Human Gene TRAPPC2L (uc002fmc.3) Description and Page Index
  Description: Homo sapiens trafficking protein particle complex 2-like (TRAPPC2L), mRNA.
RefSeq Summary (NM_016209): This gene encodes a protein that interacts with the tethering factor trafficking protein particle (TRAPP complex). TRAPP complexes mediate the contact between vescicles and target membranes, and thus, are involved in vescicle-mediated transport of proteins and lipids. The encoded protein is related to the X-linked trafficking protein particle complex 2. A related pseudogene is located on the X chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016].
Transcript (Including UTRs)
   Position: hg19 chr16:88,923,506-88,927,520 Size: 4,015 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr16:88,923,559-88,927,367 Size: 3,809 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:88,923,506-88,927,520)mRNA (may differ from genome)Protein (140 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: TPC2L_HUMAN
DESCRIPTION: RecName: Full=Trafficking protein particle complex subunit 2-like protein;
FUNCTION: May play a role in vesicular transport from endoplasmic reticulum to Golgi.
SUBUNIT: Component of the multisubunit TRAPP (transport protein particle) complex, which includes at least TRAPPC2, TRAPPC2L, TRAPPC3, TRAPPC3L, TRAPPC4, TRAPPC5, TRAPPC8, TRAPPC9, TRAPPC10, TRAPPC11 and TRAPPC12. Interacts with the heterodimer TRAPPC3- TRAPPC6A. Interacts with TRAPPC6A.
SUBCELLULAR LOCATION: Cytoplasm, perinuclear region. Endoplasmic reticulum. Golgi apparatus.
TISSUE SPECIFICITY: Expressed in testis, liver, bladder, lung, spleen and brain, several cell lines and primary chondrocytes cell line.
SIMILARITY: Belongs to the TRAPP small subunits family. Sedlin subfamily.
SEQUENCE CAUTION: Sequence=BAC86686.1; Type=Miscellaneous discrepancy; Note=Intron retention;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 33.79 RPKM in Testis
Total median expression: 650.45 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -21.4053-0.404 Picture PostScript Text
3' UTR -61.70153-0.403 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011012 - Longin-like_dom
IPR006722 - Sedlin

Pfam Domains:
PF04099 - Sybindin-like family
PF04628 - Sedlin, N-terminal conserved region

SCOP Domains:
64356 - SNARE-like

ModBase Predicted Comparative 3D Structure on Q9UL33
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0017112 Rab guanyl-nucleotide exchange factor activity

Biological Process:
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0016192 vesicle-mediated transport
GO:0048208 COPII vesicle coating
GO:0051259 protein oligomerization

Cellular Component:
GO:0000139 Golgi membrane
GO:0005622 intracellular
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0030008 TRAPP complex
GO:0043231 intracellular membrane-bounded organelle
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK307253 - Homo sapiens cDNA, FLJ97201.
AF089106 - Homo sapiens unknown mRNA, complete cds.
AX771012 - Sequence 32 from Patent WO03004532.
AK311885 - Homo sapiens cDNA, FLJ92151.
BC105809 - Homo sapiens trafficking protein particle complex 2-like, mRNA (cDNA clone MGC:111156 IMAGE:6745065), complete cds.
AK126779 - Homo sapiens cDNA FLJ44827 fis, clone BRACE3046837.
AF161524 - Homo sapiens HSPC176 mRNA, complete cds.
AX771013 - Sequence 33 from Patent WO03004532.
AK310805 - Homo sapiens cDNA, FLJ17847.
BC018024 - Homo sapiens trafficking protein particle complex 2-like, mRNA (cDNA clone MGC:24820 IMAGE:4287920), complete cds.
AX771014 - Sequence 34 from Patent WO03004532.
BC011369 - Homo sapiens trafficking protein particle complex 2-like, mRNA (cDNA clone MGC:8720 IMAGE:3868798), complete cds.
KJ902612 - Synthetic construct Homo sapiens clone ccsbBroadEn_12006 TRAPPC2L gene, encodes complete protein.
DQ595858 - Homo sapiens piRNA piR-61970, complete sequence.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UL33 (Reactome details) participates in the following event(s):

R-HSA-5694439 COPII coat binds TRAPPCII and RAB1:GDP
R-HSA-5694441 CSNK1D phosphorylates SEC23
R-HSA-5694418 RAB1:GTP binds USO1 and GORASP1:GOLGA2
R-HSA-5694409 Nucleotide exchange on RAB1
R-HSA-8877475 TRAPPC complexes exchange GTP for GDP on RAB1
R-HSA-204005 COPII-mediated vesicle transport
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-9007101 Rab regulation of trafficking
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B2R4M9, HSPC126, NM_016209, NP_057293, Q6ZTA7, Q9NZZ4, Q9UL33, TPC2L_HUMAN
UCSC ID: uc002fmc.3
RefSeq Accession: NM_016209
Protein: Q9UL33 (aka TPC2L_HUMAN)
CCDS: CCDS10971.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_016209.3
exon count: 5CDS single in 3' UTR: no RNA size: 637
ORF size: 423CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1046.00frame shift in genome: no % Coverage: 98.74
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
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