Traf3ip2 (Traf3 interacting protein 2) - Rat Genome Database
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Gene: Traf3ip2 (Traf3 interacting protein 2) Rattus norvegicus
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Symbol: Traf3ip2
Name: Traf3 interacting protein 2
RGD ID: 1593240
Description: Predicted to have signaling receptor binding activity and ubiquitin protein ligase activity. Predicted to be involved in several processes, including immunoglobulin secretion; interleukin-17-mediated signaling pathway; and positive regulation of defense response to virus by host. Human ortholog(s) of this gene implicated in chronic mucocutaneous candidiasis and psoriasis 13. Orthologous to human TRAF3IP2 (TRAF3 interacting protein 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: adapter protein CIKS; chromosome 6 open reading frame 4; E3 ubiquitin ligase TRAF3IP2; LOC294437; MGC112844; RGD1304768; similar to Adapter protein CIKS (Connection to IKK and SAPK/JNK) (Nuclear factor NF-kappa-B activator 1) (ACT1)
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
mRatBN7.22043,011,405 - 43,054,654 (+)NCBI
Rnor_6.0 Ensembl2044,680,449 - 44,722,872 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02044,679,861 - 44,722,874 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02046,401,898 - 46,445,446 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42043,747,622 - 43,792,255 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2043,727,541 - 43,769,944 (+)NCBICelera
Cytogenetic Map20q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:12477932   PMID:12761501   PMID:15485634   PMID:20554964   PMID:23066157  


Genomics

Comparative Map Data
Traf3ip2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22043,011,405 - 43,054,654 (+)NCBI
Rnor_6.0 Ensembl2044,680,449 - 44,722,872 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02044,679,861 - 44,722,874 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02046,401,898 - 46,445,446 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42043,747,622 - 43,792,255 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2043,727,541 - 43,769,944 (+)NCBICelera
Cytogenetic Map20q12NCBI
TRAF3IP2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6111,555,381 - 111,606,906 (-)EnsemblGRCh38hg38GRCh38
GRCh386111,555,381 - 111,605,878 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh376111,876,584 - 111,927,081 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh376111,876,581 - 111,927,477 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366111,986,836 - 112,034,014 (-)NCBINCBI36hg18NCBI36
Build 346111,986,835 - 112,034,014NCBI
Celera6112,626,739 - 112,674,049 (-)NCBI
Cytogenetic Map6q21NCBI
HuRef6109,448,986 - 109,500,061 (-)NCBIHuRef
CHM1_16112,139,458 - 112,190,300 (-)NCBICHM1_1
Traf3ip2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391039,488,930 - 39,531,303 (+)NCBIGRCm39mm39
GRCm381039,612,934 - 39,655,307 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1039,612,934 - 39,655,307 (+)EnsemblGRCm38mm10GRCm38
MGSCv371039,332,740 - 39,375,113 (+)NCBIGRCm37mm9NCBIm37
MGSCv361039,302,350 - 39,344,723 (+)NCBImm8
Celera1040,498,927 - 40,541,335 (+)NCBICelera
Cytogenetic Map10B1NCBI
Traf3ip2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541136,326,926 - 36,363,288 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541136,328,152 - 36,363,614 (-)NCBIChiLan1.0ChiLan1.0
TRAF3IP2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16113,443,540 - 113,490,402 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6113,444,005 - 113,485,533 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06109,367,333 - 109,414,601 (-)NCBIMhudiblu_PPA_v0panPan3
TRAF3IP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1268,030,197 - 68,058,518 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11268,029,861 - 68,070,901 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Traf3ip2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936679308,508 - 348,561 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRAF3IP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl177,480,926 - 77,541,210 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1177,483,997 - 77,541,557 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2187,044,462 - 87,102,274 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TRAF3IP2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11362,272,893 - 62,320,096 (+)NCBI
ChlSab1.1 Ensembl1362,285,589 - 62,324,312 (+)Ensembl
Traf3ip2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624933507,879 - 558,357 (+)NCBI

Position Markers
RH131445  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02044,679,570 - 44,679,775NCBIRnor6.0
Rnor_5.02046,401,019 - 46,401,224UniSTSRnor5.0
RGSC_v3.42043,746,743 - 43,746,948UniSTSRGSC3.4
Celera2043,726,662 - 43,726,867UniSTS
Cytogenetic Map20q12UniSTS
BF410372  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02044,685,702 - 44,685,903NCBIRnor6.0
Rnor_5.02046,407,176 - 46,407,377UniSTSRnor5.0
RGSC_v3.42043,752,900 - 43,753,101UniSTSRGSC3.4
Celera2043,732,755 - 43,732,956UniSTS
RH 3.4 Map20465.01UniSTS
Cytogenetic Map20q12UniSTS
RH137093  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02044,722,684 - 44,722,845NCBIRnor6.0
Rnor_5.02046,445,256 - 46,445,417UniSTSRnor5.0
RGSC_v3.42043,792,065 - 43,792,226UniSTSRGSC3.4
Celera2043,769,754 - 43,769,915UniSTS
RH 3.4 Map20460.5UniSTS
Cytogenetic Map20q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201887215049108956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)203091348156205956Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203335478345719230Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:42
Count of miRNA genes:37
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000000728
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 3 14 6 16 6 26 25 11
Low 43 43 35 3 35 8 11 74 9 16 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000728   ⟹   ENSRNOP00000000728
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2044,680,449 - 44,722,872 (+)Ensembl
RefSeq Acc Id: NM_001044248   ⟹   NP_001037713
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22043,011,450 - 43,054,654 (+)NCBI
Rnor_6.02044,680,449 - 44,722,874 (+)NCBI
Rnor_5.02046,401,898 - 46,445,446 (+)NCBI
RGSC_v3.42043,747,622 - 43,792,255 (+)RGD
Celera2043,727,541 - 43,769,944 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256532   ⟹   XP_006256594
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22043,013,075 - 43,054,379 (+)NCBI
Rnor_6.02044,681,874 - 44,722,874 (+)NCBI
Rnor_5.02046,401,898 - 46,445,446 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039098886   ⟹   XP_038954814
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22043,011,405 - 43,040,121 (+)NCBI
RefSeq Acc Id: XM_039098887   ⟹   XP_038954815
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22043,045,707 - 43,054,654 (+)NCBI
RefSeq Acc Id: XR_005497292
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22043,011,405 - 43,054,297 (+)NCBI
RefSeq Acc Id: XR_005497293
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22043,011,405 - 43,054,470 (+)NCBI
RefSeq Acc Id: XR_597418
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22043,011,405 - 43,054,470 (+)NCBI
Rnor_6.02044,679,861 - 44,722,690 (+)NCBI
Sequence:
RefSeq Acc Id: XR_597419
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02044,679,861 - 44,719,461 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001037713   ⟸   NM_001044248
- UniProtKB: Q498R8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256594   ⟸   XM_006256532
- Peptide Label: isoform X1
- UniProtKB: Q498R8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000728   ⟸   ENSRNOT00000000728
RefSeq Acc Id: XP_038954814   ⟸   XM_039098886
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038954815   ⟸   XM_039098887
- Peptide Label: isoform X3
Protein Domains
SEFIR

Transcriptome

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

Promoters
RGD ID:13701651
Promoter ID:EPDNEW_R12175
Type:initiation region
Name:Traf3ip2_1
Description:Traf3 interacting protein 2
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_6.02044,680,439 - 44,680,499EPDNEW

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)
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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:1593240 AgrOrtholog
Ensembl Genes ENSRNOG00000000595 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000728 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000728 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7376204 IMAGE-MGC_LOAD
InterPro SEFIR UniProtKB/TrEMBL
KEGG Report rno:361857 UniProtKB/TrEMBL
MGC_CLONE MGC:112844 IMAGE-MGC_LOAD
NCBI Gene 361857 ENTREZGENE
Pfam SEFIR UniProtKB/TrEMBL
PhenoGen Traf3ip2 PhenoGen
PROSITE SEFIR UniProtKB/TrEMBL
UniProt Q498R8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-06-15 Traf3ip2  Traf3 interacting protein 2  RGD1304768  similar to Adapter protein CIKS (Connection to IKK and SAPK/JNK) (Nuclear factor NF-kappa-B activator 1) (ACT1)   Data Merged 1643240 APPROVED
2008-04-30 RGD1304768  similar to Adapter protein CIKS (Connection to IKK and SAPK/JNK) (Nuclear factor NF-kappa-B activator 1) (ACT1)   RGD1304768_predicted  similar to Adapter protein CIKS (Connection to IKK and SAPK/JNK) (Nuclear factor NF-kappa-B activator 1) (ACT1) (predicted)  'predicted' is removed 2292626 APPROVED
2008-03-06 Traf3ip2  Traf3 interacting protein 2  MGC112844  chromosome 6 open reading frame 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 MGC112844  chromosome 6 open reading frame 4      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-20 RGD1304768_predicted  similar to Adapter protein CIKS (Connection to IKK and SAPK/JNK) (Nuclear factor NF-kappa-B activator 1) (ACT1) (predicted)  LOC294437_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC294437_predicted  similar to Adapter protein CIKS (Connection to IKK and SAPK/JNK) (Nuclear factor NF-kappa-B activator 1) (ACT1) (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL