Traf3 (Tnf receptor-associated factor 3) - Rat Genome Database

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Gene: Traf3 (Tnf receptor-associated factor 3) Rattus norvegicus
Analyze
Symbol: Traf3
Name: Tnf receptor-associated factor 3
RGD ID: 1304633
Description: Predicted to enable enzyme binding activity; identical protein binding activity; and tumor necrosis factor receptor binding activity. Predicted to be involved in several processes, including regulation of gene expression; regulation of intracellular signal transduction; and tumor necrosis factor-mediated signaling pathway. Predicted to be located in cytoplasm. Predicted to be part of CD40 receptor complex. Predicted to be active in cytoplasmic side of plasma membrane. Human ortholog(s) of this gene implicated in brain disease. Orthologous to human TRAF3 (TNF receptor associated factor 3); PARTICIPATES IN Toll-like receptor signaling pathway; hepatitis C pathway; Retinoic acid-inducible gene (RIG) I-like receptor signaling pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC362788
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26130,199,696 - 130,307,168 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl6135,610,743 - 135,718,564 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06135,610,698 - 135,720,247 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06144,694,225 - 144,804,047 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46135,925,375 - 136,027,270 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16136,003,658 - 136,028,793 (+)NCBI
Celera6127,764,032 - 127,864,462 (+)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-taxifolin  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acrolein  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
alpha-pinene  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP)
cannabidiol  (EXP)
capsaicin  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
curcumin  (ISO)
D-glucose  (ISO)
decabromodiphenyl ether  (EXP)
diarsenic trioxide  (ISO)
diethylstilbestrol  (ISO)
dimethylarsinic acid  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
furan  (EXP)
Fusarenone X  (ISO)
glucose  (ISO)
hydroxychloroquine  (ISO)
ibrutinib  (ISO)
isoflurane  (EXP)
lipopolysaccharide  (ISO)
metformin  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylarsonic acid  (ISO)
nickel atom  (ISO)
o-anisidine  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
pentobarbital  (EXP)
propiconazole  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (ISO)
triptonide  (ISO)
tungsten  (ISO)
urethane  (EXP)
valproic acid  (EXP,ISO)
zoledronic acid  (ISO)

References

Additional References at PubMed
PMID:11279055   PMID:11728344   PMID:16306937   PMID:17015635   PMID:17158868   PMID:17626074   PMID:20185819   PMID:20614026   PMID:22871113   PMID:23871208   PMID:24803166   PMID:30497068  
PMID:32111144  


Genomics

Comparative Map Data
Traf3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26130,199,696 - 130,307,168 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl6135,610,743 - 135,718,564 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06135,610,698 - 135,720,247 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06144,694,225 - 144,804,047 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46135,925,375 - 136,027,270 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16136,003,658 - 136,028,793 (+)NCBI
Celera6127,764,032 - 127,864,462 (+)NCBICelera
Cytogenetic Map6q32NCBI
TRAF3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl14102,777,449 - 102,911,500 (+)EnsemblGRCh38hg38GRCh38
GRCh3814102,777,449 - 102,911,500 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3714103,243,786 - 103,377,837 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3614102,313,569 - 102,442,381 (+)NCBINCBI36hg18NCBI36
Celera1483,297,948 - 83,426,752 (+)NCBI
Cytogenetic Map14q32.32NCBI
HuRef1483,420,470 - 83,553,138 (+)NCBIHuRef
CHM1_114103,181,586 - 103,315,592 (+)NCBICHM1_1
Traf3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912111,132,755 - 111,233,589 (+)NCBIGRCm39mm39
GRCm39 Ensembl12111,132,804 - 111,233,587 (+)Ensembl
GRCm3812111,166,321 - 111,267,155 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12111,166,370 - 111,267,153 (+)EnsemblGRCm38mm10GRCm38
MGSCv3712112,404,759 - 112,505,359 (+)NCBIGRCm37mm9NCBIm37
MGSCv3612111,667,619 - 111,714,956 (+)NCBImm8
Celera12112,414,118 - 112,461,451 (+)NCBICelera
Cytogenetic Map12F1NCBI
cM Map1260.94NCBI
Traf3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555381,954,152 - 2,013,367 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555381,954,152 - 2,013,367 (+)NCBIChiLan1.0ChiLan1.0
TRAF3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.114103,263,222 - 103,346,383 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl14103,263,440 - 103,340,670 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01483,392,689 - 83,530,974 (+)NCBIMhudiblu_PPA_v0panPan3
TRAF3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1870,739,389 - 70,794,448 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl870,739,417 - 70,790,645 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha870,191,158 - 70,304,538 (+)NCBI
ROS_Cfam_1.0870,955,838 - 71,067,673 (+)NCBI
UMICH_Zoey_3.1870,619,852 - 70,733,066 (+)NCBI
UNSW_CanFamBas_1.0870,684,215 - 70,797,522 (+)NCBI
UU_Cfam_GSD_1.0871,084,379 - 71,197,763 (+)NCBI
Traf3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244086403,240,015 - 3,351,172 (-)NCBI
SpeTri2.0NW_004936835844,747 - 955,900 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRAF3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.27128,912,139 - 129,006,560 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TRAF3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12480,735,234 - 80,872,104 (+)NCBI
ChlSab1.1 Ensembl2480,789,699 - 80,866,480 (+)Ensembl
Vero_WHO_p1.0NW_02366605367,926,789 - 68,064,185 (+)NCBI
Traf3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247341,728,353 - 1,820,345 (-)NCBI

Position Markers
D6Rat101  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26130,245,261 - 130,245,370 (+)MAPPERmRatBN7.2
Rnor_6.06135,658,470 - 135,658,578NCBIRnor6.0
Rnor_5.06144,755,897 - 144,756,005UniSTSRnor5.0
RGSC_v3.46135,964,407 - 135,964,844RGDRGSC3.4
RGSC_v3.46135,964,411 - 135,964,519UniSTSRGSC3.4
RGSC_v3.16135,970,598 - 135,970,706RGD
Celera6127,802,576 - 127,802,684UniSTS
RH 3.4 Map6781.7RGD
RH 3.4 Map6781.7UniSTS
RH 2.0 Map61118.0RGD
SHRSP x BN Map681.7698RGD
Cytogenetic Map6q32UniSTS
AI528849  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26130,306,850 - 130,306,963 (+)MAPPERmRatBN7.2
Rnor_6.06135,719,934 - 135,720,046NCBIRnor6.0
Rnor_5.06144,694,429 - 144,694,541UniSTSRnor5.0
RGSC_v3.46136,026,957 - 136,027,069UniSTSRGSC3.4
Celera6127,864,149 - 127,864,261UniSTS
Cytogenetic Map6q32UniSTS
BE119065  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26130,264,923 - 130,265,073 (+)MAPPERmRatBN7.2
Rnor_6.06135,678,011 - 135,678,160NCBIRnor6.0
Rnor_5.06144,736,315 - 144,736,464UniSTSRnor5.0
RGSC_v3.46135,984,077 - 135,984,226UniSTSRGSC3.4
Celera6127,822,242 - 127,822,391UniSTS
Cytogenetic Map6q32UniSTS
TRAF3_1584  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26130,301,628 - 130,302,520 (+)MAPPERmRatBN7.2
Rnor_6.06135,714,712 - 135,715,603NCBIRnor6.0
Rnor_5.06144,698,872 - 144,699,763UniSTSRnor5.0
RGSC_v3.46136,021,735 - 136,022,626UniSTSRGSC3.4
Celera6127,858,939 - 127,859,830UniSTS
Cytogenetic Map6q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)692879510137879510Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6104363890147991367Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6104381930138066274Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6111134524138065254Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6117355600147991367Rat
1298087Iddm18Insulin dependent diabetes mellitus QTL 180.0001urine glucose amount (VT:0001758)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)6121224054135658578Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)6127286494144745573Rat
2293085Iddm29Insulin dependent diabetes mellitus QTL 297.66blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)6127286494147249902Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)6127286494147991367Rat
2312560Pur20Proteinuria QTL 202.10.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)6130561943144745573Rat
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6132652096138068606Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:532
Count of miRNA genes:238
Interacting mature miRNAs:323
Transcripts:ENSRNOT00000010906
Prediction methods: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.


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 10 17 2 18 2 74 20 31 2
Low 1 33 40 39 1 39 8 11 15 10 9 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010906   ⟹   ENSRNOP00000010906
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6135,610,743 - 135,718,564 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077770   ⟹   ENSRNOP00000074381
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6135,680,615 - 135,715,273 (+)Ensembl
RefSeq Acc Id: NM_001108724   ⟹   NP_001102194
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,206,484 - 130,307,164 (+)NCBI
Rnor_6.06135,610,743 - 135,720,247 (+)NCBI
Rnor_5.06144,694,225 - 144,804,047 (-)NCBI
RGSC_v3.46135,925,375 - 136,027,270 (+)RGD
Celera6127,764,032 - 127,864,462 (+)RGD
Sequence:
RefSeq Acc Id: XM_039112583   ⟹   XP_038968511
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,267,323 - 130,307,168 (+)NCBI
RefSeq Acc Id: XM_039112584   ⟹   XP_038968512
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,267,320 - 130,307,168 (+)NCBI
RefSeq Acc Id: XM_039112585   ⟹   XP_038968513
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,205,836 - 130,307,168 (+)NCBI
RefSeq Acc Id: XM_039112587   ⟹   XP_038968515
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,205,836 - 130,307,168 (+)NCBI
RefSeq Acc Id: XM_039112588   ⟹   XP_038968516
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,206,657 - 130,307,168 (+)NCBI
RefSeq Acc Id: XM_039112589   ⟹   XP_038968517
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,206,133 - 130,307,168 (+)NCBI
RefSeq Acc Id: XM_039112590   ⟹   XP_038968518
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,242,840 - 130,307,168 (+)NCBI
RefSeq Acc Id: XM_039112591   ⟹   XP_038968519
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,199,696 - 130,307,168 (+)NCBI
RefSeq Acc Id: XM_039112592   ⟹   XP_038968520
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,238,936 - 130,307,168 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001102194   ⟸   NM_001108724
- Sequence:
RefSeq Acc Id: ENSRNOP00000074381   ⟸   ENSRNOT00000077770
RefSeq Acc Id: ENSRNOP00000010906   ⟸   ENSRNOT00000010906
RefSeq Acc Id: XP_038968519   ⟸   XM_039112591
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968513   ⟸   XM_039112585
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968515   ⟸   XM_039112587
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968517   ⟸   XM_039112589
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968516   ⟸   XM_039112588
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968520   ⟸   XM_039112592
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968518   ⟸   XM_039112590
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968512   ⟸   XM_039112584
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038968511   ⟸   XM_039112583
- Peptide Label: isoform X1
Protein Domains
MATH   RING-type   TRAF-type

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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304633 AgrOrtholog
Ensembl Genes ENSRNOG00000008145 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000010906 UniProtKB/TrEMBL
  ENSRNOP00000074381 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010906 UniProtKB/TrEMBL
  ENSRNOT00000077770 UniProtKB/TrEMBL
Gene3D-CATH 2.60.210.10 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
InterPro MATH UniProtKB/TrEMBL
  TNF_rcpt-assoc_TRAF UniProtKB/TrEMBL
  TNF_recpt_TRAF UniProtKB/TrEMBL
  TRAF-like UniProtKB/TrEMBL
  TRAF3 UniProtKB/TrEMBL
  TRAF3_MATH UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
  Znf_RING_CS UniProtKB/TrEMBL
  Znf_TRAF UniProtKB/TrEMBL
KEGG Report rno:362788 UniProtKB/TrEMBL
NCBI Gene 362788 ENTREZGENE
PANTHER PTHR10131 UniProtKB/TrEMBL
  PTHR10131:SF76 UniProtKB/TrEMBL
Pfam zf-TRAF UniProtKB/TrEMBL
PhenoGen Traf3 PhenoGen
PIRSF TRAF UniProtKB/TrEMBL
PROSITE MATH UniProtKB/TrEMBL
  ZF_RING_1 UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/TrEMBL
  ZF_TRAF UniProtKB/TrEMBL
SMART MATH UniProtKB/TrEMBL
Superfamily-SCOP Traf_like UniProtKB/TrEMBL
UniProt A0A0G2K7X2_RAT UniProtKB/TrEMBL
  D3Z9G0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Traf3  Tnf receptor-associated factor 3   Traf3_predicted  Tnf receptor-associated factor 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Traf3_predicted  Tnf receptor-associated factor 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED