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TRAPPC2P1 Gene

pseudogene   GIFtS: 29
GCID: GC19P057874

Trafficking Protein Particle Complex 2 Pseudogene 1

(Previous names: spondyloepiphyseal dysplasia, late, pseudogene)
(Previous symbol: SEDLP)
  See TRAPPC2P1-related disease
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
Trafficking Protein Particle Complex 2 Pseudogene 11 2     Spondyloepiphyseal Dysplasia, Late, Pseudogene1
SEDLP1 2     TRAPPC2.193
MIP-2A2 3     MBP-1-Interacting Protein 2A3
SEDLP12 3     

External Ids:    HGNC: 107101   Entrez Gene: 105972   Ensembl: ENSG000002560607   UniProtKB: P0DI823   

Export aliases for TRAPPC2P1 gene to outside databases

Previous GC identifers: GC19U901030 GC19P054199


(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 TRAPPC2P1 Gene:
This gene has been described as a transcribed retropseudogene (or retro-xaptonuon) based on its structure which
lacks most of the introns of SEDL and the detection of transcripts from this locus. Most retropseudogenes are
thought to not express protein products. A protein product could potentially be encoded by this retropseudogene
that would be identical to the protein product of the SEDL gene. However, it remains unclear whether this gene
encodes a protein product or is a transcribed retropseudogene. (provided by RefSeq, Jul 2008)

GeneCards Summary for TRAPPC2P1 Gene:
TRAPPC2P1 (trafficking protein particle complex 2 pseudogene 1) is a pseudogene. Diseases associated with TRAPPC2P1 include x-linked spondyloepiphyseal dysplasia tarda. An important paralog of this gene is TRAPPC2.

UniProtKB/Swiss-Prot: TPC2B_HUMAN, P0DI82
Function: Prevents transcriptional repression and induction of cell death by ENO1. May play a role in vesicular
transport from endoplasmic reticulum to Golgi

Gene Wiki entry for TRAPPC2P1 (SEDLP) 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000019.9  NC_018930.2  NT_011109.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the TRAPPC2P1 gene promoter:
         Nkx3-1   Nkx3-1 v4   RFX1   Nkx3-1 v1   RORalpha2   Nkx3-1 v2   Nkx3-1 v3   Msx-1   MRF-2   En-1   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TRAPPC2P1


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

Entrez Gene cytogenetic band: 19q13.4   Ensembl cytogenetic band:  19q13.43   HGNC cytogenetic band: 19q13.43

TRAPPC2P1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TRAPPC2P1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P057874:  view genomic region     (about GC identifiers)

Start:
57,874,879 bp from pter      End:
57,876,721 bp from pter
Size:
1,843 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,
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UniProtKB/Swiss-Prot: TPC2B_HUMAN, P0DI82 (See protein sequence)
Recommended Name: Trafficking protein particle complex subunit 2 protein TRAPPC2P1  
Size: 140 amino acids; 16445 Da
Subunit: Interacts with PITX1, SF1, and TRAPPC3 (By similarity). Can homodimerize (By similarity). Part of the
multisubunit TRAPP (transport protein particle) complex. Interacts with ENO1 and TRAPPC2L
Miscellaneous: The gene encoding this protein appears to have arisen by retrotransposition of a cDNA from the
X-linked locus TRAPPC2. The site of integration of this retrotransposed cDNA appears to lie within an intron of
the ZNF547 gene, which provides a promoter and non-coding 5' exon. TRAPPC2 and this protein are indistinguishable
at protein level, and both proteins have been identified and functionally characterized
Secondary accessions: A6NEG0 O14582 Q9HD16

Explore the universe of human proteins at neXtProt for TRAPPC2P1: NX_P0DI82


ENSEMBL proteins: 
 ENSP00000442778   ENSP00000469888  

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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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2 InterPro protein domains:
 IPR006722 Sedlin
 IPR011012 Longin-like_dom

Graphical View of Domain Structure for InterPro Entry P0DI82

ProtoNet protein and cluster: P0DI82

UniProtKB/Swiss-Prot: TPC2B_HUMAN, P0DI82
Similarity: Belongs to the TRAPP small subunits family. Sedlin subfamily


Find genes that share domains with TRAPPC2P1           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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Molecular Function:

     UniProtKB/Swiss-Prot Summary: TPC2B_HUMAN, P0DI82
Function: Prevents transcriptional repression and induction of cell death by ENO1. May play a role in vesicular
transport from endoplasmic reticulum to Golgi

     Gene Ontology (GO): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding ----
GO:0008134transcription factor binding ----
GO:0044325ion channel binding ----
     
Find genes that share ontologies with TRAPPC2P1           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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Subcellular locations from UniProtKB/Swiss-Prot
TPC2B_HUMAN, P0DI82: Nucleus (By similarity). Cytoplasm, perinuclear region. Endoplasmic reticulum. Golgi
apparatus. Note=Localized in perinuclear granular structures

Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005622intracellular ----
GO:0005634nucleus IEA--
GO:0005783endoplasmic reticulum IEA--
GO:0005794Golgi apparatus IEA--
GO:0005801cis-Golgi network ----

Find genes that share ontologies with TRAPPC2P1           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:

    GeneGlobe Interaction Network for TRAPPC2P1

Selected Interacting proteins for TRAPPC2P1 (P0DI823) via UniProtKB, MINT, STRING, and/or I2D (see all 53)
InteractantInteraction Details
GeneCardExternal ID(s)
CLIC1O002993I2D: score=2 
ENSG00000206394O002993I2D: score=2 
ENSG00000223639O002993I2D: score=2 
ENSG00000226248O002993I2D: score=2 
ENSG00000226417O002993I2D: score=2 
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Gene Ontology (GO): 5 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0001501skeletal system development ----
GO:0006351transcription, DNA-templated IEA--
GO:0006355regulation of transcription, DNA-templated ----
GO:0006810transport ----
GO:0006888ER to Golgi vesicle-mediated transport IEA--

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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 TRAPPC2P1 (TPC2B)



(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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Unigene Cluster for TRAPPC2P1:

Trafficking protein particle complex 2 pseudogene 1
Hs.446620  [show with all ESTs]
Unigene Representative Sequence: NM_173631
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000543226(uc002qok.1) ENST00000596755
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Additional mRNA sequence: 

AF058918.1 AK055662.1 AK291464.1 AL832545.1 BC008889.2 BC032809.1 BC042681.1 BC064426.1 
CR456859.1 NR_002166.1 

11 DOTS entries:

DT.92428765  DT.92046519  DT.92428766  DT.100747344  DT.92428767  DT.97804556  DT.100741438  DT.95143702 
DT.100741440  DT.95143704  DT.40244361 

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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TRAPPC2P1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ACATAAGACA
TRAPPC2P1 Expression
About this image

TRAPPC2P1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.446620

UniProtKB/Swiss-Prot: TPC2B_HUMAN, P0DI82
Tissue specificity: Expressed in brain, heart, kidney, liver, lung, pancreas, placenta, skeletal muscle, fetal
cartilage, fibroblasts, placenta and lymphocytes

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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 animals and fungi.

Orthologs for TRAPPC2P1 gene from Selected species (see all 13)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves TRAPPC26
Gallus gallus trafficking protein particle complex...
93(a)
1 → many
1(122421140-122426804)
lizard
(Anolis carolinensis)
Reptilia --
--
Uncharacterized protein
96(a)
90(a)
many ↔ many
many ↔ many
3(120465834-120470547)
GL343610.1(164247-164669)
zebrafish
(Danio rerio)
Actinopterygii trappc26
egfl66
EGF-like-domain, multiple 6
96(a)
92(a)
many ↔ many
many ↔ many
9(56717697-56719061) ENSDARG00000097660
9(56709489-56718790) ENSDARG00000068831
fruit fly
(Drosophila melanogaster)
Insecta l(3)72Dh6
lethal (3) 72Dh
58(a)
1 → many
3L(16124094-16124732)
worm
(Caenorhabditis elegans)
Secernentea sedl-16
Protein SEDL-1 (sedl-1) mRNA, complete cds
53(a)
1 → many
X(1439276-1440263) WBGene00021046
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRS206
One of 10 subunits of the transport protein partic...
32(a)
1 → many
II(723736-724263) YBR254C
        Species with no ortholog for TRAPPC2P1

ENSEMBL Gene Tree for TRAPPC2P1 (if available)
TreeFam Gene Tree for TRAPPC2P1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TRAPPC2P1 gene
TRAPPC22  
1 SIMAP similar gene for TRAPPC2P1 using alignment to 1 protein entry:     TPC2B_HUMAN:
TRAPPC2

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(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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Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing TRAPPC2P1
DNA2.0 Custom Variant and Variant Library Synthesis for TRAPPC2P1

(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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1 disease for TRAPPC2P1:    
About MalaCards
x-linked spondyloepiphyseal dysplasia tarda


Find genes that share disorders with TRAPPC2P1           About GenesLikeMe


Export disorders for TRAPPC2P1 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 TRAPPC2P1 gene, integrated from 10 sources (see all 15):
(articles sorted by number of sources associating them with TRAPPC2P1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Functional organization of the yeast proteome by systematic analysis of protein complexes. (PubMed id 11805826)1, 2 Gavin A.-C....Superti-Furga G. (Nature 2002)
  2. A novel 16-kilodalton cellular protein physically interacts with and antagonizes the functional activity of c-myc promoter-binding protein 1. (PubMed id 11134351)1, 2 Ghosh A.K.... Ray R.B. (Mol. Cell. Biol. 2001)
  3. Gene structure and expression study of the SEDL gene for spondyloepiphyseal dysplasia tarda. (PubMed id 11031107)1, 2 Gecz J.... Mulley J.C. (Genomics 2000)
  4. Identification of the gene (SEDL) causing X-linked spondyloepiphyseal dysplasia tarda. (PubMed id 10431248)1, 2 Gedeon A.K.... Gecz J. (Nat. Genet. 1999)
  5. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
  6. TRAPPC2L is a novel, highly conserved TRAPP-interacting protein. (PubMed id 19416478)2 Scrivens P.J.... Sacher M. (Traffic 2009)
  7. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (Nature 2005)
  8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  9. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)2 Grimwood J.... Lucas S.M. (Nature 2004)
  10. Membrane traffic fuses with cartilage development. (PubMed id 12935876)1 Sacher M. (FEBS Lett. 2003)

(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: 10597 HGNC: 10710 Ensembl:ENSG00000256060 euGenes: HUgn10597 ECgene: TRAPPC2P1
H-InvDB: TRAPPC2P1

(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 TRAPPC2P1 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 TRAPPC2P1 gene:
Search GeneIP for patents involving TRAPPC2P1

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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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

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