TRIM56 Gene
protein-coding GIFtS: 45
GCID: GC07P100728
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|
tripartite motif containing 56(Previous name: tripartite motif-containing 56 )
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Aliases
for TRIM56 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Tripartite Motif Containing 561 2 | | RING Finger Protein 1092 3 | | RNF1091 2 3 | | E3 Ubiquitin-Protein Ligase TRIM562 | | Tripartite Motif-Containing 561 2 | | EC 6.3.2.-3 | | Tripartite Motif-Containing Protein 562 3 | | |
Export aliases for TRIM56 gene to outside databasesPrevious GC identifers: GC07P099213 GC07P100275 GC07P100288 GC07P100322 GC07P100515 GC07P095322 |
Summaries
for TRIM56 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
UniProtKB/Swiss-Prot: TRI56_HUMAN, Q9BRZ2Function: E3 ubiquitin-protein ligase that mediates 'Lys-63'-linked polyubiquitination of TMEM173/STING, therebyplaying a key role in innate immunity. TMEM173/STING 'Lys-63'-linked ubiquitination activates the production of type Iinterferon IFN-beta following detection of pathogen- and host-derived double-stranded DNA (By similarity)
|
Genomic Views
for TRIM56 gene
(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 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000007.13 NC_018918.1 NT_007933.15 NT_079596.2
Regulatory elements:
 Search SABiosciences Regulatory transcription factor binding sites for TRIM56
Other transcription factors
Search SABiosciences Chromatin IP Primers for TRIM56
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TRIM56 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 7q22.1 Ensembl cytogenetic band: 7q22.1 HGNC cytogenetic band: 7q11.2TRIM56 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 7 GeneLoc Exon Structure GeneLoc location for GC07P100728: view genomic region
(about GC identifiers)
Start:
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100,728,720 bp from pter |
End:
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100,735,017 bp from pter |
Size:
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6,298 bases |
Orientation:
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plus strand |
1 alternative location:
| Chr7+,CRA_TCAG 100,087,175-100,092,298 |
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Proteins
for TRIM56 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
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, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: TRI56_HUMAN, Q9BRZ2 (See
protein sequence)Recommended Name: E3 ubiquitin-protein ligase TRIM56 Size: 755 amino acids; 81488 Da
Subunit: Interacts with TMEM173/STING (By similarity)
Subcellular location: Cytoplasm (By similarity)
Sequence caution: Sequence=AAH11882.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;Sequence=BAC11500.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: Q6PJS5 Q86VT6 Q8N2H8 Q8NAC0 Q9H031Alternative splicing: 3 isoforms: Q9BRZ2-1 Q9BRZ2-2 Q9BRZ2-3 (No experimental confirmation available)Explore the universe of human proteins at neXtProt for TRIM56: NX_Q9BRZ2
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9BRZ2
TRIM56 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_112223.1
ENSEMBL proteins: ENSP00000305161 ENSP00000404186
Human Recombinant Protein Products for TRIM56:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table
TRIM56 for ontologies About GeneDecksing
TRIM56 Antibody Products:
Assay Products for TRIM56: |
Protein
Domains /
Families
for TRIM56 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
TRIM56 for domains About GeneDecksing
5 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9BRZ2ProtoNet protein and cluster: Q9BRZ2 3 Blocks protein families: IPB000315 B-box zinc finger signature IPB000504 RNA-binding region RNP-1 (RNA recognition motif) IPB001841 Zn-finger
UniProtKB/Swiss-Prot: TRI56_HUMAN, Q9BRZ2Similarity: Belongs to the TRIM/RBCC familySimilarity: Contains 2 B box-type zinc fingersSimilarity: Contains 1 RING-type zinc finger |
Function
for TRIM56 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Sirion Biotech,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Molecular Function:
UniProtKB/Swiss-Prot Summary: TRI56_HUMAN, Q9BRZ2Function: E3 ubiquitin-protein ligase that mediates 'Lys-63'-linked polyubiquitination of TMEM173/STING, therebyplaying a key role in innate immunity. TMEM173/STING 'Lys-63'-linked ubiquitination activates the production of type Iinterferon IFN-beta following detection of pathogen- and host-derived double-stranded DNA (By similarity) Enzyme Number (IUBMB): EC 6.3.2.-1
Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0004842 | ubiquitin-protein ligase activity |
ISS | -- | | GO:0005515 | protein binding |
-- | -- | | GO:0008270 | zinc ion binding |
IEA | -- |
TRIM56 for ontologies About GeneDecksing
Animal Models:
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for TRIM56 (see all 2)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for TRIM56
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
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| |  | GenScript: all cDNA clones in your preferred vector: TRIM56 (NM_030961) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for TRIM56 | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TRIM56 |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRIM56 |
|
Pathways & Interactions
for TRIM56 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
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 Mar 2013 via
Entrez Gene).
About This Section
|
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TRIM56
STRING Interaction
Network Preview (showing 3 interactants - click image to see more details)
5 Interacting proteins for TRIM56 (Q9BRZ23 ENSP000003051614) via UniProtKB, MINT, STRING, and/or I2DAbout this table
Gene Ontology (GO): 4 biological process terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0032608 | interferon-beta production |
ISS | -- | | GO:0034340 | response to type I interferon |
ISS | -- | | GO:0051607 | defense response to virus |
ISS | -- | | GO:0070534 | protein K63-linked ubiquitination |
ISS | -- |
TRIM56 for ontologies About GeneDecksing
|
Drugs & Compounds
for TRIM56 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for TRIM56
Search CenterWatch for drugs/clinical trials and news about TRIM56 / TRI56
|
Transcripts
for TRIM56 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 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,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
Sirion Biotech,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for TRIM56 gene: NM_030961.1 Unigene Cluster for TRIM56: Tripartite motif containing 56 Hs.521092 [show with all ESTs]Unigene Representative Sequence: BC0058474 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000306085(uc003uxq.3) ENST00000412507(uc003uxr.3) ENST00000467847
ENST00000487252
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for TRIM56 (see all 2)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for TRIM56
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: TRIM56 (NM_030961) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for TRIM56 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TRIM56 |
Additional cDNA sequence: AK075255.1 AL512757.1 BC005847.2 BC011882.2 BC048194.1 BC128050.1 6 DOTS entries: DT.435379 DT.97806615 DT.100031169 DT.95300058 DT.100752520 DT.121117792 24/145 AceView cDNA sequences (see all 145): BE301071 BE876112 BM352587 BM272584 NM_030961 BG943871 AW328506 BQ223903 BM894020 BE302899 AI031714 BQ929018 AI089989 BM313880 BU687184 BE301033 BG574808 BI467347 BC048194 BC011882 AI474342 BU688360 BQ049558 CA443882
GeneLoc Exon Structure
|
Expression
for TRIM56 gene
(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™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| TRIM56 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GTTTCCCACG
About this image
See TRIM56 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for TRIM56
SOURCE GeneReport for Unigene cluster: Hs.521092
SABiosciences Expression via Pathway-Focused PCR Array including TRIM56: | Ubiquitin Ligases in human mouse rat |
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for TRIM56
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse / rat TRIM56 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat TRIM56 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat TRIM56 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRIM56 |
Orthologs
for TRIM56 gene
(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)
About This Section
|
This gene was present in the common ancestor of chordates.
Orthologs for TRIM56 gene from 1/9 species (see all 9) About this table
| Organism |
Taxonomic
classification |
Gene |
Description |
Human
Similarity |
Orthology
Type |
Details |
lizard
(Anolis carolinensis) |
Reptilia |
TRIM566 |
-- |
45(a) |
1 ↔ 1 |
GL344173.1(55697-58061) |
ENSEMBL Gene Tree for TRIM56 (if available)
TreeFam Gene Tree for TRIM56 (if available) |
Paralogs
for TRIM56 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for TRIM56 gene
- TRIM32 TRIM712 NHLRC12 TRIM452 TRIM22 TRIM322
2 SIMAP similar genes for TRIM56 using alignment to 2 protein entries: TRI56_HUMAN (see all proteins):TRIM39 TRIM5
TRIM56 for paralogs About GeneDecksing
|
Genomic Variants
for TRIM56 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, 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) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 7 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for TRIM56 (100728720 - 100735017 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for TRIM56
1 CNV: 3692 | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing TRIM56 |
|
Disorders
/ Diseases
for TRIM56 gene
(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.)
About This Section
|
TRIM56 for disorders About GeneDecksing
1  disease for TRIM56: About MalaCardsneuronitis
Export disorders for TRIM56 gene to outside databases
|
Publications
for TRIM56 gene (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)
About This Section
|
PubMed articles for TRIM56 gene, integrated from 9 sources (see all 16):
(articles sorted by number of sources associating them with TRIM56) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
- 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. (2004)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
- The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (2003)
- The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation. (PubMed id 22797925)1 Aichem A....Groettrup M. (2012)
- A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
- Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
- TRIM56 is an essential component of the TLR3 antiviral signaling pathway. (PubMed id 22948160)1 Shen Y....Li K. (2012)
- The BTB and CNC homology 1 (BACH1) target genes are i nvolved in the oxidative stress response and in control of the cell cycle. (PubMed id 21555518)1 Warnatz H.J....Yaspo M.L. (2011)
- TRIM56 is a virus- and interferon-inducible E3 ubiqui tin ligase that restricts pestivirus infection. (PubMed id 21289118)1 Wang J....Li K. (2011)
|
External Searches for TRIM56 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing TRIM56 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing TRIM56 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing TRIM56 gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for TRIM56 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for TRIM56 gene:
Search GeneIP for patents involving TRIM56
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for TRIM56 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
About This Section
|
 | |
 | |
 |
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| |
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 | | | TRIM56 Proteins, Antibodies, CLIAs, and ELISAs |
| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRIM56 |
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