Tnfrsf13c (TNF receptor superfamily member 13C) - Rat Genome Database

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Gene: Tnfrsf13c (TNF receptor superfamily member 13C) Rattus norvegicus
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Symbol: Tnfrsf13c
Name: TNF receptor superfamily member 13C
RGD ID: 1560810
Description: Predicted to enable signaling receptor activity. Predicted to be involved in positive regulation of lymphocyte activation. Predicted to act upstream of or within B cell homeostasis; positive regulation of germinal center formation; and positive regulation of type II interferon production. Predicted to be located in membrane. Predicted to be active in external side of plasma membrane. Human ortholog(s) of this gene implicated in common variable immunodeficiency 4. Orthologous to human TNFRSF13C (TNF receptor superfamily member 13C); PARTICIPATES IN cytokine mediated signaling pathway; primary immunodeficiency pathway; INTERACTS WITH 1,2-dimethylhydrazine; 17beta-estradiol; alpha-Zearalanol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC500910; RGD1560810; similar to tumor necrosis factor receptor superfamily, member 13c; tumor necrosis factor receptor superfamily member 13C; tumor necrosis factor receptor superfamily, member 13c
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87115,616,139 - 115,618,647 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7115,616,303 - 115,618,620 (-)EnsemblGRCr8
mRatBN7.27113,736,046 - 113,738,523 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7113,736,055 - 113,738,517 (-)EnsemblmRatBN7.2
Rnor_6.07123,453,799 - 123,456,289 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7123,453,788 - 123,456,268 (-)Ensemblrn6Rnor6.0
Rnor_5.07123,438,591 - 123,439,975 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47120,596,571 - 120,597,836 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7110,051,209 - 110,053,699 (-)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14557413   PMID:15240667   PMID:15368291   PMID:22124120   PMID:22391142  


Genomics

Comparative Map Data
Tnfrsf13c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87115,616,139 - 115,618,647 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7115,616,303 - 115,618,620 (-)EnsemblGRCr8
mRatBN7.27113,736,046 - 113,738,523 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7113,736,055 - 113,738,517 (-)EnsemblmRatBN7.2
Rnor_6.07123,453,799 - 123,456,289 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7123,453,788 - 123,456,268 (-)Ensemblrn6Rnor6.0
Rnor_5.07123,438,591 - 123,439,975 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47120,596,571 - 120,597,836 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7110,051,209 - 110,053,699 (-)NCBICelera
Cytogenetic Map7q34NCBI
TNFRSF13C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382241,922,032 - 41,926,806 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2241,922,032 - 41,926,806 (-)Ensemblhg38GRCh38
GRCh372242,318,036 - 42,322,810 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362240,650,982 - 40,652,728 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342240,645,535 - 40,647,282NCBI
Celera2226,127,271 - 26,129,056 (-)NCBICelera
Cytogenetic Map22q13.2NCBI
HuRef2225,286,634 - 25,288,419 (-)NCBIHuRef
CHM1_12242,281,235 - 42,283,020 (-)NCBICHM1_1
T2T-CHM13v2.02242,400,895 - 42,405,666 (-)NCBIT2T-CHM13v2.0
Tnfrsf13c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391582,105,943 - 82,108,581 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1582,105,944 - 82,108,570 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381582,221,742 - 82,224,380 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1582,221,743 - 82,224,369 (-)Ensemblmm10GRCm38
MGSCv371582,052,174 - 82,054,766 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361582,048,999 - 82,051,591 (-)NCBIMGSCv36mm8
Celera1584,345,398 - 84,346,929 (-)NCBICelera
Cytogenetic Map15E1NCBI
cM Map1538.56NCBI
Tnfrsf13c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495541327,341,977 - 27,344,009 (-)NCBIChiLan1.0ChiLan1.0
TNFRSF13C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22351,751,774 - 51,758,115 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12254,449,100 - 54,457,327 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02222,816,504 - 22,819,584 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
TNFRSF13C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11023,430,960 - 23,434,972 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1023,433,052 - 23,438,946 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1023,365,041 - 23,369,055 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01024,175,948 - 24,179,962 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1024,178,192 - 24,179,471 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11023,892,942 - 23,896,956 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01024,214,176 - 24,218,207 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01024,388,325 - 24,392,339 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tnfrsf13c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049457,088,464 - 7,089,921 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493649298,878 - 101,920 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNFRSF13C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl56,699,878 - 6,703,656 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.156,699,812 - 6,703,403 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TNFRSF13C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11924,457,381 - 24,459,438 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666045100,952,971 - 100,954,833 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tnfrsf13c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247526,797,983 - 6,799,097 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247526,797,453 - 6,799,437 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Tnfrsf13c
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11251,951,579 - 251,952,857 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tnfrsf13c
21 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:177
Count of miRNA genes:95
Interacting mature miRNAs:102
Transcripts:ENSRNOT00000010086, ENSRNOT00000056037
Prediction methods:Microtar, Miranda, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)792388565119280177Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)782111245123048330Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7104186212135371468Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)773618702118618702Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)793302009131686183Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)795485047137014596Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7115313999136544683Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)746307490127866166Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)785043242130043242Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)785497398130497398Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)792362341137014596Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)783626689128626689Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)782111382132099989Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)798549867137014596Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)773557047118557047Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)782111245123048330Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)740540077123682549Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)796700404118618702Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)749682832115766396Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7110725024135371468Rat
10450862Kidm55Kidney mass QTL 554.9kidney mass (VT:0002707)kidney weight (CMO:0000081)772725037117725037Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)7100548246137014596Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)782111245134948181Rat
10450856Livw4Liver weight QTL 43.8liver mass (VT:0003402)liver weight (CMO:0000092)772725037117725037Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)749682832115766396Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)778682549123682549Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)749682832115766396Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)771621154119349044Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)771827901136544683Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
14 12 40 108 79 78 47 90 47 6 297 163 11 83 65 60 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000056037   ⟹   ENSRNOP00000052889
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7115,616,303 - 115,618,620 (-)Ensembl
mRatBN7.2 Ensembl7113,736,055 - 113,738,517 (-)Ensembl
Rnor_6.0 Ensembl7123,453,788 - 123,456,268 (-)Ensembl
RefSeq Acc Id: XM_576316   ⟹   XP_576316
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87115,616,139 - 115,618,647 (-)NCBI
mRatBN7.27113,736,046 - 113,738,523 (-)NCBI
Rnor_6.07123,453,799 - 123,456,289 (-)NCBI
Rnor_5.07123,438,591 - 123,439,975 (-)NCBI
RGSC_v3.47120,596,571 - 120,597,836 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001418900 (Get FASTA)   NCBI Sequence Viewer  
  XP_576316 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000052889
  ENSRNOP00000052889.3
RefSeq Acc Id: XP_576316   ⟸   XM_576316
- Sequence:
Ensembl Acc Id: ENSRNOP00000052889   ⟸   ENSRNOT00000056037
Protein Domains
Tumour necrosis factor receptor 13C TALL-1 binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A281-F1-model_v2 AlphaFold D4A281 1-175 view protein structure

Transcriptome

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

Promoters
RGD ID:13695533
Promoter ID:EPDNEW_R6054
Type:multiple initiation site
Name:Tnfrsf13c_1
Description:TNF receptor superfamily member 13C
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_6.07123,456,258 - 123,456,318EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560810 AgrOrtholog
BioCyc Gene G2FUF-32637 BioCyc
Ensembl Genes ENSRNOG00000007664 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000056037 ENTREZGENE
  ENSRNOT00000056037.5 UniProtKB/TrEMBL
InterPro TNFR_13C UniProtKB/TrEMBL
  TNFR_13C/17 UniProtKB/TrEMBL
  TNFR_13C_TALL-1-bd UniProtKB/TrEMBL
KEGG Report rno:500910 UniProtKB/TrEMBL
NCBI Gene 500910 ENTREZGENE
PANTHER PTHR20437 UniProtKB/TrEMBL
  PTHR20437:SF2 UniProtKB/TrEMBL
Pfam BaffR-Tall_bind UniProtKB/TrEMBL
PhenoGen Tnfrsf13c PhenoGen
PRINTS TNFACTORR13C UniProtKB/TrEMBL
RatGTEx ENSRNOG00000007664 RatGTEx
Superfamily-SCOP TNF receptor-like UniProtKB/TrEMBL
UniProt D4A281 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-05 Tnfrsf13c  TNF receptor superfamily member 13C  Tnfrsf13c  tumor necrosis factor receptor superfamily, member 13c  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-28 Tnfrsf13c  tumor necrosis factor receptor superfamily, member 13c  RGD1560810_predicted  similar to tumor necrosis factor receptor superfamily, member 13c (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560810_predicted  similar to tumor necrosis factor receptor superfamily, member 13c (predicted)  LOC500910  similar to tumor necrosis factor receptor superfamily, member 13c  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC500910  similar to tumor necrosis factor receptor superfamily, member 13c      Symbol and Name status set to provisional 70820 PROVISIONAL