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TRIM49D2P Gene

pseudogene   GIFtS: 20
GCID: GC11P089659

Tripartite Motif Containing 49D2, Pseudogene

(Previous names: tripartite motif-containing 49-like, tripartite motif containing...)
(Previous symbols: TRIM49L, TRIM49L1)
  Search for TRIM49D2P
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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 49D2, Pseudogene1 2     TRIM48L12
TRIM49L1 2 3     TRIM49D12
TRIM49L11 2 3     Tripartite Motif-Containing 49-Like 12
Tripartite Motif Containing 49-Like 11 2     Tripartite Motif-Containing Protein 49-Like Protein 12
Tripartite Motif-Containing Protein 49D2 Pseudogene2 3     Tripartite Motif-Containing Protein 49D12
Tripartite Motif-Containing 49-Like1     Tripartite Motif-Containing Protein 49-Like Protein3

External Ids:    HGNC: 372171   Entrez Gene: 7293842   Ensembl: ENSG000002338027   UniProtKB: C9J1S83   

Export aliases for TRIM49D2P gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TRIM49D2P Gene:
TRIM49D2P (tripartite motif containing 49D2, pseudogene) is a pseudogene. An important paralog of this gene is TRIM49D1.


(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 TRIM49D2P
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TRIM49D2P


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

Entrez Gene cytogenetic band: 11q14.3   Ensembl cytogenetic band:  11q14.3   HGNC cytogenetic band: 11q14.3

TRIM49D2P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TRIM49D2P gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P089659:  view genomic region     (about GC identifiers)

Start:
89,657,232 bp from pter      End:
89,666,231 bp from pter
Size:
9,000 bases      Orientation:
plus 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., 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/Swiss-Prot: T49D1_HUMAN, C9J1S8 (See protein sequence)
Recommended Name: Tripartite motif-containing protein 49D1  
Size: 452 amino acids; 52496 Da
Secondary accessions: I1YAP9

Explore the universe of human proteins at neXtProt for TRIM49D2P: NX_C9J1S8

REFSEQ proteins: NP_001098992.1  

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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:
TRIMP: Triparite motif-containing / Pseudogenes

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 C9J1S8

ProtoNet protein and cluster: C9J1S8

UniProtKB/Swiss-Prot: T49D1_HUMAN, C9J1S8
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 TRIM49D2P           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 IEA--
     
Find genes that share ontologies with TRIM49D2P           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 IEA--

Find genes that share ontologies with TRIM49D2P           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 TRIM49D2P (T49D1)



(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 TRIM49D2P gene: 
NM_001105522.1  

2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000526396(uc009yvv.3) ENST00000605881
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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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See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

TRIM49D2P Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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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 human and chimp.

Orthologs for TRIM49D2P gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia TRIM491 tripartite motif-containing 49 98.85(n)
97.53(a)
  748950  XM_001164346.2  XP_001164346.2 


ENSEMBL Gene Tree for TRIM49D2P (if available)
TreeFam Gene Tree for TRIM49D2P (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TRIM49D2P gene
TRIM49D1  
16 SIMAP similar genes for TRIM49D2P using alignment to 1 protein entry:     T49D1_HUMAN:
TRIM49B    TRIM49C    TRIM51    TRIM49    TRIM43    TRIM43B
TRIM48    TRIM64    TRIM64B    TRIM64C    TRIM77    TRIML1
TRIM21    TRIM58    TRIM38    TRIM68

Find genes that share paralogs with TRIM49D2P           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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Selected SNPs for TRIM49D2P (see all 11)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs2021037351,2
--89658369(+) ATAAG-/TATAT 
        
TATAT
1 -- int10--------
rs1912526541,2
--89665248(+) TGTGCA/TAATTT 1 -- int10--------
rs1455174521,2
--89665511(+) TCTTTC/TTATTT 1 -- int10--------
rs2010862561,2
----89658076(+) AGGGCC/TCTCCA 1 -- int10--------
rs2011069371,2
----89665555(+) GCAGTA/GGATAT 2 V syn10--------
rs2002757031,2
----89662611(+) AAAGAA/TATTTT 2 E D mis10--------
rs2019448171,2
----89658456(+) CGTGGC/TGGGCA 1 -- int10--------
rs3772159061,2
----89665515(+) TTTATC/TTATTT 1 -- int10--------
rs2005710051,2
----89658645(+) GCCGAG/TATTGC 1 -- int10--------
rs2002844591,2
----89657837(+) TTTTGA/GCCAAA 1 -- int10--------

HapMap Linkage Disequilibrium report for TRIM49D2P (89657232 - 89666231 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for TRIM49D2P: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing TRIM49D2P
DNA2.0 Custom Variant and Variant Library Synthesis for TRIM49D2P

(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 TRIM49D2P gene integrated from 10 sources:
(articles sorted by number of sources associating them with TRIM49D2P)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Identification of a genomic reservoir for new TRIM genes in primate genomes. (PubMed id 22144910)1, 2, 3 Han K.... Sawyer S.L. (PLoS Genet. 2011)
  2. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)2 Taylor T.D....Sakaki Y. (Nature 2006)

(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: 729384 HGNC: 37217 Ensembl:ENSG00000233802 euGenes: HUgn729384 ECgene: TRIM49D2P
H-InvDB: TRIM49D2P

(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 TRIM49D2P Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for TRIM49D2P gene:
Search GeneIP for patents involving TRIM49D2P

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
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