Tnfsf13b (TNF superfamily member 13b) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Tnfsf13b (TNF superfamily member 13b) Rattus norvegicus
Analyze
Symbol: Tnfsf13b
Name: TNF superfamily member 13b
RGD ID: 1561519
Description: Predicted to have signaling receptor binding activity. Predicted to be involved in several processes, including immunoglobulin secretion; positive regulation of germinal center formation; and positive regulation of lymphocyte activation. Predicted to localize to extracellular space; perinuclear region of cytoplasm; and plasma membrane. Orthologous to human TNFSF13B (TNF superfamily member 13b); PARTICIPATES IN cytokine mediated signaling pathway; rheumatoid arthritis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: B-cell-activating factor; BAFF; LOC498666; RGD1561519; similar to NZB B-cell activating factor; Tnlg7a; tumor necrosis factor (ligand) superfamily, member 13b; tumor necrosis factor ligand 7a; tumor necrosis factor ligand superfamily member 13B; tumor necrosis factor superfamily member 13b
Orthologs:
Homo sapiens (human) : TNFSF13B (TNF superfamily member 13b)  HGNC  Alliance
Mus musculus (house mouse) : Tnfsf13b (tumor necrosis factor (ligand) superfamily, member 13b)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Tnfsf13b (TNF superfamily member 13b)
Pan paniscus (bonobo/pygmy chimpanzee) : TNFSF13B (TNF superfamily member 13b)
Canis lupus familiaris (dog) : TNFSF13B (TNF superfamily member 13b)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Tnfsf13b (TNF superfamily member 13b)
Sus scrofa (pig) : TNFSF13B (TNF superfamily member 13b)
Chlorocebus sabaeus (African green monkey) : TNFSF13B (TNF superfamily member 13b)
Heterocephalus glaber (naked mole-rat) : Tnfsf13b (TNF superfamily member 13b)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01685,275,690 - 85,306,419 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1685,275,678 - 85,306,366 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01684,714,936 - 84,745,392 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41684,837,266 - 84,856,103 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1677,261,395 - 77,279,849 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View


Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:14557413   PMID:15240667   PMID:15368291   PMID:15485634   PMID:17499850   PMID:19828625   PMID:22124120   PMID:22391142   PMID:25598291   PMID:26417991   PMID:26646413   PMID:26688104  
PMID:27196292  


Genomics

Comparative Map Data
Tnfsf13b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01685,275,690 - 85,306,419 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1685,275,678 - 85,306,366 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01684,714,936 - 84,745,392 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41684,837,266 - 84,856,103 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1677,261,395 - 77,279,849 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
TNFSF13B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl13108,251,240 - 108,308,484 (+)EnsemblGRCh38hg38GRCh38
GRCh3813108,268,240 - 108,308,484 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3713108,921,875 - 108,960,832 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3613107,719,978 - 107,757,366 (+)NCBINCBI36hg18NCBI36
Build 3413107,719,977 - 107,757,366NCBI
Celera1389,766,721 - 89,804,112 (+)NCBI
Cytogenetic Map13q33.3NCBI
HuRef1389,512,942 - 89,552,797 (+)NCBIHuRef
CHM1_113108,891,226 - 108,925,602 (+)NCBICHM1_1
Tnfsf13b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39810,056,229 - 10,086,000 (+)NCBI
GRCm38810,006,229 - 10,036,000 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl810,006,467 - 10,039,072 (+)EnsemblGRCm38mm10GRCm38
MGSCv37810,006,633 - 10,036,000 (+)NCBIGRCm37mm9NCBIm37
MGSCv36810,006,605 - 10,035,972 (+)NCBImm8
Celera810,182,059 - 10,211,354 (+)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map84.55NCBI
Tnfsf13b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554043,536,868 - 3,569,750 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554043,536,041 - 3,573,242 (-)NCBIChiLan1.0ChiLan1.0
TNFSF13B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.113108,536,617 - 108,575,739 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13108,536,617 - 108,574,296 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01389,399,044 - 89,438,837 (+)NCBI
TNFSF13B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2257,036,292 - 57,068,320 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12257,036,307 - 57,069,053 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tnfsf13b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364723,789,111 - 3,834,163 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNFSF13B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1175,599,598 - 75,633,041 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11175,599,296 - 75,633,044 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21183,014,191 - 83,048,071 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TNFSF13B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl386,638,302 - 86,675,772 (+)Ensembl
ChlSab1.1386,637,988 - 86,675,774 (+)NCBI
Tnfsf13b
(Heterocephalus glaber - naked mole-rat)
No map positions available.

Position Markers
RH131199  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01685,275,736 - 85,275,918NCBIRnor6.0
Rnor_5.01684,714,982 - 84,715,164UniSTSRnor5.0
RGSC_v3.41684,825,181 - 84,825,363UniSTSRGSC3.4
Celera1677,249,701 - 77,249,883UniSTS
Cytogenetic Map16q12.5UniSTS
RH 3.4 Map16769.4UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164151271086512710Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164151271086512710Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164655818890668790Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165781635790668790Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165781635790668790Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165781635790668790Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165928577589248943Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:10
Count of miRNA genes:10
Interacting mature miRNAs:10
Transcripts:ENSRNOT00000067511
Prediction methods: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.


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 2 1 1 5
Low 2 12 49 35 18 35 2 2 5 14 20 6 2
Below cutoff 25 4 4 4 6 9 65 21 19 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067511   ⟹   ENSRNOP00000062950
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1685,287,828 - 85,305,782 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076737   ⟹   ENSRNOP00000068118
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1685,275,678 - 85,305,839 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089650   ⟹   ENSRNOP00000073755
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1685,275,689 - 85,306,366 (-)Ensembl
RefSeq Acc Id: NM_001109112   ⟹   NP_001102582
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01685,287,516 - 85,306,088 (-)NCBI
Rnor_5.01684,714,936 - 84,745,392 (-)NCBI
RGSC_v3.41684,837,266 - 84,856,103 (-)RGD
Celera1677,261,395 - 77,279,849 (-)RGD
Sequence:
RefSeq Acc Id: XM_006253480   ⟹   XP_006253542
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01685,275,690 - 85,306,419 (-)NCBI
Rnor_5.01684,714,936 - 84,745,392 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253481   ⟹   XP_006253543
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01685,275,690 - 85,306,419 (-)NCBI
Rnor_5.01684,714,936 - 84,745,392 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253482   ⟹   XP_006253544
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01685,275,690 - 85,306,418 (-)NCBI
Rnor_5.01684,714,936 - 84,745,392 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253483   ⟹   XP_006253545
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01685,275,690 - 85,306,417 (-)NCBI
Rnor_5.01684,714,936 - 84,745,392 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001102582   ⟸   NM_001109112
- UniProtKB: D3ZFD8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253543   ⟸   XM_006253481
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006253542   ⟸   XM_006253480
- Peptide Label: isoform X1
- UniProtKB: A0A096MJG3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253544   ⟸   XM_006253482
- Peptide Label: isoform X3
- UniProtKB: A0A0U5JXV5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253545   ⟸   XM_006253483
- Peptide Label: isoform X4
- UniProtKB: A0A0G2K6C2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000062950   ⟸   ENSRNOT00000067511
RefSeq Acc Id: ENSRNOP00000073755   ⟸   ENSRNOT00000089650
RefSeq Acc Id: ENSRNOP00000068118   ⟸   ENSRNOT00000076737
Protein Domains
TNF_2

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 84848985 84848986 A G snv FHL/EurMcwi (MCW), LCR/2Mco (UMich), HCR/1Mco (UMich), SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561519 AgrOrtholog
Ensembl Genes ENSRNOG00000014464 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000062950 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068118 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073755 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067511 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000076737 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000089650 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.40 UniProtKB/TrEMBL
InterPro TNF_dom UniProtKB/TrEMBL
  Tumour_necrosis_fac-like_dom UniProtKB/TrEMBL
KEGG Report rno:498666 UniProtKB/TrEMBL
NCBI Gene 498666 ENTREZGENE
Pfam TNF UniProtKB/TrEMBL
PhenoGen Tnfsf13b PhenoGen
PROSITE TNF_2 UniProtKB/TrEMBL
Superfamily-SCOP SSF49842 UniProtKB/TrEMBL
UniGene Rn.219918 ENTREZGENE
UniProt A0A096MJG3 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K6C2 ENTREZGENE, UniProtKB/TrEMBL
  A0A0U5JXV5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZFD8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-21 Tnfsf13b  TNF superfamily member 13b  Tnfsf13b  tumor necrosis factor superfamily member 13b  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-25 Tnfsf13b  tumor necrosis factor superfamily member 13b  Tnfsf13b  tumor necrosis factor (ligand) superfamily, member 13b  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 Tnfsf13b  tumor necrosis factor (ligand) superfamily, member 13b  RGD1561519_predicted  similar to NZB B-cell activating factor (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561519_predicted  similar to NZB B-cell activating factor (predicted)  LOC498666  similar to NZB B-cell activating factor  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498666  similar to NZB B-cell activating factor      Symbol and Name status set to provisional 70820 PROVISIONAL

 



Contact Us |  About Us |  License CC BY 4.0 |  Legal Disclaimer |  © Medical College of Wisconsin
NHLBI Logo

RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.