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2024-03-28 21:34:45, GGRNA : RefSeq release 60 (20130726)

LOCUS       NM_001136473            2577 bp    mRNA    linear   PRI 07-JUL-2013
DEFINITION  Homo sapiens lipopolysaccharide-induced TNF factor (LITAF),
            transcript variant 3, mRNA.
ACCESSION   NM_001136473
VERSION     NM_001136473.1  GI:210147506
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 2577)
  AUTHORS   Smith JG, Avery CL, Evans DS, Nalls MA, Meng YA, Smith EN, Palmer
            C, Tanaka T, Mehra R, Butler AM, Young T, Buxbaum SG, Kerr KF,
            Berenson GS, Schnabel RB, Li G, Ellinor PT, Magnani JW, Chen W, Bis
            JC, Curb JD, Hsueh WC, Rotter JI, Liu Y, Newman AB, Limacher MC,
            North KE, Reiner AP, Quibrera PM, Schork NJ, Singleton AB, Psaty
            BM, Soliman EZ, Solomon AJ, Srinivasan SR, Alonso A, Wallace R,
            Redline S, Zhang ZM, Post WS, Zonderman AB, Taylor HA, Murray SS,
            Ferrucci L, Arking DE, Evans MK, Fox ER, Sotoodehnia N, Heckbert
            SR, Whitsel EA and Newton-Cheh C.
  CONSRTM   CARe and COGENT consortia
  TITLE     Impact of ancestry and common genetic variants on QT interval in
            African Americans
  JOURNAL   Circ Cardiovasc Genet 5 (6), 647-655 (2012)
   PUBMED   23166209
REFERENCE   2  (bases 1 to 2577)
  AUTHORS   Lee,S.M., Chin,L.S. and Li,L.
  TITLE     Charcot-Marie-Tooth disease-linked protein SIMPLE functions with
            the ESCRT machinery in endosomal trafficking
  JOURNAL   J. Cell Biol. 199 (5), 799-816 (2012)
   PUBMED   23166352
  REMARK    GeneRIF: The findings indicate a function of SIMPLE as a regulator
            of endosomal trafficking and provide evidence linking dysregulated
            endosomal trafficking to CMT pathogenesis.
REFERENCE   3  (bases 1 to 2577)
  AUTHORS   Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee
            JC, Schumm LP, Sharma Y, Anderson CA, Essers J, Mitrovic M, Ning K,
            Cleynen I, Theatre E, Spain SL, Raychaudhuri S, Goyette P, Wei Z,
            Abraham C, Achkar JP, Ahmad T, Amininejad L, Ananthakrishnan AN,
            Andersen V, Andrews JM, Baidoo L, Balschun T, Bampton PA, Bitton A,
            Boucher G, Brand S, Buning C, Cohain A, Cichon S, D'Amato M, De
            Jong D, Devaney KL, Dubinsky M, Edwards C, Ellinghaus D, Ferguson
            LR, Franchimont D, Fransen K, Gearry R, Georges M, Gieger C, Glas
            J, Haritunians T, Hart A, Hawkey C, Hedl M, Hu X, Karlsen TH,
            Kupcinskas L, Kugathasan S, Latiano A, Laukens D, Lawrance IC, Lees
            CW, Louis E, Mahy G, Mansfield J, Morgan AR, Mowat C, Newman W,
            Palmieri O, Ponsioen CY, Potocnik U, Prescott NJ, Regueiro M,
            Rotter JI, Russell RK, Sanderson JD, Sans M, Satsangi J, Schreiber
            S, Simms LA, Sventoraityte J, Targan SR, Taylor KD, Tremelling M,
            Verspaget HW, De Vos M, Wijmenga C, Wilson DC, Winkelmann J, Xavier
            RJ, Zeissig S, Zhang B, Zhang CK, Zhao H, Silverberg MS, Annese V,
            Hakonarson H, Brant SR, Radford-Smith G, Mathew CG, Rioux JD,
            Schadt EE, Daly MJ, Franke A, Parkes M, Vermeire S, Barrett JC and
            Cho JH.
  CONSRTM   International IBD Genetics Consortium (IIBDGC)
  TITLE     Host-microbe interactions have shaped the genetic architecture of
            inflammatory bowel disease
  JOURNAL   Nature 491 (7422), 119-124 (2012)
   PUBMED   23128233
REFERENCE   4  (bases 1 to 2577)
  AUTHORS   Liu,J., Xing,H., Chen,Y., Wang,L., Wang,D., Rao,Q., Tang,K.,
            Tian,Z., He,K., Wang,M. and Wang,J.
  TITLE     PIG7, transactivated by AML1, promotes apoptosis and
            differentiation of leukemia cells with AML1-ETO fusion gene
  JOURNAL   Leukemia 26 (1), 117-126 (2012)
   PUBMED   21836606
  REMARK    GeneRIF: PIG7 could be transactivated by AML1, which subsequently
            induces differentiation and apoptosis of leukemia cells, especially
            those with AML1-ETO fusion gene
REFERENCE   5  (bases 1 to 2577)
  AUTHORS   Lee,S.M., Olzmann,J.A., Chin,L.S. and Li,L.
  TITLE     Mutations associated with Charcot-Marie-Tooth disease cause SIMPLE
            protein mislocalization and degradation by the proteasome and
            aggresome-autophagy pathways
  JOURNAL   J. Cell. Sci. 124 (PT 19), 3319-3331 (2011)
   PUBMED   21896645
  REMARK    GeneRIF: Our findings suggest that SIMPLE mutations cause
            Charcot-Marie-Tooth type 1 C peripheral neuropathy by a combination
            of loss-of-function and toxic gain-of-function mechanisms
REFERENCE   6  (bases 1 to 2577)
  AUTHORS   Street,V.A., Bennett,C.L., Goldy,J.D., Shirk,A.J., Kleopa,K.A.,
            Tempel,B.L., Lipe,H.P., Scherer,S.S., Bird,T.D. and Chance,P.F.
  TITLE     Mutation of a putative protein degradation gene LITAF/SIMPLE in
            Charcot-Marie-Tooth disease 1C
  JOURNAL   Neurology 60 (1), 22-26 (2003)
   PUBMED   12525712
REFERENCE   7  (bases 1 to 2577)
  AUTHORS   Street,V.A., Goldy,J.D., Golden,A.S., Tempel,B.L., Bird,T.D. and
            Chance,P.F.
  TITLE     Mapping of Charcot-Marie-Tooth disease type 1C to chromosome 16p
            identifies a novel locus for demyelinating neuropathies
  JOURNAL   Am. J. Hum. Genet. 70 (1), 244-250 (2002)
   PUBMED   11713717
REFERENCE   8  (bases 1 to 2577)
  AUTHORS   Moriwaki,Y., Begum,N.A., Kobayashi,M., Matsumoto,M., Toyoshima,K.
            and Seya,T.
  TITLE     Mycobacterium bovis Bacillus Calmette-Guerin and its cell wall
            complex induce a novel lysosomal membrane protein, SIMPLE, that
            bridges the missing link between lipopolysaccharide and
            p53-inducible gene, LITAF(PIG7), and estrogen-inducible gene, EET-1
  JOURNAL   J. Biol. Chem. 276 (25), 23065-23076 (2001)
   PUBMED   11274176
REFERENCE   9  (bases 1 to 2577)
  AUTHORS   Myokai,F., Takashiba,S., Lebo,R. and Amar,S.
  TITLE     A novel lipopolysaccharide-induced transcription factor regulating
            tumor necrosis factor alpha gene expression: molecular cloning,
            sequencing, characterization, and chromosomal assignment
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 96 (8), 4518-4523 (1999)
   PUBMED   10200294
REFERENCE   10 (bases 1 to 2577)
  AUTHORS   Polyak,K., Xia,Y., Zweier,J.L., Kinzler,K.W. and Vogelstein,B.
  TITLE     A model for p53-induced apoptosis
  JOURNAL   Nature 389 (6648), 300-305 (1997)
   PUBMED   9305847
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK095955.1, AB034747.1 and
            AA625937.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            Summary: Lipopolysaccharide is a potent stimulator of monocytes and
            macrophages, causing secretion of tumor necrosis factor-alpha
            (TNF-alpha) and other inflammatory mediators. This gene encodes
            lipopolysaccharide-induced TNF-alpha factor, which is a DNA-binding
            protein and can mediate the TNF-alpha expression by direct binding
            to the promoter region of the TNF-alpha gene. The transcription of
            this gene is induced by tumor suppresor p53 and has been implicated
            in the p53-induced apoptotic pathway. Mutations in this gene cause
            Charcot-Marie-Tooth disease type 1C (CMT1C) and may be involved in
            the carcinogenesis of extramammary Paget's disease (EMPD). Multiple
            alternatively spliced transcript variants have been found for this
            gene. [provided by RefSeq, Oct 2008].
            
            Transcript Variant: This variant (3) has an alternate 5' UTR exon
            and an additional exon in the 3' region, as compared to variant 1.
            The resulting isoform (2) has a different and shorter C-terminus,
            as compared to isoform 1.
            
            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 :: AK095955.1, BP294739.1 [ECO:0000332]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1236              AK095955.1         1-1236
            1237-2291           AB034747.1         1302-2356
            2292-2577           AA625937.1         1-286               c
FEATURES             Location/Qualifiers
     source          1..2577
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="16"
                     /map="16p13.13"
     gene            1..2577
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /note="lipopolysaccharide-induced TNF factor"
                     /db_xref="GeneID:9516"
                     /db_xref="HGNC:16841"
                     /db_xref="MIM:603795"
     exon            1..65
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /inference="alignment:Splign:1.39.8"
     exon            66..290
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /inference="alignment:Splign:1.39.8"
     CDS             71..529
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /note="isoform 2 is encoded by transcript variant 3; small
                     integral membrane protein of lysosome/late endosome; tumor
                     protein p53 inducible protein 7; LPS-induced TNF-alpha
                     factor; lipopolysaccharide-induced tumor necrosis
                     factor-alpha factor; p53-induced gene 7 protein;
                     lipopolysaccharide-induced TNF-alpha factor"
                     /codon_start=1
                     /product="lipopolysaccharide-induced tumor necrosis
                     factor-alpha factor isoform 2"
                     /protein_id="NP_001129945.1"
                     /db_xref="GI:210147507"
                     /db_xref="CCDS:CCDS45411.1"
                     /db_xref="GeneID:9516"
                     /db_xref="HGNC:16841"
                     /db_xref="MIM:603795"
                     /translation="
MSVPGPYQAATGPSSAPSAPPSYEETVAVNSYYPTPPAPMPGPTTGLVTGPDGKGMNPPSYYTQPAPIPNNNPITVQTVYVQHPITFLDRPIQMCCPSCNKMIVSQLSYNAGALTWLSCGSLCLLGQECSGTIVALRSFDLLGSCNPPSSAS
"
     misc_feature    128..139
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="propagated from UniProtKB/Swiss-Prot (Q99732.2);
                     Region: WW-binding"
     misc_feature    329..>448
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /note="LITAF-like zinc ribbon domain; Region:
                     zf-LITAF-like; pfam10601"
                     /db_xref="CDD:204526"
     exon            291..447
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /inference="alignment:Splign:1.39.8"
     variation       304
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:9282774"
     variation       342
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:11544251"
     variation       344
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:4280262"
     variation       403
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /replace="c"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:34448402"
     exon            448..545
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /inference="alignment:Splign:1.39.8"
     exon            546..2569
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /inference="alignment:Splign:1.39.8"
     variation       797
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:1801977"
     variation       1224
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:79834068"
     STS             1420..1676
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /standard_name="SHGC-61147"
                     /db_xref="UniSTS:21213"
     variation       1471
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:15035"
     STS             1829..2004
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /standard_name="G62064"
                     /db_xref="UniSTS:139179"
     variation       2007
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:5031040"
     STS             2020..2144
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /standard_name="D16S3304"
                     /db_xref="UniSTS:23420"
     STS             2219..2281
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /standard_name="D16S2671"
                     /db_xref="UniSTS:152420"
     polyA_signal    2268..2273
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
     polyA_site      2291
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
     STS             2336..2517
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
                     /standard_name="RH70306"
                     /db_xref="UniSTS:19202"
     polyA_signal    2549..2554
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
     polyA_site      2569
                     /gene="LITAF"
                     /gene_synonym="PIG7; SIMPLE; TP53I7"
ORIGIN      
ccttttctcggggcgcccgagaggccagctcagacctcccggctcgacaggcggcgcgggcggcggtaaaatgtcggttccaggaccttaccaggcggccactgggccttcctcagcaccatccgcacctccatcctatgaagagacagtggctgttaacagttattaccccacacctccagctcccatgcctgggccaactacggggcttgtgacggggcctgatgggaagggcatgaatcctccttcgtattatacccagccagcgcccatccccaataacaatccaattaccgtgcagacggtctacgtgcagcaccccatcacctttttggaccgccctatccaaatgtgttgtccttcctgcaacaagatgatcgtgagtcagctgtcctataacgccggtgctctgacctggctgtcctgcgggagcctgtgcctgctggggcaggagtgcagtggtacgatcgtagctctccgcagctttgatctcctgggctcctgcaatccgcccagctcagcctcctgagtacctgggaccacaggtgcatagcgggctgctgcttcatccccttctgcgtggatgccctgcaggacgtggaccattactgtcccaactgcagagctctcctgggcacctacaagcgtttgtaggactcagccagacgtggagggagccgggtgccgcaggaagtcctttccacctctcatccagcttcacgcctggtggaggttctgccctggtggtctcacctctccagggggcccaccttcatgtcttcttttggggggaatacgtcgcaaaactaacaaatctccaaaccccagaaattgctgcttggagtcgtgcataggacttgcaaagacattccccttgagtgtcagttccacggtttcctgcctccctgagaccctgagtcctgccatctaactgtgatcattgccctatccgaatatcttcctgtgatctgccatcagtggctcttttttcctgcttccatgggcctttctggtggcagtctcaaactgagaagccacagttgccttatttttgaggctgttctgcccagagctcggctgaaccagcctttagtgcctaccattatcttatccgtctcttcccgtccctgatgacaaagatcttgccttacagactttacaggcttggctttgagattctgtaactgcagacttcattagcacacagattcactttaatttcttaattttttttttaaatacaaggagggggctattaacacccagtacagacatatccacaaggtcgtaaatgcatgctagaaaaatagggctggatcttatcactgccctgtctccccttgtttctctgtgccagatcttcagtgcccctttccatacagggatttttttctcatagagtaattatatgaacagtttttatgacctccttttggtctgaaatacttttgaacagaatttcttttttttaaaaaaaaacagagatggggtcttactatgttgcccaggctggtgtcgaactcctgggctcaagcgatccttctgccttggcctcccgaagtgctgggattgcaggcataagctaccatgctgggcctgaacataatttcaagaggaggatttataaaaccattttctgtaatcaaatgattggtgtcattttcccatttgccaatgtagtctcacttaaaaaaaaaaaaaagaaaaagaaatggataatttcatctactgcctttacttggggttaatgtgattcttaaacaccttcatcatggaactctcagagtggggtccgttttggtttcctggtggtgggttttgaaagataagggaaagcacattttgagcatgtctgggtaccatggtgcggatgcttgggaaccagaactgtttcagaggaatctaaagtctgattttagttttcagagacacagcttgttgtaaaacatgagaagacatgatttctaggactcaagcagcaagccaggattctaggttggctgctgtgtcatctttgaagtcaagacaaagctgggctcgaccttcaagggtcctcgttttgataatacttcagaatagggaactcatgtgaatactactatgtagaaataaaacctagaccttgagcgaacatctgtatattggttgaaaacgatagtggtaaccattgatcccccttcatttgatgtttggaaaattccagtaattatcatttttgcaacgaatatggataccacatagtactttggtgttacctgcttttgaaaaataaagtctttggttcacccggtgaactatttatgagttcttttggtgtgaagaaagggctcatgttgcatttccagccattgctacaaagaacctttatttgttcagtaacggtagaaaatccttcccgattaaaaacttcagacttgctgaatatcctgcaatgtcaagatgaccgatgttgagttgggtggatttgctaacgagtcagatttgaacatgaggctattggaacccaataggcgtcattgatggcggcaagccatagctttcaagttttaataaaatgcacaaaagagaaaaaaaaaa
//

Annotations:

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:9516 -> Molecular function: GO:0004871 [signal transducer activity] evidence: IMP
            GeneID:9516 -> Molecular function: GO:0005515 [protein binding] evidence: IPI
            GeneID:9516 -> Molecular function: GO:0050699 [WW domain binding] evidence: IPI
            GeneID:9516 -> Biological process: GO:0001817 [regulation of cytokine production] evidence: IEA
            GeneID:9516 -> Biological process: GO:0006351 [transcription, DNA-dependent] evidence: IEA
            GeneID:9516 -> Biological process: GO:0006357 [regulation of transcription from RNA polymerase II promoter] evidence: TAS
            GeneID:9516 -> Biological process: GO:0006915 [apoptotic process] evidence: IEA
            GeneID:9516 -> Biological process: GO:0007165 [signal transduction] evidence: IMP
            GeneID:9516 -> Biological process: GO:0042347 [negative regulation of NF-kappaB import into nucleus] evidence: IEA
            GeneID:9516 -> Biological process: GO:0043123 [positive regulation of I-kappaB kinase/NF-kappaB cascade] evidence: IMP
            GeneID:9516 -> Biological process: GO:0071222 [cellular response to lipopolysaccharide] evidence: IEA
            GeneID:9516 -> Cellular component: GO:0005765 [lysosomal membrane] evidence: IDA
            GeneID:9516 -> Cellular component: GO:0005794 [Golgi apparatus] evidence: IDA
            GeneID:9516 -> Cellular component: GO:0005794 [Golgi apparatus] evidence: IMP
            GeneID:9516 -> Cellular component: GO:0005886 [plasma membrane] evidence: IMP

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