Trappc2 (trafficking protein particle complex subunit 2) - Rat Genome Database

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Gene: Trappc2 (trafficking protein particle complex subunit 2) Rattus norvegicus
Analyze
Symbol: Trappc2
Name: trafficking protein particle complex subunit 2
RGD ID: 1306925
Description: Predicted to enable transcription corepressor binding activity; transcription regulator inhibitor activity; and transmembrane transporter binding activity. Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; positive regulation of gene expression; and skeletal system development. Predicted to be located in endoplasmic reticulum; nucleus; and perinuclear region of cytoplasm. Predicted to be part of TRAPP complex. Predicted to be active in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in X-linked spondyloepiphyseal dysplasia tarda. Orthologous to several human genes including TRAPPC2 (trafficking protein particle complex subunit 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; furan.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC287274; MGC109621; RGD1306925; sedlin; similar to RIKEN cDNA 0610009B22; trafficking protein particle complex 2; trafficking protein particle complex protein 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X28,004,051 - 28,015,336 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX27,994,054 - 28,015,346 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX29,038,597 - 29,049,838 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X32,473,731 - 32,484,938 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X28,653,239 - 28,664,478 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X29,550,871 - 29,562,135 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX29,550,873 - 29,556,610 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X29,944,161 - 29,955,426 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X48,690,381 - 48,701,588 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X48,743,851 - 48,755,057 (-)NCBI
CeleraX28,376,813 - 28,388,017 (-)NCBICelera
Cytogenetic MapXq13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10431248   PMID:11134351   PMID:12477932   PMID:12681486   PMID:17027922   PMID:21525244   PMID:25918224  


Genomics

Comparative Map Data
Trappc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X28,004,051 - 28,015,336 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX27,994,054 - 28,015,346 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX29,038,597 - 29,049,838 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X32,473,731 - 32,484,938 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X28,653,239 - 28,664,478 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X29,550,871 - 29,562,135 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX29,550,873 - 29,556,610 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X29,944,161 - 29,955,426 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X48,690,381 - 48,701,588 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X48,743,851 - 48,755,057 (-)NCBI
CeleraX28,376,813 - 28,388,017 (-)NCBICelera
Cytogenetic MapXq13NCBI
TRAPPC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X13,712,245 - 13,734,620 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX13,712,244 - 13,734,635 (-)EnsemblGRCh38hg38GRCh38
GRCh37X13,730,364 - 13,752,739 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X13,640,282 - 13,662,648 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X13,490,017 - 13,512,384NCBI
CeleraX17,847,442 - 17,869,835 (-)NCBICelera
Cytogenetic MapXp22.2NCBI
HuRefX11,488,878 - 11,510,859 (-)NCBIHuRef
CHM1_1X13,761,181 - 13,783,572 (-)NCBICHM1_1
T2T-CHM13v2.0X13,293,643 - 13,316,052 (-)NCBIT2T-CHM13v2.0
Trappc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X165,223,747 - 165,236,136 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX165,223,570 - 165,236,136 (+)EnsemblGRCm39 Ensembl
GRCm38X166,440,702 - 166,453,140 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX166,440,574 - 166,453,140 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X162,878,757 - 162,890,475 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X161,784,906 - 161,797,243 (+)NCBIMGSCv36mm8
CeleraX149,620,616 - 149,632,365 (+)NCBICelera
Cytogenetic MapXF5NCBI
cM MapX77.43NCBI
Trappc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555194,470,906 - 4,485,969 (+)NCBIChiLan1.0ChiLan1.0
TRAPPC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1X15,495,495 - 15,517,527 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X6,321,264 - 6,341,650 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X13,609,852 - 13,629,926 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX13,609,852 - 13,629,916 (-)Ensemblpanpan1.1panPan2
LOC480840
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X10,128,169 - 10,140,386 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX10,128,849 - 10,140,351 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX10,104,804 - 10,108,924 (-)NCBIDog10K_Boxer_Tasha
Trappc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X3,278,413 - 3,292,930 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049364703,278,415 - 3,292,905 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRAPPC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX10,353,419 - 10,366,106 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X10,353,417 - 10,366,095 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X11,307,155 - 11,319,835 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TRAPPC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X12,206,192 - 12,222,303 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX12,206,289 - 12,211,834 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605614,020,889 - 14,039,703 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Trappc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624882417,101 - 431,170 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Trappc2
39 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:941
Count of miRNA genes:322
Interacting mature miRNAs:431
Transcripts:ENSRNOT00000006006, ENSRNOT00000068113, ENSRNOT00000073738
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1529780260297802Rat
1598873Memor2Memory QTL 22.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)X2099094741052531Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2099094741203591Rat

Markers in Region
RH128656  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X28,004,243 - 28,004,452 (+)MAPPERmRatBN7.2
Rnor_6.0X29,551,064 - 29,551,272NCBIRnor6.0
Rnor_5.0X29,944,357 - 29,944,565UniSTSRnor5.0
RGSC_v3.4X48,690,574 - 48,690,782UniSTSRGSC3.4
CeleraX28,377,006 - 28,377,214UniSTS
RH 3.4 MapX360.3UniSTS
Cytogenetic MapXq21UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 32 32 16 19 16 1 1 74 33 36 11 1
Low 1 11 25 25 25 7 10 2 5 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000068113   ⟹   ENSRNOP00000062350
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX28,004,054 - 28,015,346 (-)Ensembl
Rnor_6.0 EnsemblX29,550,873 - 29,556,610 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102365   ⟹   ENSRNOP00000086382
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX27,994,054 - 28,015,299 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102526   ⟹   ENSRNOP00000090564
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX28,005,063 - 28,015,346 (-)Ensembl
RefSeq Acc Id: NM_001024965   ⟹   NP_001020136
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X28,004,051 - 28,015,260 (-)NCBI
Rnor_6.0X29,550,871 - 29,562,078 (-)NCBI
Rnor_5.0X29,944,161 - 29,955,426 (-)NCBI
RGSC_v3.4X48,690,381 - 48,701,588 (-)RGD
CeleraX28,376,813 - 28,388,017 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256857   ⟹   XP_006256919
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X28,004,051 - 28,015,336 (-)NCBI
Rnor_6.0X29,550,871 - 29,562,135 (-)NCBI
Rnor_5.0X29,944,161 - 29,955,426 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001020136 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256919 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL90550 (Get FASTA)   NCBI Sequence Viewer  
  EDL90551 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001020136   ⟸   NM_001024965
- UniProtKB: Q5BJL8 (UniProtKB/TrEMBL),   A6K2H9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256919   ⟸   XM_006256857
- Peptide Label: isoform X1
- UniProtKB: Q5BJL8 (UniProtKB/TrEMBL),   A6K2H9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000062350   ⟸   ENSRNOT00000068113
RefSeq Acc Id: ENSRNOP00000090564   ⟸   ENSRNOT00000102526
RefSeq Acc Id: ENSRNOP00000086382   ⟸   ENSRNOT00000102365

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5BJL8-F1-model_v2 AlphaFold Q5BJL8 1-140 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306925 AgrOrtholog
BioCyc Gene G2FUF-2609 BioCyc
Ensembl Genes ENSRNOG00000042276 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000062350 ENTREZGENE
  ENSRNOP00000062350.1 UniProtKB/TrEMBL
  ENSRNOP00000086382 ENTREZGENE
  ENSRNOP00000086382.1 UniProtKB/TrEMBL
  ENSRNOP00000090564.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068113 ENTREZGENE
  ENSRNOT00000068113.2 UniProtKB/TrEMBL
  ENSRNOT00000102365 ENTREZGENE
  ENSRNOT00000102365.1 UniProtKB/TrEMBL
  ENSRNOT00000102526.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.450.70 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7367127 IMAGE-MGC_LOAD
InterPro Longin-like UniProtKB/TrEMBL
  Sedlin UniProtKB/TrEMBL
KEGG Report rno:501550 UniProtKB/TrEMBL
MGC_CLONE MGC:109621 IMAGE-MGC_LOAD
NCBI Gene 501550 ENTREZGENE
PANTHER Sedlin UniProtKB/TrEMBL
  TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 2-RELATED UniProtKB/TrEMBL
Pfam Sedlin_N UniProtKB/TrEMBL
PhenoGen Trappc2 PhenoGen
Superfamily-SCOP Longin_like UniProtKB/TrEMBL
UniProt A0A8I6AEJ6_RAT UniProtKB/TrEMBL
  A6K2H9 ENTREZGENE
  A6K2I0_RAT UniProtKB/TrEMBL
  Q5BJL8 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A6K2H9 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-02-18 Trappc2  trafficking protein particle complex subunit 2  Trappc2  trafficking protein particle complex 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Trappc2  trafficking protein particle complex 2  RGD1306925  similar to RIKEN cDNA 0610009B22  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1306925  similar to RIKEN cDNA 0610009B22  RGD1306925_predicted  similar to RIKEN cDNA 0610009B22 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1306925_predicted  similar to RIKEN cDNA 0610009B22 (predicted)  LOC287274_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC287274_predicted  similar to RIKEN cDNA 0610009B22 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL