Cish (cytokine inducible SH2-containing protein) - Rat Genome Database
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Gene: Cish (cytokine inducible SH2-containing protein) Rattus norvegicus
Analyze
Symbol: Cish
Name: cytokine inducible SH2-containing protein
RGD ID: 69261
Description: Predicted to have 1-phosphatidylinositol-3-kinase regulator activity. Involved in cytokine-mediated signaling pathway. Predicted to localize to phosphatidylinositol 3-kinase complex and plasma membrane. Human ortholog(s) of this gene implicated in malaria and tuberculosis. Orthologous to human CISH (cytokine inducible SH2 containing protein); PARTICIPATES IN granulocyte-macrophage colony-stimulating factor signaling pathway; interleukin-2 signaling pathway; interleukin-3 signaling pathway; INTERACTS WITH 1,3-dinitrobenzene; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Cis; CIS-1; cytokine inducible SH2-containing protein 1; cytokine-inducible SH2-containing protein; SOCS; suppressor of cytokine signaling
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
mRatBN7.28107,972,306 - 107,977,254 (+)NCBI
Rnor_6.0 Ensembl8116,054,465 - 116,060,723 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08116,054,547 - 116,059,494 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08115,411,027 - 115,415,974 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48112,541,034 - 112,545,982 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18112,560,606 - 112,564,500 (+)NCBI
Celera8107,282,095 - 107,287,043 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butoxyethanol  (ISO)
2-nitrotoluene  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxynon-2-enal  (ISO)
4-nitrotoluene  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
ammonium chloride  (EXP)
andrographolide  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[ghi]perylene  (ISO)
benzoates  (ISO)
beta-naphthoflavone  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
chromium(6+)  (ISO)
chrysene  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (EXP)
copper(II) sulfate  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dibenz[a,h]anthracene  (ISO)
doxorubicin  (EXP,ISO)
endosulfan  (EXP)
entinostat  (ISO)
eugenol  (ISO)
fenofibrate  (ISO)
fenvalerate  (EXP)
folic acid  (ISO)
furan  (EXP)
gamma-hexachlorocyclohexane  (EXP)
genistein  (ISO)
glycidol  (EXP)
hexachlorobenzene  (EXP)
hydrogen peroxide  (ISO)
indole-3-methanol  (EXP)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
manganese(II) chloride  (EXP)
melatonin  (ISO)
metformin  (EXP)
methotrexate  (ISO)
methylmercury(1+)  (EXP)
N-acetyl-L-cysteine  (EXP)
N-methylformamide  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
O-methyleugenol  (ISO)
orphenadrine  (EXP)
oxazepam  (ISO)
paracetamol  (ISO)
PCB138  (ISO)
phenformin  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
progesterone  (EXP)
raloxifene  (ISO)
rotenone  (EXP)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
Soman  (EXP)
stattic  (ISO)
sulpiride  (EXP)
sunitinib  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triphenyl phosphate  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:12586763   PMID:12618484   PMID:15118263   PMID:15378659   PMID:16154995   PMID:16357045   PMID:16956890  


Genomics

Comparative Map Data
Cish
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28107,972,306 - 107,977,254 (+)NCBI
Rnor_6.0 Ensembl8116,054,465 - 116,060,723 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08116,054,547 - 116,059,494 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08115,411,027 - 115,415,974 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48112,541,034 - 112,545,982 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18112,560,606 - 112,564,500 (+)NCBI
Celera8107,282,095 - 107,287,043 (+)NCBICelera
Cytogenetic Map8q32NCBI
CISH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl350,606,490 - 50,611,831 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl350,606,489 - 50,611,774 (-)EnsemblGRCh38hg38GRCh38
GRCh38350,606,454 - 50,611,774 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37350,643,885 - 50,649,262 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh37350,643,920 - 50,649,205 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36350,618,924 - 50,624,207 (-)NCBINCBI36hg18NCBI36
Build 34350,618,929 - 50,624,207NCBI
Celera350,616,686 - 50,622,064 (-)NCBI
Cytogenetic Map3p21.2NCBI
HuRef350,699,815 - 50,705,193 (-)NCBIHuRef
CHM1_1350,596,124 - 50,601,502 (-)NCBICHM1_1
Cish
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399107,173,858 - 107,179,983 (+)NCBIGRCm39mm39
GRCm389107,296,659 - 107,302,784 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9107,296,026 - 107,302,784 (+)EnsemblGRCm38mm10GRCm38
MGSCv379107,199,020 - 107,204,292 (+)NCBIGRCm37mm9NCBIm37
MGSCv369107,154,790 - 107,160,062 (+)NCBImm8
Celera9106,902,900 - 106,908,144 (+)NCBICelera
Cytogenetic Map9F1NCBI
cM Map957.99NCBI
Cish
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555322,378,088 - 2,386,000 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555322,380,380 - 2,386,000 (-)NCBIChiLan1.0ChiLan1.0
CISH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1351,769,194 - 51,774,548 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl351,769,194 - 51,774,548 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0350,531,870 - 50,537,319 (-)NCBIMhudiblu_PPA_v0panPan3
CISH
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2038,762,378 - 38,766,620 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12038,762,239 - 38,767,701 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cish
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365292,116,786 - 2,124,469 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CISH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1333,084,873 - 33,090,615 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11333,086,280 - 33,090,540 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21336,354,834 - 36,358,941 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CISH
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12211,993,212 - 11,998,625 (-)NCBI
ChlSab1.1 Ensembl2211,993,242 - 11,995,375 (-)Ensembl
Cish
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247304,434,817 - 4,440,269 (-)NCBI

Position Markers
BE107841  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08116,054,117 - 116,054,290NCBIRnor6.0
Rnor_5.08115,410,597 - 115,410,770UniSTSRnor5.0
RGSC_v3.48112,540,604 - 112,540,777UniSTSRGSC3.4
Celera8107,281,665 - 107,281,838UniSTS
RH 3.4 Map81124.0UniSTS
Cytogenetic Map8q32UniSTS
PMC156147P14  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08116,054,090 - 116,054,341NCBIRnor6.0
Rnor_5.08115,410,570 - 115,410,821UniSTSRnor5.0
RGSC_v3.48112,540,577 - 112,540,828UniSTSRGSC3.4
Celera8107,281,638 - 107,281,889UniSTS
Cytogenetic Map8q32UniSTS
PMC156147P15  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08116,054,281 - 116,054,439NCBIRnor6.0
Rnor_5.08115,410,761 - 115,410,919UniSTSRnor5.0
RGSC_v3.48112,540,768 - 112,540,926UniSTSRGSC3.4
Celera8107,281,829 - 107,281,987UniSTS
Cytogenetic Map8q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)89531047119211942Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810938911120496129Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)844458129118087517Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)850529480128036471Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)865717449128033050Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)872849686117849686Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight as a percentage of body weight (CMO:0000654)874917593121080545Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)876103982127182642Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)878805083123805083Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)878805083123805083Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)878805083123805083Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)878805083123805083Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)880697934125697934Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)883894304128894304Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)889058229132243842Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)895963141122354314Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102051964133307652Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8104682575133307652Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)8104682575133307652Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8107769005129956433Rat
631217Activ1Activity QTL 115.9voluntary movement trait (VT:0003491)number of photobeam interruptions in an experimental apparatus (CMO:0001517)8110212979116947981Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:149
Count of miRNA genes:103
Interacting mature miRNAs:122
Transcripts:ENSRNOT00000040056
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 1 13 7 7 1 7 3 12 2 3
Low 2 30 49 33 18 33 8 8 74 23 38 8 8
Below cutoff 1 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000040056   ⟹   ENSRNOP00000041734
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8116,054,465 - 116,060,723 (+)Ensembl
RefSeq Acc Id: NM_031804   ⟹   NP_113992
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28107,972,306 - 107,977,254 (+)NCBI
Rnor_6.08116,054,547 - 116,059,494 (+)NCBI
Rnor_5.08115,411,027 - 115,415,974 (+)NCBI
RGSC_v3.48112,541,034 - 112,545,982 (+)RGD
Celera8107,282,095 - 107,287,043 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_113992   ⟸   NM_031804
- UniProtKB: B1WBX9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000041734   ⟸   ENSRNOT00000040056
Protein Domains
SH2   SOCS box

Transcriptome

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

Promoters
RGD ID:13696264
Promoter ID:EPDNEW_R6789
Type:multiple initiation site
Name:Cish_1
Description:cytokine inducible SH2-containing protein
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_6.08116,054,541 - 116,054,601EPDNEW

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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 115414921 115414922 C G snv LN/MavRrrc (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 116058441 116058442 C G snv LN/MavRrrc (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 112544929 112544930 C G snv LN/MavRrrc (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69261 AgrOrtholog
Ensembl Genes ENSRNOG00000029543 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000041734 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000040056 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.505.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8375557 IMAGE-MGC_LOAD
InterPro CIS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CIS_SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS_box-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:83681 UniProtKB/TrEMBL
MGC_CLONE MGC:187704 IMAGE-MGC_LOAD
NCBI Gene 83681 ENTREZGENE
PANTHER PTHR10155:SF9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cish PhenoGen
PRINTS SH2DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF158235 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF55550 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B1WBX9 ENTREZGENE, UniProtKB/TrEMBL
  CISH_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9ERQ1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Cish  cytokine inducible SH2-containing protein      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference