Trappc2b (trafficking protein particle complex 2B) - Rat Genome Database

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Gene: Trappc2b (trafficking protein particle complex 2B) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Trappc2b
Name: trafficking protein particle complex 2B
RGD ID: 6499350
Description: Predicted to be located in nucleus. Human ortholog(s) of this gene implicated in X-linked spondyloepiphyseal dysplasia tarda. Orthologous to human TRAPPC2 (trafficking protein particle complex subunit 2) and TRAPPC2B (trafficking protein particle complex subunit 2B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; paracetamol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC100910318; sedlin-like; trafficking protein particle complex 2; trafficking protein particle complex subunit 2; trafficking protein particle complex subunit 2-like; trafficking protein particle complex subunit 2B
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81036,439,185 - 36,443,432 (-)NCBIGRCr8
mRatBN7.21035,938,225 - 35,942,869 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1035,938,039 - 35,942,975 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1040,631,983 - 40,636,237 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01040,122,261 - 40,126,515 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01035,625,680 - 35,629,935 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01035,036,176 - 35,040,918 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1035,036,176 - 35,040,423 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1037,130,499 - 37,130,921 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01034,808,875 - 34,813,524 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1035,293,575 - 35,297,819 (-)NCBICelera
Cytogenetic Map10q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15057822  


Genomics

Variants

.
Variants in Trappc2b
12 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:21
Count of miRNA genes:14
Interacting mature miRNAs:14
Transcripts:ENSRNOT00000006006, ENSRNOT00000073738
Prediction methods:Microtar, Rnahybrid
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
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101790711351786432Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
631531Iresp2Immunoglobin response QTL26.3blood immunoglobulin E amount (VT:0002492)serum immunoglobulin E level (CMO:0002101)102291826836400810Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102887565052200160Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103449055945579777Rat
1354614Hpcl1Hepatic cholesterol level QTL 13.3liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)103539226751793994Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat


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 3 4 43 32 12 32 50 35 41 11
Low 39 14 9 7 9 8 11 24 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006006   ⟹   ENSRNOP00000006006
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1037,130,499 - 37,130,921 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000073738   ⟹   ENSRNOP00000066171
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1035,938,039 - 35,942,975 (-)Ensembl
Rnor_6.0 Ensembl1035,036,176 - 35,040,423 (-)Ensembl
RefSeq Acc Id: NM_001271111   ⟹   NP_001258040
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81036,439,185 - 36,443,432 (-)NCBI
mRatBN7.21035,938,225 - 35,942,474 (-)NCBI
Rnor_6.01035,036,176 - 35,040,423 (-)NCBI
Rnor_5.01034,808,875 - 34,813,524 (-)NCBI
Celera1035,293,575 - 35,297,819 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001271112   ⟹   NP_001258041
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81036,439,185 - 36,443,432 (-)NCBI
mRatBN7.21035,938,225 - 35,942,474 (-)NCBI
Rnor_6.01035,036,176 - 35,040,423 (-)NCBI
Rnor_5.01034,808,875 - 34,813,524 (-)NCBI
Celera1035,293,575 - 35,297,819 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001258041   ⟸   NM_001271112
- UniProtKB: D3ZVF4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001258040   ⟸   NM_001271111
- UniProtKB: D3ZVF4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006006   ⟸   ENSRNOT00000006006
RefSeq Acc Id: ENSRNOP00000066171   ⟸   ENSRNOT00000073738

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZVF4-F1-model_v2 AlphaFold D3ZVF4 1-140 view protein structure

Transcriptome

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

Promoters
RGD ID:13697142
Promoter ID:EPDNEW_R7667
Type:initiation region
Name:Trappc2b_1
Description:trafficking protein particle complex 2B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01035,040,345 - 35,040,405EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:6499350 AgrOrtholog
BioCyc Gene G2FUF-25190 BioCyc
Ensembl Genes ENSRNOG00000004419 Ensembl
  ENSRNOG00000049062 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055005219 UniProtKB/Swiss-Prot
  ENSRNOG00060024463 UniProtKB/Swiss-Prot
  ENSRNOG00065005348 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000073738 ENTREZGENE
  ENSRNOT00000073738.3 UniProtKB/Swiss-Prot
  ENSRNOT00055008370 UniProtKB/Swiss-Prot
  ENSRNOT00060042349 UniProtKB/Swiss-Prot
  ENSRNOT00065007892 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.450.70 UniProtKB/Swiss-Prot
InterPro Longin-like_dom_sf UniProtKB/Swiss-Prot
  Sedlin UniProtKB/Swiss-Prot
KEGG Report rno:100910318 UniProtKB/Swiss-Prot
NCBI Gene LOC100910318 ENTREZGENE
PANTHER PTHR12403 UniProtKB/Swiss-Prot
  RIKEN CDNA 0610009B22 GENE UniProtKB/Swiss-Prot
Pfam Sedlin_N UniProtKB/Swiss-Prot
PhenoGen Trappc2b PhenoGen
RatGTEx ENSRNOG00000004419 RatGTEx
  ENSRNOG00000049062 RatGTEx
  ENSRNOG00055005219 RatGTEx
  ENSRNOG00060024463 RatGTEx
  ENSRNOG00065005348 RatGTEx
Superfamily-SCOP SSF64356 UniProtKB/Swiss-Prot
UniProt D3ZVF4 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-06-10 Trappc2b  trafficking protein particle complex 2B  LOC100910318  trafficking protein particle complex subunit 2-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100910318  trafficking protein particle complex subunit 2-like      Symbol and Name status set to provisional 70820 PROVISIONAL