Tnfrsf17 (TNF receptor superfamily member 17) - Rat Genome Database

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Gene: Tnfrsf17 (TNF receptor superfamily member 17) Rattus norvegicus
Analyze
Symbol: Tnfrsf17
Name: TNF receptor superfamily member 17
RGD ID: 1304703
Description: Predicted to enable signaling receptor activity. Predicted to be involved in tumor necrosis factor-mediated signaling pathway. Predicted to act upstream of or within lymphocyte homeostasis. Human ortholog(s) of this gene implicated in colon carcinoma and multiple myeloma. Orthologous to human TNFRSF17 (TNF receptor superfamily member 17); PARTICIPATES IN cytokine mediated signaling pathway; INTERACTS WITH cadmium dichloride; furan; phenacetin.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC287034; tumor necrosis factor receptor superfamily member 17; tumor necrosis factor receptor superfamily, member 17
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
mRatBN7.2104,301,023 - 4,306,889 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl104,301,038 - 4,306,788 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx108,997,717 - 9,003,465 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0108,518,792 - 8,524,540 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0104,157,040 - 4,162,788 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0104,252,097 - 4,258,335 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl104,251,941 - 4,257,868 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0103,118,168 - 3,123,990 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4104,187,672 - 4,193,420 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1104,187,670 - 4,249,349 (-)NCBI
Celera103,324,770 - 3,330,518 (-)NCBICelera
Cytogenetic Map10q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Graft-versus-tumor response in patients with multiple myeloma is associated with antibody response to BCMA, a plasma-cell membrane receptor. Bellucci R, etal., Blood. 2005 May 15;105(10):3945-50. Epub 2005 Feb 3.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. A soluble form of B cell maturation antigen, a receptor for the tumor necrosis factor family member APRIL, inhibits tumor cell growth. Rennert P, etal., J Exp Med. 2000 Dec 4;192(11):1677-84.
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:14707116  


Genomics

Comparative Map Data
Tnfrsf17
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2104,301,023 - 4,306,889 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl104,301,038 - 4,306,788 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx108,997,717 - 9,003,465 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0108,518,792 - 8,524,540 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0104,157,040 - 4,162,788 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0104,252,097 - 4,258,335 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl104,251,941 - 4,257,868 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0103,118,168 - 3,123,990 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4104,187,672 - 4,193,420 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1104,187,670 - 4,249,349 (-)NCBI
Celera103,324,770 - 3,330,518 (-)NCBICelera
Cytogenetic Map10q11NCBI
TNFRSF17
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381611,965,210 - 11,968,068 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1611,965,210 - 11,968,068 (+)EnsemblGRCh38hg38GRCh38
GRCh371612,059,067 - 12,061,925 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361611,966,465 - 11,969,426 (+)NCBINCBI36Build 36hg18NCBI36
Build 341611,966,464 - 11,969,426NCBI
Celera1612,233,004 - 12,235,957 (+)NCBICelera
Cytogenetic Map16p13.13NCBI
HuRef1611,974,961 - 11,977,914 (+)NCBIHuRef
CHM1_11612,059,016 - 12,061,977 (+)NCBICHM1_1
T2T-CHM13v2.01612,001,328 - 12,004,186 (+)NCBIT2T-CHM13v2.0
Tnfrsf17
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391611,131,131 - 11,137,938 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1611,131,676 - 11,137,938 (+)EnsemblGRCm39 Ensembl
GRCm381611,313,232 - 11,320,074 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1611,313,812 - 11,320,074 (+)EnsemblGRCm38mm10GRCm38
MGSCv371611,313,902 - 11,320,161 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361611,227,387 - 11,233,646 (+)NCBIMGSCv36mm8
Celera1611,945,271 - 11,951,530 (+)NCBICelera
Cytogenetic Map16A1NCBI
cM Map166.42NCBI
Tnfrsf17
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554426,626,399 - 6,629,931 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554426,626,434 - 6,651,193 (-)NCBIChiLan1.0ChiLan1.0
TNFRSF17
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan11616,280,960 - 16,293,206 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01610,903,795 - 10,906,542 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11612,333,254 - 12,336,219 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1612,333,254 - 12,336,219 (+)Ensemblpanpan1.1panPan2
TNFRSF17
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1630,842,269 - 30,846,124 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl630,841,152 - 30,845,905 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha632,222,917 - 32,226,766 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0631,020,231 - 31,024,149 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl631,019,743 - 31,024,148 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1630,834,283 - 30,838,159 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0630,708,920 - 30,712,730 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0631,132,189 - 31,135,999 (-)NCBIUU_Cfam_GSD_1.0
Tnfrsf17
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344112,750,164 - 112,812,235 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936501907,009 - 909,878 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936501907,059 - 910,084 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNFRSF17
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl331,137,682 - 31,141,735 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1331,137,672 - 31,141,862 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2332,122,943 - 32,130,379 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TNFRSF17
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1511,435,306 - 11,438,573 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl511,435,842 - 11,438,351 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606818,695,580 - 18,698,526 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tnfrsf17
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247826,338,087 - 6,341,090 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247826,337,914 - 6,375,242 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tnfrsf17
18 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:175
Count of miRNA genes:145
Interacting mature miRNAs:154
Transcripts:ENSRNOT00000035886
Prediction methods:Microtar, Miranda, 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
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
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
1549898Neuinf3Neuroinflammation QTL 326.4nervous system integrity trait (VT:0010566)MHC Class II RT1A-positive spinal cord ventral horn area to total spinal cord ventral horn area ratio (CMO:0001980)1034063205387112Rat

Markers in Region
RH132261  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2104,306,076 - 4,306,277 (+)MAPPERmRatBN7.2
Rnor_6.0104,257,135 - 4,257,335NCBIRnor6.0
Rnor_5.0103,123,206 - 3,123,406UniSTSRnor5.0
RGSC_v3.4104,192,709 - 4,192,909UniSTSRGSC3.4
Celera103,329,807 - 3,330,007UniSTS
Cytogenetic Map10q11UniSTS
RH139044  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2104,301,122 - 4,301,305 (+)MAPPERmRatBN7.2
Rnor_6.0104,252,183 - 4,252,365NCBIRnor6.0
Rnor_5.0103,118,254 - 3,118,436UniSTSRnor5.0
RGSC_v3.4104,187,757 - 4,187,939UniSTSRGSC3.4
Celera103,324,855 - 3,325,037UniSTS
Cytogenetic Map10q11UniSTS


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 1
Low 2 31 15 18 1 1 11 9 9 11 1
Below cutoff 1 12 13 12 12 6 7 18 8 19 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000035886   ⟹   ENSRNOP00000034356
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl104,301,038 - 4,306,788 (-)Ensembl
Rnor_6.0 Ensembl104,251,941 - 4,257,868 (-)Ensembl
RefSeq Acc Id: NM_001105761   ⟹   NP_001099231
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2104,301,038 - 4,306,788 (-)NCBI
Rnor_6.0104,252,098 - 4,257,846 (-)NCBI
Rnor_5.0103,118,168 - 3,123,990 (-)NCBI
RGSC_v3.4104,187,672 - 4,193,420 (-)RGD
Celera103,324,770 - 3,330,518 (-)RGD
Sequence:
RefSeq Acc Id: XM_017597054   ⟹   XP_017452543
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2104,301,023 - 4,306,889 (-)NCBI
Rnor_6.0104,252,097 - 4,258,335 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001099231 (Get FASTA)   NCBI Sequence Viewer  
  XP_017452543 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL96195 (Get FASTA)   NCBI Sequence Viewer  
  EDL96196 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000034356
  ENSRNOP00000034356.4
Reference Protein Sequences
RefSeq Acc Id: NP_001099231   ⟸   NM_001105761
- UniProtKB: D3ZKQ8 (UniProtKB/TrEMBL),   A6K4H4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017452543   ⟸   XM_017597054
- Peptide Label: isoform X1
- UniProtKB: D3ZKQ8 (UniProtKB/TrEMBL),   A6K4H4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000034356   ⟸   ENSRNOT00000035886
Protein Domains
BCMA TALL-1 binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZKQ8-F1-model_v2 AlphaFold D3ZKQ8 1-184 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:1304703 AgrOrtholog
BioCyc Gene G2FUF-26173 BioCyc
Ensembl Genes ENSRNOG00000021987 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035886 ENTREZGENE
  ENSRNOT00000035886.6 UniProtKB/TrEMBL
Gene3D-CATH Tumor necrosis factor receptor superfamily UniProtKB/TrEMBL
InterPro BCMA_Tall-1-bd UniProtKB/TrEMBL
  TNFR_13C/17 UniProtKB/TrEMBL
  TNFR_17 UniProtKB/TrEMBL
KEGG Report rno:287034 UniProtKB/TrEMBL
NCBI Gene 287034 ENTREZGENE
PANTHER PTHR20437 UniProtKB/TrEMBL
  TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 17 UniProtKB/TrEMBL
Pfam BCMA-Tall_bind UniProtKB/TrEMBL
PharmGKB TNFRSF17 RGD
PhenoGen Tnfrsf17 PhenoGen
PRINTS TNFACTORR17 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000021987 RatGTEx
Superfamily-SCOP TNF receptor-like UniProtKB/TrEMBL
UniProt A6K4H4 ENTREZGENE, UniProtKB/TrEMBL
  D3ZKQ8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-05 Tnfrsf17  TNF receptor superfamily member 17  Tnfrsf17  tumor necrosis factor receptor superfamily, member 17  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Tnfrsf17  tumor necrosis factor receptor superfamily, member 17   Tnfrsf17_predicted  tumor necrosis factor receptor superfamily, member 17 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Tnfrsf17_predicted  tumor necrosis factor receptor superfamily, member 17 (predicted)      Symbol and Name status set to approved 70820 APPROVED