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TRIM39-RPP21 Gene

protein-coding   GIFtS: 22
GCID: GC06P030423

TRIM39-RPP21 Readthrough

  Search for TRIM39-RPP21
at  

(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
TRIM39-RPP21 Readthrough1 2
TRIM39R2
Rpp21 Domain-Containing TRIM Protein2
TRIM39-RPP21 Protein2
TRIM39-RPP21 Read-Through Transcript2
TRIM39-Like Protein4

External Ids:    HGNC: 388451   Entrez Gene: 2026582   Ensembl: ENSG000002481677   UniProtKB: A6ZJ124   

Export aliases for TRIM39-RPP21 gene to outside databases

Previous GC identifers: GC06U902092 GC06P030296


(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 TRIM39-RPP21 Gene:
This locus represents naturally occurring read-through transcription between the neighboring TRIM39 (tripartite
motif-containing 39) and RPP21 (ribonuclease P/MRP 21kDa subunit) genes on chromosome 6. The read-through
transcript encodes a fusion protein that shares sequence identity with each individual gene product. (provided by
RefSeq, Nov 2010)

GeneCards Summary for TRIM39-RPP21 Gene:
TRIM39-RPP21 (TRIM39-RPP21 readthrough) is a protein-coding gene. An important paralog of this gene is TRIM7.




(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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Regulatory elements:
   Search for regulatory transcription factor binding sites for TRIM39-RPP21
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TRIM39-RPP21


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

Ensembl cytogenetic band:  6p22.1   HGNC cytogenetic band: 6p22.1

TRIM39-RPP21 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TRIM39-RPP21 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P030423:  view genomic region     (about GC identifiers)

Start:
30,297,088 bp from pter      End:
30,314,635 bp from pter
Size:
17,548 bases      Orientation:
plus strand

6 alternative locations:
Chr6+,NT_167245 1,590,737-1,608,289      Chr6+,NT_113891.2 1,809,095-1,826,645      Chr6+,NT_167248 1,589,983-1,607,536     
Chr6+,NT_167249 1,627,064-1,644,613      Chr6+,NT_167244 1,608,718-1,626,270      Chr6+,NT_167246 1,645,157-1,662,712     

(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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/TrEMBL: A6ZJ12 (See protein sequence)
Recommended Name: Protein TRIM39-RPP21  
Size: 415 amino acids; 48096 Da

Explore proteomics data for TRIM39-RPP21 at MOPED


See TRIM39-RPP21 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001186048.1  
ENSEMBL proteins: 
 ENSP00000424048  

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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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Selected InterPro protein domains (see all 6):
 IPR007175 Rpr2
 IPR006574 PRY
 IPR001870 B30.2/SPRY
 IPR000315 Znf_B-box
 IPR003879 Butyrophylin

Graphical View of Domain Structure for InterPro Entry A6ZJ12

ProtoNet protein and cluster: A6ZJ12

UniProtKB/TrEMBL: A6ZJ12
Similarity: Contains B30.2/SPRY domain


Find genes that share domains with TRIM39-RPP21           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0008270zinc ion binding ----
     
Find genes that share ontologies with TRIM39-RPP21           About GenesLikeMe


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

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

Find genes that share ontologies with TRIM39-RPP21           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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Interactions:

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(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 Tocris compounds for TRIM39-RPP21



(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 TRIM39-RPP21 gene: 
NM_001199119.1  

1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000513556(uc010jsa.2)
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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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TRIM39-RPP21 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
TRIM39-RPP21 Expression
About this image

TRIM39-RPP21 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TRIM39-RPP21 Protein Expression
    Custom PCR Arrays for TRIM39-RPP21
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In Situ
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(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 TRIM39-RPP21 gene from Selected species (see all 4)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
40(a)
1 → many
2(192582206-192599704)
        Species with no ortholog for TRIM39-RPP21

ENSEMBL Gene Tree for TRIM39-RPP21 (if available)
TreeFam Gene Tree for TRIM39-RPP21 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TRIM39-RPP21 gene
TRIM72  TRIM42  TRIM392  TRIM342  TRIML12  TRIM272  TRIM582  TRIM682  
TRIM602  TRIM222  TRIM172  TRIM52  TRIM62  TRIM6-TRIM342  TRIM212  TRIM382  
TRIM112  

Find genes that share paralogs with TRIM39-RPP21           About GenesLikeMe



(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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Structural Variations
     Database of Genomic Variants (DGV) 1 variation for TRIM39-RPP21:    About this table    
Variant IDTypeSubtypePubMed ID
nsv5241CNV Insertion18451855

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing TRIM39-RPP21
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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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  --

(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 TRIM39-RPP21 gene integrated from 10 sources:
(articles sorted by number of sources associating them with TRIM39-RPP21)
    Utopia: connect your pdf to the dynamic
world of online information

  1. TRIM39R, but not TRIM39B, regulates type I interferon response. (PubMed id 23707810)1 Kurata R....Inoko H. (Biochem. Biophys. Res. Commun. 2013)
  2. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
  3. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
  4. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. (PubMed id 20967262)1 Prakash T....Taylor T.D. (PLoS ONE 2010)
  5. cGMP-dependent protein kinase I interacts with TRIM39R, a novel Rpp21 domain-containing TRIM protein. (PubMed id 17601797)1 Roberts J.D.Jr.... Bloch K.D. (Am. J. Physiol. Lung Cell. Mol. Physiol. 2007)

(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: 202658 HGNC: 38845 Ensembl:ENSG00000248167 euGenes: HUgn202658 ECgene: TRIM39-RPP21
H-InvDB: TRIM39-RPP21

(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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  --

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for TRIM39-RPP21 gene:
Search GeneIP for patents involving TRIM39-RPP21

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, LSBio, eBioscience, 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 inGenious Targeting Laboratory, genOway)
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