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TRIM49 Gene

protein-coding   GIFtS: 44
GCID: GC11M089530

Tripartite Motif Containing 49

(Previous names: ring finger protein 18, tripartite motif-containing 49)
(Previous symbol: RNF18)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Tripartite Motif Containing 491 2     TRIM49A2
RNF181 2 3 5     TRIM49L22
RING Finger Protein 181 2 3     Testis-Specific RING Finger Protein2
Tripartite Motif-Containing 491 2     Tripartite Motif-Containing Protein 492
Testis-Specific RING-Finger Protein2 3     

External Ids:    HGNC: 134311   Entrez Gene: 570932   Ensembl: ENSG000001689307   OMIM: 6061245   UniProtKB: P0CI253   

Export aliases for TRIM49 gene to outside databases

Previous GC identifers: GC11M089171 GC11M085755


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for TRIM49 Gene:
The protein encoded by this gene contains a RING zinc finger, a motif known to be involved in protein-protein
interactions. This gene has been found to be preferentially expressed in testis. Related pseudogenes and gene
duplicates have also been identified on chromosome 11. (provided by RefSeq, Aug 2010)

GeneCards Summary for TRIM49 Gene:
TRIM49 (tripartite motif containing 49) is a protein-coding gene. An important paralog of this gene is TRIM43.




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000011.9  NC_018922.2  NT_033899.9  
Regulatory elements:
   Regulatory transcription factor binding sites in the TRIM49 gene promoter:
         IRF-2   NCX/Ncx   IRF-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for TRIM49

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TRIM49


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11p11.12-q12   Ensembl cytogenetic band:  11q14.3   HGNC cytogenetic band: 11p11.12-q12

TRIM49 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TRIM49 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M089530:  view genomic region     (about GC identifiers)

Start:
89,530,823 bp from pter      End:
89,541,743 bp from pter
Size:
10,921 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: TRI49_HUMAN, P0CI25 (See protein sequence)
Recommended Name: Tripartite motif-containing protein 49  
Size: 452 amino acids; 52888 Da
Secondary accessions: A0AVR7 A0AVR9 Q6DJV1 Q9NS80

Explore the universe of human proteins at neXtProt for TRIM49: NX_P0CI25

Explore proteomics data for TRIM49 at MOPED


See TRIM49 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_065091.1  
ENSEMBL proteins: 
 ENSP00000327604   ENSP00000431618  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
TRIM: Tripartite motif containing / Tripartite motif containing
RNF: RING-type (C3HC4) zinc fingers

Selected InterPro protein domains (see all 7):
 IPR001841 Znf_RING
 IPR001870 B30.2/SPRY
 IPR003877 SPRY_rcpt
 IPR000315 Znf_B-box
 IPR013083 Znf_RING/FYVE/PHD

Graphical View of Domain Structure for InterPro Entry P0CI25

ProtoNet protein and cluster: P0CI25

UniProtKB/Swiss-Prot: TRI49_HUMAN, P0CI25
Similarity: Belongs to the TRIM/RBCC family
Similarity: Contains 1 B box-type zinc finger
Similarity: Contains 1 B30.2/SPRY domain
Similarity: Contains 1 RING-type zinc finger


Find genes that share domains with TRIM49           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003677DNA binding ----
GO:0005515protein binding ----
GO:0008270zinc ion binding IEA--
     
Find genes that share ontologies with TRIM49           About GenesLikeMe


Phenotypes:
     2 GenomeRNAi human phenotypes for TRIM49:
 Decreased viability of wild-ty  Increased gamma-H2AX phosphory 

Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for TRIM49

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol2
nucleus2
mitochondrion1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005622intracellular IEA--

Find genes that share ontologies with TRIM49           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TRIM49
Interactions:

    Search GeneGlobe Interaction Network for TRIM49

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for TRIM49 (TRI49)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for TRIM49 gene: 
NM_020358.2  

Unigene Cluster for TRIM49:

Tripartite motif containing 49
Hs.534218
Unigene Representative Sequence: NM_020358
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000329758(uc001pdb.3) ENST00000532501
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Additional mRNA sequence: 

AB037682.1 BC075019.2 BC075020.2 BC126472.1 JF968461.1 

1 DOTS entry:

DT.91741373 

4 AceView cDNA sequences:

BV199056 BV195728 BC075020 BC075019 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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TRIM49 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TCTGAATGAA
TRIM49 Expression
About this image

TRIM49 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TRIM49 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.534218

UniProtKB/Swiss-Prot: TRI49_HUMAN, P0CI25
Tissue specificity: Preferentially expressed in testis

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRIM49

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of chordates.

Orthologs for TRIM49 gene from Selected species (see all 6)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
dog
(Canis familiaris)
Mammalia LOC4851401 tripartite motif-containing protein 77-like 63.84(n)
50(a)
  485140  XM_542258.2  XP_542258.1 
lizard
(Anolis carolinensis)
Reptilia --
--
(see all 7)
Uncharacterized protein
(see all 7)
29(a)
28(a)
(see all 7)
many ↔ many
many ↔ many
(see all 7)
2(193472385-193473600)
GL344228.1(12866-17397)
zebrafish
(Danio rerio)
Actinopterygii FP015862.16
Uncharacterized protein
17(a)
many ↔ many
16(23978442-23984417) ENSDARG00000059905


ENSEMBL Gene Tree for TRIM49 (if available)
TreeFam Gene Tree for TRIM49 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TRIM49 gene
TRIM49C1 2  TRIM432  TRIM772  TRIM612  TRIM64B2  TRIM49B2  TRIM64C2  TRIM512  
TRIM49D12  TRIM482  
Selected SIMAP similar genes for TRIM49 using alignment to 2 protein entries:     TRI49_HUMAN (see all proteins) (see all similar genes):
TRIM49B    TRIM49C    TRIM49D1    TRIM49D2P    TRIM51    TRIM48
TRIM41    TRIM43    TRIM43B    BFAR    MEFV    TRIM77
TRIM64    TRIM64B    TRIM39    TRIM60    TRIM61    TRIM64C

Find genes that share paralogs with TRIM49           About GenesLikeMe


1 Pseudogenes.org Pseudogene for TRIM49
PGOHUM00000258095


(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for TRIM49 (see all 158)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs2004228591,2
C--89530916(+) TATCAC/TTGAGA 1 -- ut310--------
rs2009810441,2
C--89530963(+) CGACTC/GTCTTC 1 -- ut310--------
rs2011450611,2
C--89530998(+) ATGTCA/TGTCAT 1 -- ut310--------
rs2006395181,2
C,F--89531476(+) GGGAGG/TTGGTA 2 N T mis11Minor allele frequency- T:0.00EU 1289
rs1867836961,2
--89531512(+) TAACAC/TACCCA 2 Y C mis10--------
rs1468987801,2
C,F--89531533(+) GTCCCG/TCCTTT 2 E A mis11Minor allele frequency- T:0.01EU 985
rs124179801,2,,4
C,F,H--89531540(+) CTTTCC/TATCTA 2 R G mis17Minor allele frequency- T:0.30NA WA EA EU 1545
rs1485279081,2
C,F--89531543(+) TCCATC/TTATCT 2 N D mis12Minor allele frequency- T:0.00NA EU 5759
rs1510265111,2
F--89531572(+) CTTTCC/TGATAC 2 Q R mis11Minor allele frequency- T:0.00NA 4438
rs1444898341,2
C,F--89531613(+) GAGTCC/ACCTAC 2 /G syn12Minor allele frequency- A:0.00NA EU 5239

HapMap Linkage Disequilibrium report for TRIM49 (89530823 - 89541743 bp)

Structural Variations
     Database of Genomic Variants (DGV) 9 variations for TRIM49:    About this table    
Variant IDTypeSubtypePubMed ID
nsv426CNV Insertion18451855
dgv1257n71CNV Loss21882294
nsv508644CNV Loss20534489
dgv1256n71CNV Loss21882294
dgv233n67CNV Gain20364138
nsv898094CNV Gain21882294
nsv832225CNV Gain17160897
nsv826025CNV Gain20364138
dgv412e1CNV Complex17122850

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 606124    OMIM disorders: --


Find genes that share disorders with TRIM49           About GenesLikeMe


Export disorders for TRIM49 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for TRIM49 gene integrated from 10 sources:
(articles sorted by number of sources associating them with TRIM49)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Isolation of a cDNA for a novel human RING finger protein gene, RNF18, by the virtual transcribed sequence (VTS) approach. (PubMed id 11018261)1, 2, 3 Yoshikawa T....Saito T. (Biochim. Biophys. Acta 2000)
  2. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)1, 2 Taylor T.D....Sakaki Y. (Nature 2006)
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  4. Ubiquitin-dependent recruitment of the Bloom syndrome helicase upon replication stress is required to suppress homologous recombination. (PubMed id 23708797)1 Tikoo S....Sengupta S. (EMBO J. 2013)
  5. Quantitative analysis of HSP90-client interactions reveals principles of substrate recognition. (PubMed id 22939624)1 Taipale M....Lindquist S. (Cell 2012)
  6. Genetic association with overall survival of taxane-treated lung cancer patients - a genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study. (PubMed id 23006423)1 Niu N....Wang L. (BMC Cancer 2012)
  7. Identification of a genomic reservoir for new TRIM genes in primate genomes. (PubMed id 22144910)1 Han K.... Sawyer S.L. (PLoS Genet. 2011)
  8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 57093 HGNC: 13431 AceView: RNF18.1 Ensembl:ENSG00000168930 euGenes: HUgn57093
ECgene: TRIM49 H-InvDB: TRIM49

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for TRIM49 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for TRIM49 Genetics and Cytogenetics in Oncology and Haematology

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for TRIM49 gene:
Search GeneIP for patents involving TRIM49

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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 Search Tocris compounds for TRIM49 (TRI49)
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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

 Novus Tissue Slides
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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