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

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Gene: Tnfrsf13c (TNF receptor superfamily member 13C) Rattus norvegicus
Analyze
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 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: MODEL
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
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87115,616,139 - 115,618,647 (-)NCBIGRCr8
mRatBN7.27113,736,046 - 113,738,523 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7113,736,055 - 113,738,517 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.07123,453,799 - 123,456,289 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7123,453,788 - 123,456,268 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07123,438,591 - 123,439,975 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47120,596,571 - 120,597,836 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7110,051,209 - 110,053,699 (-)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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 (-)NCBIGRCr8
mRatBN7.27113,736,046 - 113,738,523 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7113,736,055 - 113,738,517 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.07123,453,799 - 123,456,289 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7123,453,788 - 123,456,268 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07123,438,591 - 123,439,975 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47120,596,571 - 120,597,836 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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 (-)EnsemblGRCh38hg38GRCh38
GRCh372242,318,036 - 42,322,810 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362240,650,982 - 40,652,728 (-)NCBINCBI36Build 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 Ensembl
GRCm381582,221,742 - 82,224,380 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1582,221,743 - 82,224,369 (-)EnsemblGRCm38mm10GRCm38
MGSCv371582,052,174 - 82,054,766 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1023,365,041 - 23,369,055 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01024,175,948 - 24,179,962 (+)NCBIROS_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_1.0
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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247526,797,453 - 6,799,437 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tnfrsf13c
16 total Variants
miRNA Target Status

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 (mRatBN7.2)
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)743747012135012528Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)794811326116294265Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7103146217116738842Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)794811085116738842Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)768938720113886318Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)768938720113886318Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)768938720113886318Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)769736226117455174Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat


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 11
Low 1 6 26 10 8 10 4 5 9 9 11 11 4
Below cutoff 21 19 19 19 4 6 12 18 24 4

Sequence


Ensembl Acc Id: ENSRNOT00000056037   ⟹   ENSRNOP00000052889
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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 XP_576316 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000052889.3
RefSeq Acc Id: XP_576316   ⟸   XM_576316
- UniProtKB: D4A281 (UniProtKB/TrEMBL)
- 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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000056037.4 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