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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TRAPPC2P1 Gene

pseudogene   GIFtS: 33
GCID: GC19P057874

trafficking protein particle complex 2 pseudogene 1

(Previous names: spondyloepiphyseal dysplasia, late, pseudogene )
(Previous symbol: SEDLP)
 Explore 4 diseases affiliated with
TRAPPC2P1 via our new
 Human Malady Compendium 
Biological research products
for TRAPPC2P1
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Trafficking Protein Particle Complex 2 Pseudogene 11 2     Spondyloepiphyseal Dysplasia, Late, Pseudogene1
SEDLP11 2 3     TRAPPC2.193
SEDLP1 2     MBP-1-Interacting Protein 2A3
MIP-2A2 3     

External Ids:    HGNC: 107101   Entrez Gene: 105972   Ensembl: ENSG000002560607   UniProtKB: P0DI823   
ORGUL members:         
NONCODE:n405416    

Export aliases for TRAPPC2P1 gene to outside databases

Previous GC identifers: GC19U901030 GC19P054199


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for TRAPPC2P1:
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)

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)


(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_000019.9  NC_018930.1  NT_011109.16  
Regulatory elements:
   SABiosciences 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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   Search SABiosciences Chromatin IP Primers for TRAPPC2P1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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, 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: 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
Subcellular location: Nucleus (By similarity). Cytoplasm, perinuclear region. Endoplasmic reticulum. Golgi apparatus.
Note=Localized in perinuclear granular structures
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

TRAPPC2P1 Protein expression data from MOPED and PaxDb:    About this image 

Estimated protein expression log10 (pmol).


ENSEMBL proteins: 
 ENSP00000442778  

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Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005622intracellular ----
GO:0005634nucleus IEA--
GO:0005783endoplasmic reticulum IEA--
GO:0005794Golgi apparatus IEA--
GO:0048471perinuclear region of cytoplasm IEA--


TRAPPC2P1 for ontologies           About GeneDecksing



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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

TRAPPC2P1 for domains           About GeneDecksing

2 InterPro domains/families:
 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


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

     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

miRNA
Products:
    
miRTarBase miRNAs that target TRAPPC2P1:
hsa-mir-192 (MIRT004862), hsa-mir-200a (MIRT004867), hsa-mir-769-5p (MIRT004869), hsa-mir-603 (MIRT004864), hsa-mir-217 (MIRT004866), hsa-mir-27b (MIRT004863), hsa-mir-532-5p (MIRT004865), hsa-mir-141 (MIRT004868)

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Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding ----
GO:0008134transcription factor binding ----


TRAPPC2P1 for ontologies           About GeneDecksing



(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:

    SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for TRAPPC2P1

5/47 Interacting proteins for TRAPPC2P1 (P0DI823) via UniProtKB, MINT, STRING, and/or I2D (see all 47)
InteractantInteraction Details
GeneCardExternal ID(s)
TRAPPC5Q8IUR03I2D: score=5 
RUVBL2Q9Y2303I2D: score=4 
TRAPPC2P0DI813I2D: score=3 
CLIC1O002993I2D: score=2 
CLIC2O152473I2D: score=2 
About this table

Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

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


TRAPPC2P1 for ontologies           About GeneDecksing



(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 Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for TRAPPC2P1
Search CenterWatch for drugs/clinical trials and news about TRAPPC2P1 

(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,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

Unigene Cluster for TRAPPC2P1:

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

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Additional cDNA 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™, 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

TRAPPC2P1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: ACATAAGACA

Microarray
RNAseq (Illumina Body Map)
(100×FPKM)½
SAGE (Serial Analysis of Gene Expression)

About this image
See TRAPPC2P1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for TRAPPC2P1

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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In Situ
Assay Products:
 

 
Search Advanced Cell Diagnostics for RNAscope RNA in situ hybridization assays for TRAPPC2P1

(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 eukaryotes.

Orthologs for TRAPPC2P1 gene from 7/22 species (see all 22)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves TPPC2_CHICK6
Trafficking protein particle complex subunit 2
93(a)
1 → many
1(126388987-126394651)
lizard
(Anolis carolinensis)
Reptilia --
--
--
96(a)
90(a)
many ↔ many
many ↔ many
3(120465835-120470539)
GL343610.1(164247-164669)
zebrafish
(Danio rerio)
Actinopterygii trappc26
trafficking protein particle complex 2
92(a)
1 → many
9(56709490-56719061)
fruit fly
(Drosophila melanogaster)
Insecta l(3)72Dh6
lethal (3) 72Dh
59(a)
1 → many
3L(16124094-16124732)
worm
(Caenorhabditis elegans)
Secernentea sedl-16
Probable trafficking protein particle complex subu...
55(a)
1 → many
X(1439271-1440258)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G805006
SNARE-like protein
49(a)
1 → many
1(30270529-30272668)
rice
(Oryza sativa)
Liliopsida --
--
trafficking protein particle complex subunit, puta...
trafficking protein particle complex subunit, puta...
49(a)
29(a)
many ↔ many
many ↔ many
2(24190188-24195562)
4(24965221-24967734)
        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)
About This Section
Paralogs for TRAPPC2P1 gene
TRAPPC22  
1 SIMAP similar gene for TRAPPC2P1 using alignment to 1 protein entry:     TPC2B_HUMAN:
TRAPPC2

TRAPPC2P1 for paralogs           About GeneDecksing



(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

10/80 NCBI SNPs in TRAPPC2P1 are shown (see all 80    About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1860506461,2
--57872903(+) GAAATA/GCATAT 2 -- us2k10--------
rs1462033481,2
--57872904(+) AAATAA/CATATA 2 -- us2k10--------
rs1391064561,2
--57872905(+) AATACA/GTATAG 2 -- us2k10--------
rs1889050481,2
--57872909(+) CATATA/GGGAGA 2 -- us2k10--------
rs8627111,2
C,F,H,--57872997(+) TCTACT/CGTAAC 2 -- us2k121Minor allele frequency- C:0.09NS EA NA WA 2762
rs730632611,2
--57873188(+) TGCCCA/GACTGC 2 -- us2k10--------
rs1498664691,2
--57873308(+) GCCGGA/GTGCTG 2 -- us2k10--------
rs1122977981,2
--57873376(+) GTCAGG/AAATTC 2 -- us2k13Minor allele frequency- A:0.15CSA WA 120
rs1819932831,2
--57873384(+) TTCCAG/TACTGG 2 -- us2k10--------
rs8627121,2
F,--57873599(+) aaaaaA/Ccccac 2 -- us2k15Minor allele frequency- C:0.11NA CSA WA 243

HapMap Linkage Disequilibrium report for TRAPPC2P1 (57874879 - 57876721 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
      Database of Genomic Variants (DGV) variations for TRAPPC2P1: --

SABiosciences Cancer Mutation PCR Assays
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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.)
About This Section

TRAPPC2P1 for disorders           About GeneDecksing

4 diseases for TRAPPC2P1:    About MalaCards
spondyloepiphyseal dysplasia    x-linked spondyloepiphyseal dysplasia tarda    spondyloepiphyseal dysplasia tarda    malaria


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)
About This Section

PubMed articles for TRAPPC2P1 gene, integrated from 9 sources (see all 14):
(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. (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. (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. (2000)
  4. Identification of the gene (SEDL) causing X-linked spondyloepiphyseal dysplasia tarda. (PubMed id 10431248)1, 2 Gedeon A.K.... Gecz J. (1999)
  5. TRAPPC2L is a novel, highly conserved TRAPP-interacting protein. (PubMed id 19416478)2 Scrivens P.J.... Sacher M. (2009)
  6. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (2005)
  7. 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. (2004)
  8. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)2 Grimwood J.... Lucas S.M. (2004)
  9. Membrane traffic fuses with cartilage development. (PubMed id 12935876)1 Sacher M. (2003)
  10. Human wild-type SEDL protein functionally complements yeast Trs20p but some naturally occurring SEDL mutants do not. (PubMed id 14597397)1 Gecz J....de Barros Lopes M. (2003)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 10597 HGNC: 10710 Ensembl:ENSG00000256060 euGenes: HUgn10597 ECgene: TRAPPC2P1
H-InvDB: TRAPPC2P1

(According to HUGE)
About This Section
  --

(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
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

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