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2024-04-19 14:00:02, GGRNA : RefSeq release 60 (20130726)
LOCUS NM_152311 1174 bp mRNA linear PRI 17-APR-2013
DEFINITION Homo sapiens clarin 3 (CLRN3), mRNA.
ACCESSION NM_152311
VERSION NM_152311.3 GI:219521912
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 1174)
AUTHORS Chung,S.J., Armasu,S.M., Biernacka,J.M., Anderson,K.J.,
Lesnick,T.G., Rider,D.N., Cunningham,J.M., Eric Ahlskog,J.,
Frigerio,R. and Maraganore,D.M.
TITLE Genomic determinants of motor and cognitive outcomes in Parkinson's
disease
JOURNAL Parkinsonism Relat. Disord. 18 (7), 881-886 (2012)
PUBMED 22658654
REMARK GeneRIF: The SNP rs6482992 in the CLRN3 gene had the smallest p
value in analyses of the cognitive outcome.
REFERENCE 2 (bases 1 to 1174)
AUTHORS Lamesch,P., Li,N., Milstein,S., Fan,C., Hao,T., Szabo,G., Hu,Z.,
Venkatesan,K., Bethel,G., Martin,P., Rogers,J., Lawlor,S.,
McLaren,S., Dricot,A., Borick,H., Cusick,M.E., Vandenhaute,J.,
Dunham,I., Hill,D.E. and Vidal,M.
TITLE hORFeome v3.1: a resource of human open reading frames representing
over 10,000 human genes
JOURNAL Genomics 89 (3), 307-315 (2007)
PUBMED 17207965
REFERENCE 3 (bases 1 to 1174)
AUTHORS Grupe,A., Li,Y., Rowland,C., Nowotny,P., Hinrichs,A.L., Smemo,S.,
Kauwe,J.S., Maxwell,T.J., Cherny,S., Doil,L., Tacey,K., van
Luchene,R., Myers,A., Wavrant-De Vrieze,F., Kaleem,M.,
Hollingworth,P., Jehu,L., Foy,C., Archer,N., Hamilton,G.,
Holmans,P., Morris,C.M., Catanese,J., Sninsky,J., White,T.J.,
Powell,J., Hardy,J., O'Donovan,M., Lovestone,S., Jones,L.,
Morris,J.C., Thal,L., Owen,M., Williams,J. and Goate,A.
TITLE A scan of chromosome 10 identifies a novel locus showing strong
association with late-onset Alzheimer disease
JOURNAL Am. J. Hum. Genet. 78 (1), 78-88 (2006)
PUBMED 16385451
REMARK GeneRIF: Observational study of gene-disease association. (HuGE
Navigator)
REFERENCE 4 (bases 1 to 1174)
AUTHORS Oh,J.H., Yang,J.O., Hahn,Y., Kim,M.R., Byun,S.S., Jeon,Y.J.,
Kim,J.M., Song,K.S., Noh,S.M., Kim,S., Yoo,H.S., Kim,Y.S. and
Kim,N.S.
TITLE Transcriptome analysis of human gastric cancer
JOURNAL Mamm. Genome 16 (12), 942-954 (2005)
PUBMED 16341674
REFERENCE 5 (bases 1 to 1174)
AUTHORS Deloukas,P., Earthrowl,M.E., Grafham,D.V., Rubenfield,M.,
French,L., Steward,C.A., Sims,S.K., Jones,M.C., Searle,S.,
Scott,C., Howe,K., Hunt,S.E., Andrews,T.D., Gilbert,J.G.,
Swarbreck,D., Ashurst,J.L., Taylor,A., Battles,J., Bird,C.P.,
Ainscough,R., Almeida,J.P., Ashwell,R.I., Ambrose,K.D.,
Babbage,A.K., Bagguley,C.L., Bailey,J., Banerjee,R., Bates,K.,
Beasley,H., Bray-Allen,S., Brown,A.J., Brown,J.Y., Burford,D.C.,
Burrill,W., Burton,J., Cahill,P., Camire,D., Carter,N.P.,
Chapman,J.C., Clark,S.Y., Clarke,G., Clee,C.M., Clegg,S., Corby,N.,
Coulson,A., Dhami,P., Dutta,I., Dunn,M., Faulkner,L., Frankish,A.,
Frankland,J.A., Garner,P., Garnett,J., Gribble,S., Griffiths,C.,
Grocock,R., Gustafson,E., Hammond,S., Harley,J.L., Hart,E.,
Heath,P.D., Ho,T.P., Hopkins,B., Horne,J., Howden,P.J., Huckle,E.,
Hynds,C., Johnson,C., Johnson,D., Kana,A., Kay,M., Kimberley,A.M.,
Kershaw,J.K., Kokkinaki,M., Laird,G.K., Lawlor,S., Lee,H.M.,
Leongamornlert,D.A., Laird,G., Lloyd,C., Lloyd,D.M., Loveland,J.,
Lovell,J., McLaren,S., McLay,K.E., McMurray,A.,
Mashreghi-Mohammadi,M., Matthews,L., Milne,S., Nickerson,T.,
Nguyen,M., Overton-Larty,E., Palmer,S.A., Pearce,A.V., Peck,A.I.,
Pelan,S., Phillimore,B., Porter,K., Rice,C.M., Rogosin,A.,
Ross,M.T., Sarafidou,T., Sehra,H.K., Shownkeen,R., Skuce,C.D.,
Smith,M., Standring,L., Sycamore,N., Tester,J., Thorpe,A.,
Torcasso,W., Tracey,A., Tromans,A., Tsolas,J., Wall,M., Walsh,J.,
Wang,H., Weinstock,K., West,A.P., Willey,D.L., Whitehead,S.L.,
Wilming,L., Wray,P.W., Young,L., Chen,Y., Lovering,R.C.,
Moschonas,N.K., Siebert,R., Fechtel,K., Bentley,D., Durbin,R.,
Hubbard,T., Doucette-Stamm,L., Beck,S., Smith,D.R. and Rogers,J.
TITLE The DNA sequence and comparative analysis of human chromosome 10
JOURNAL Nature 429 (6990), 375-381 (2004)
PUBMED 15164054
REFERENCE 6 (bases 1 to 1174)
AUTHORS Fields,R.R., Zhou,G., Huang,D., Davis,J.R., Moller,C.,
Jacobson,S.G., Kimberling,W.J. and Sumegi,J.
TITLE Usher syndrome type III: revised genomic structure of the USH3 gene
and identification of novel mutations
JOURNAL Am. J. Hum. Genet. 71 (3), 607-617 (2002)
PUBMED 12145752
REFERENCE 7 (bases 1 to 1174)
AUTHORS Adato,A., Vreugde,S., Joensuu,T., Avidan,N., Hamalainen,R.,
Belenkiy,O., Olender,T., Bonne-Tamir,B., Ben-Asher,E., Espinos,C.,
Millan,J.M., Lehesjoki,A.E., Flannery,J.G., Avraham,K.B.,
Pietrokovski,S., Sankila,E.M., Beckmann,J.S. and Lancet,D.
TITLE USH3A transcripts encode clarin-1, a four-transmembrane-domain
protein with a possible role in sensory synapses
JOURNAL Eur. J. Hum. Genet. 10 (6), 339-350 (2002)
PUBMED 12080385
COMMENT VALIDATED REFSEQ: This record has undergone validation or
preliminary review. The reference sequence was derived from
BC029478.1, BM830163.1 and BX640823.1.
On Jan 3, 2009 this sequence version replaced gi:142352526.
##Evidence-Data-START##
Transcript exon combination :: BC029478.1, BG427068.1 [ECO:0000332]
RNAseq introns :: single sample supports all introns
ERS025082, ERS025084 [ECO:0000348]
##Evidence-Data-END##
PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
1-273 BC029478.1 1-273
274-877 BM830163.1 27-630
878-1102 BC029478.1 878-1102
1103-1142 BX640823.1 1383-1422
1143-1174 BC029478.1 1143-1174
FEATURES Location/Qualifiers
source 1..1174
/organism="Homo sapiens"
/mol_type="mRNA"
/db_xref="taxon:9606"
/chromosome="10"
/map="10q26.2"
gene 1..1174
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/note="clarin 3"
/db_xref="GeneID:119467"
/db_xref="HGNC:20795"
/db_xref="HPRD:14553"
exon 1..392
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/inference="alignment:Splign:1.39.8"
misc_feature 140..142
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/note="upstream in-frame stop codon"
variation 141
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/replace="a"
/replace="g"
/db_xref="dbSNP:3802693"
CDS 164..844
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/note="transmembrane protein 12; usher syndrome
type-3A-like protein 1"
/codon_start=1
/product="clarin-3"
/protein_id="NP_689524.1"
/db_xref="GI:22748685"
/db_xref="CCDS:CCDS7656.1"
/db_xref="GeneID:119467"
/db_xref="HGNC:20795"
/db_xref="HPRD:14553"
/translation="
MPTTKKTLMFLSSFFTSLGSFIVICSILGTQAWITSTIAVRDSASNGSIFITYGLFRGESSEELSHGLAEPKKKFAVLEILNNSSQKTLHSVTILFLVLSLITSLLSSGFTFYNSISNPYQTFLGPTGVYTWNGLGASFVFVTMILFVANTQSNQLSEELFQMLYPATTSKGTTHSYGYSFWLILLVILLNIVTVTIIIFYQKARYQRKQEQRKPMEYAPRDGILF
"
misc_feature 185..247
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/inference="non-experimental evidence, no additional
details recorded"
/note="propagated from UniProtKB/Swiss-Prot (Q8NCR9.1);
transmembrane region"
misc_feature 245..709
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/note="PMP-22/EMP/MP20/Claudin family; Region:
PMP22_Claudin; cl15797"
/db_xref="CDD:210197"
misc_feature 437..499
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/inference="non-experimental evidence, no additional
details recorded"
/note="propagated from UniProtKB/Swiss-Prot (Q8NCR9.1);
transmembrane region"
misc_feature 548..610
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/inference="non-experimental evidence, no additional
details recorded"
/note="propagated from UniProtKB/Swiss-Prot (Q8NCR9.1);
transmembrane region"
misc_feature 704..766
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/inference="non-experimental evidence, no additional
details recorded"
/note="propagated from UniProtKB/Swiss-Prot (Q8NCR9.1);
transmembrane region"
variation 375
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/replace="a"
/replace="c"
/db_xref="dbSNP:35890579"
variation 386
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/replace="a"
/replace="t"
/db_xref="dbSNP:35070529"
exon 393..572
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/inference="alignment:Splign:1.39.8"
exon 573..1143
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/inference="alignment:Splign:1.39.8"
STS 676..814
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/standard_name="RH102083"
/db_xref="UniSTS:96417"
variation 678
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/replace="a"
/replace="g"
/db_xref="dbSNP:35146970"
variation 737
/gene="CLRN3"
/gene_synonym="TMEM12; USH3AL1"
/replace="a"
/replace="g"
/db_xref="dbSNP:34656572"
ORIGIN
aatgtccattagcataacccttcctcaggaagagtgagattttatatttgacaataaagtgttagactccatttctaaataccagacttcaaaagataaggttcaaaagtgttataagaagatattcctttttttgtcctagagaacttattttcctgtgaaaatgcctaccacaaagaagacattgatgttcttatcaagctttttcaccagccttgggtccttcattgtaatttgctctattcttgggacacaagcatggatcaccagtacaattgctgttagagactctgcttcaaatgggagcattttcatcacttacggactttttcgtggggagagtagtgaagaattgagtcacggacttgcagaaccaaagaaaaagtttgcagttttagagatactgaataattcttcccaaaaaactctgcattcggtgactatcctgttcctggtcctgagtttgatcacgtcgctgctgagctctgggtttaccttctacaacagcatcagcaacccttaccagacattcctggggccgacgggggtgtacacctggaacgggctcggtgcatccttcgtttttgtgaccatgatactgtttgtggcgaacacgcagtccaaccaactctccgaagagttgttccaaatgctttacccggcaaccaccagtaaaggaacgacccacagttacggatactcgttctggctcatactgctcgtcattcttctaaatatagtcactgtaaccatcatcattttctaccagaaggccagataccagcggaagcaggagcagagaaagccaatggaatatgctccaagggacggaattttattctgaattctctttcatctcattttggcgttgcatctattgtacatcagccctgagtagtaactggttagcttctctggacaattcagcatggtaacgtgactgtcatctgtgacagcatttgtgtttcatgacactgtgttcttcattgatgctgtactcctgaaaatttttcccacaaggttggggaaatgaatgggaaatgtcgctggtctgtgtggtattcaaagcagtagtatcatgatgagcgtaacgacccttctgacctggtctcacgatctgaaataataaaaggctgtgtcatgcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
//
ANNOTATIONS from NCBI Entrez Gene (20130726):
GeneID:119467 -> Cellular component: GO:0016021 [integral to membrane] evidence: IEA
by
@meso_cacase at
DBCLS
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