper,J.D., Howson,J.M., Walker,N.M., Plagnol,V.,
            Stevens,H., Clayton,D.G. and Todd,J.A.
  TITLE     PTPN22 Trp620 explains the association of chromosome 1p13 with type
            1 diabetes and shows a statistical interaction with HLA class II
            genotypes
  JOURNAL   Diabetes 57 (6), 1730-1737 (2008)
   PUBMED   18305142
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   5  (bases 1 to 3244)
  AUTHORS   Todd,J.A., Walker,N.M., Cooper,J.D., Smyth,D.J., Downes,K.,
            Plagnol,V., Bailey,R., Nejentsev,S., Field,S.F., Payne,F.,
            Lowe,C.E., Szeszko,J.S., Hafler,J.P., Zeitels,L., Yang,J.H.,
            Vella,A., Nutland,S., Stevens,H.E., Schuilenburg,H., Coleman,G.,
            Maisuria,M., Meadows,W., Smink,L.J., Healy,B., Burren,O.S.,
            Lam,A.A., Ovington,N.R., Allen,J., Adlem,E., Leung,H.T.,
            Wallace,C., Howson,J.M., Guja,C., Ionescu-Tirgoviste,C.,
            Simmonds,M.J., Heward,J.M., Gough,S.C., Dunger,D.B., Wicker,L.S.
            and Clayton,D.G.
  CONSRTM   Genetics of Type 1 Diabetes in Finland; Wellcome Trust Case Control
            Consortium
  TITLE     Robust associations of four new chromosome regions from genome-wide
            analyses of type 1 diabetes
  JOURNAL   Nat. Genet. 39 (7), 857-864 (2007)
   PUBMED   17554260
REFERENCE   6  (bases 1 to 3244)
  AUTHORS   Manuel,A., Beaupain,D., Romeo,P.H. and Raich,N.
  TITLE     Molecular characterization of a novel gene family (PHTF) conserved
            from Drosophila to mammals
  JOURNAL   Genomics 64 (2), 216-220 (2000)
   PUBMED   10729229
REFERENCE   7  (bases 1 to 3244)
  AUTHORS   Raich,N., Mattei,M.G., Romeo,P.H. and Beaupain,D.
  TITLE     PHTF, a novel atypical homeobox gene on chromosome 1p13, is
            evolutionarily conserved
  JOURNAL   Genomics 59 (1), 108-109 (1999)
   PUBMED   10395808
REFERENCE   8  (bases 1 to 3244)
  AUTHORS   Siegele,D.A. and Kolter,R.
  TITLE     Life after log
  JOURNAL   J. Bacteriol. 174 (2), 345-348 (1992)
   PUBMED   1729229
  REMARK    Review article
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DB457884.1, CX763183.1, AJ011863.1, BC002447.2, DA728266.1 and
            AK126773.1.
            On Jan 29, 2008 this sequence version replaced gi:5729975.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AJ011863.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           ERS025084 [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-334               DB457884.1         4-337
            335-421             CX763183.1         211-297
            422-1075            AJ011863.1         1-654
            1076-2342           BC002447.2         1220-2486
            2343-2720           DA728266.1         266-643
            2721-3244           AK126773.1         3420-3943
FEATURES             Location/Qualifiers
     source          1..3244
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1p13"
     gene            1..3244
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /note="putative homeodomain transcription factor 1"
                     /db_xref="GeneID:10745"
                     /db_xref="HGNC:8939"
                     /db_xref="MIM:604950"
     exon            1..497
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    423..425
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /note="upstream in-frame stop codon"
     CDS             453..2741
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /codon_start=1
                     /product="putative homeodomain transcription factor 1"
                     /protein_id="NP_006599.2"
                     /db_xref="GI:166197666"
                     /db_xref="CCDS:CCDS861.1"
                     /db_xref="GeneID:10745"
                     /db_xref="HGNC:8939"
                     /db_xref="MIM:604950"
                     /translation="
MASNERDAISWYQKKIGAYDQQIWEKSIEQTQIKGLKNKPKKMGHIKPDLIDVDLIRGSTFAKAKPEIPWTSLTRKGLVRVVFFPLFSNWWIQVTSLRIFVWLLLLYFMQVIAIVLYLMMPIVNISEVLGPLCLMLLMGTVHCQIVSTQITRPSGNNGNRRRRKLRKTVNGDGSRENGNNSSDKVRGIETLESVPIIGGFWETIFGNRIKRVKLISNKGTETDNDPSCVHPIIKRRQCRPEIRMWQTREKAKFSDGEKCRREAFRRLGNGVSDDLSSEEDGEARTQMILLRRSVEGASSDNGCEVKNRKSILSRHLNSQVKKTTTRWCHIVRDSDSLAESEFESAAFSQGSRSGVSGGSRSLNMSRRDSESTRHDSETEDMLWDDLLHGPECRSSVTSDSEGAHVNTLHSGTKRDPKEDVFQQNHLFWLQNSSPSSDRVSAIIWEGNECKKMDMSVLEISGIIMSRVNAYQQGVGYQMLGNVVTIGLAFFPFLHRLFREKSLDQLKSISAEEILTLFCGAPPVTPIIVLSIINFFERLCLTWMFFFMMCVAERTYKQRFLFAKLFSHITSARKARKYEIPHFRLKKVENIKIWLSLRSYLKRRGPQRSVDVVVSSVFLLTLSIAFICCAQVLQGHKTFLNDAYNWEFLIWETALLLFLLRLASLGSETNKKYSNVSILLTEQINLYLKMEKKPNKKEQLTLVNNVLKLSTKLLKELDTPFRLYGLTMNPLIYNITRVVILSAVSGVISDLLGFNIRLWKIKS
"
     misc_feature    459..914
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /note="Male germ-cell putative homeodomain transcription
                     factor; Region: Phtf-FEM1B_bdg; pfam12129"
                     /db_xref="CDD:152564"
     exon            498..554
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            555..624
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            625..783
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     variation       734
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:2273757"
     exon            784..940
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            941..1075
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            1076..1235
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            1236..1409
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            1410..1499
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            1500..1721
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            1722..1850
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            1851..2123
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     variation       2038
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:1141014"
     exon            2124..2255
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            2256..2342
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            2343..2498
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            2499..2594
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            2595..2720
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     exon            2721..3244
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /inference="alignment:Splign:1.39.8"
     STS             3040..3162
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /standard_name="SHGC-75355"
                     /db_xref="UniSTS:30547"
     STS             3072..3217
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /standard_name="D1S3609"
                     /db_xref="UniSTS:34839"
     STS             3088..3237
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /standard_name="SHGC-75358"
                     /db_xref="UniSTS:29463"
     variation       3105
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:1141015"
     variation       3106
                     /gene="PHTF1"
                     /gene_synonym="PHTF"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:1141016"
ORIGIN      
ctctccggcgtctccgcctggaggggaagatgcggcctgcctggcccgccgcctcgcccccggcctcacggtgggaccccgggcactgaggacggaggtcccgggcgccggcccgcggggcaacgggcactaggtgagagccggacgcgggcgagcgaaggaggcgggtgccgggcgactccagcggcggcccctgcccctcccccgcacccacgaacacgctcgcccgatatattgcagaggcttctccggtcgccgctgcgccagtttttttttgtttgtttgttgtgttttccctggcaaacagctggagaaagagcagctcatggagaggctgagagaagcggttttcgcgtcctacccaaactgggagagtaaccttcagcagctggactcaccgattggttttccttcattttcagtgaaatcccattctctggctggagacacagatggcctcaaatgagagagatgctatatcgtggtaccaaaagaagattggagcctacgatcagcagatatgggaaaagtcaatcgaacagactcagattaagggtttgaaaaacaaaccgaaaaagatgggccacataaagccagacttgattgacgttgacttaatcagagggtcaacatttgccaaagcaaaacctgaaattccatggacatctctgactcggaaggggcttgttcgagttgtattttttccattgttcagcaattggtggattcaggttacctctttaagaatctttgtttggctgttactactttatttcatgcaagttatagcaattgtcttatatttgatgatgcctattgtgaacataagtgaagtacttggacccttgtgccttatgctactcatgggaactgtccactgtcaaattgtgtctactcagataacaagaccatcaggaaacaatggaaatcgaagaagaagaaaattacgaaaaactgtaaatggtgatgggagccgagaaaatggaaataactcctctgataaagtcagaggaatagaaactttggaatctgtacccattattggtggtttttgggagactatctttggcaacaggattaaaagagtaaaattaatatctaacaaagggactgaaactgacaatgacccaagttgtgtccatcctatcattaagaggagacaatgtcgaccagagattagaatgtggcaaacaagagagaaagcaaaattttcagatggagaaaagtgccgtagggaggcttttaggcgtttgggtaatggggtgtctgatgacctgtcaagtgaagaagatggtgaagcacggacacagatgatattattgcgtaggagtgtggaaggggcctcaagtgacaatggttgtgaagttaagaatagaaaatcaatactttcaaggcacctaaactctcaggtaaagaaaaccactacaaggtggtgtcatattgtgcgggattcagatagtctggctgaatcagaatttgaatcagcagccttcagccagggctctagatcgggtgtgagtggtggctctcgaagcctcaacatgtcaagaagagactcagaaagcacccgccatgactcggagactgaggacatgttatgggacgacctgctacatggcccagagtgccggtcatctgtcaccagtgacagtgagggggcccatgtgaatacccttcactcagggaccaaacgtgaccccaaagaggatgtttttcagcagaatcatttattctggcttcagaattcaagtccttcctctgatcgagttagtgcaataatctgggaggggaatgagtgcaaaaagatggatatgtctgtgttggaaataagtggcatcatcatgagcagggtcaatgcctatcagcaaggagtaggttatcagatgctgggaaatgttgtcactattggattagcattttttccattcttacatcgacttttccgtgagaagagccttgaccaactaaagtccatttcagctgaggagatcttgactctcttttgtggggcaccacctgttacacctattattgttttgtcgataattaatttttttgaaagattgtgtcttacttggatgttttttttcatgatgtgtgtggcagagagaacatataaacagagatttttatttgcaaaactcttcagccatattacttctgccaggaaagctaggaaatatgaaatacctcatttcagacttaagaaggtggagaatattaaaatatggttatcactgcgttcctatctaaagagacgggggccacagcgttcagttgatgtggttgtatcctcggttttcctactgacactttcgattgctttcatttgttgtgctcaggttctccaaggacataaaactttcctgaatgatgcttataactgggagtttttgatctgggaaacagctttactactttttttattgcgtctggcctcactggggtctgaaaccaataagaaatacagcaatgtttcaatattacttacagaacagattaatttatatcttaagatggaaaaaaagccaaataagaaagaacagcttactctagtaaacaatgtattaaagctgtccaccaagttgttgaaagagctggacacaccatttagactctatggactgacaatgaatcccttaatctacaatatcacaagagtagttatcctttctgctgtctcaggtgttataagtgatcttctaggatttaatataagactgtggaaaattaaatcataagctgagtaaatgcctggactctcccctggctggtatcaaaacttacctatcaaggaaagtgatgactgcagaaaccagtgagatacccacctgcttgttcacatgcacaggtgctctcagctctgccaaagcgaatgaatggtgtttccggaggagcaagtccttttccaactgggtgtgcatgctaaaaacctgtattttcatgcttttcaaacaacatgaatagtcagctgactaaagactgtgtgtgttgtggtaacacaaagacaattttgtaagtttgcgcttcagtactgtgacagttatgtttactggacatagtcttttgggcaactatgatagatgcccaaagcatgaagcaaatatcttttattggaaatatgcaaattcaatacttttccattatagtctatagaactggagatttcatttctctatcaaagagagatcaagcgaactattttaggttaaatccgaataaaagaactttactggagactttc
//

Annotations:

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:10745 -> Molecular function: GO:0003677 [DNA binding] evidence: IEA
            GeneID:10745 -> Molecular function: GO:0003700 [sequence-specific DNA binding transcription factor activity] evidence: TAS
            GeneID:10745 -> Biological process: GO:0006351 [transcription, DNA-dependent] evidence: IEA
            GeneID:10745 -> Cellular component: GO:0005634 [nucleus] evidence: IEA

by @meso_cacase at DBCLS
This page is licensed under a Creative Commons Attribution 2.1 Japan License.