Cyth4 (cytohesin 4) - Rat Genome Database
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Gene: Cyth4 (cytohesin 4) Rattus norvegicus
Analyze
Symbol: Cyth4
Name: cytohesin 4
RGD ID: 1564842
Description: Predicted to have guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of ARF protein signal transduction and regulation of catalytic activity. Predicted to localize to several cellular components, including centriolar satellite; cytosol; and intercellular bridge. Orthologous to human CYTH4 (cytohesin 4); INTERACTS WITH acetamide; bisphenol A; methylmercury chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cytohesin-4; LOC500906; pleckstrin homology, Sec7 and coiled/coil domains 4; Pscd4; RGD1564842; similar to cytohesin-4
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
mRatBN7.27110,152,232 - 110,176,741 (+)NCBI
Rnor_6.0 Ensembl7119,820,537 - 119,845,003 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07119,820,521 - 119,845,003 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07119,809,471 - 119,833,941 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47116,557,797 - 116,582,215 (+)NCBIRGSC3.4rn4RGSC3.4
Celera7106,489,779 - 106,514,242 (+)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
centriolar satellite  (IEA,ISO)
cytosol  (IEA,ISO)
intercellular bridge  (IEA,ISO)
plasma membrane  (IEA,ISO)

Molecular Function

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10652308   PMID:12477932   PMID:17398095  


Genomics

Comparative Map Data
Cyth4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27110,152,232 - 110,176,741 (+)NCBI
Rnor_6.0 Ensembl7119,820,537 - 119,845,003 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07119,820,521 - 119,845,003 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07119,809,471 - 119,833,941 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47116,557,797 - 116,582,215 (+)NCBIRGSC3.4rn4RGSC3.4
Celera7106,489,779 - 106,514,242 (+)NCBICelera
Cytogenetic Map7q34NCBI
CYTH4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2237,282,027 - 37,315,341 (+)EnsemblGRCh38hg38GRCh38
GRCh382237,282,508 - 37,315,341 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372237,678,549 - 37,711,382 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362236,008,370 - 36,041,328 (+)NCBINCBI36hg18NCBI36
Build 342236,002,923 - 36,035,880NCBI
Celera2221,479,377 - 21,512,272 (+)NCBI
Cytogenetic Map22q13.1NCBI
HuRef2220,643,760 - 20,676,655 (+)NCBIHuRef
CHM1_12237,637,401 - 37,670,270 (+)NCBICHM1_1
Cyth4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391578,481,247 - 78,506,219 (+)NCBIGRCm39mm39
GRCm39 Ensembl1578,481,247 - 78,506,219 (+)Ensembl
GRCm381578,597,047 - 78,622,019 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1578,597,047 - 78,622,019 (+)EnsemblGRCm38mm10GRCm38
MGSCv371578,427,477 - 78,452,449 (+)NCBIGRCm37mm9NCBIm37
MGSCv361578,424,373 - 78,448,141 (+)NCBImm8
Celera1580,059,894 - 80,084,897 (+)NCBICelera
Cytogenetic Map15E1NCBI
Cyth4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541323,745,777 - 23,768,387 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541323,745,797 - 23,774,397 (+)NCBIChiLan1.0ChiLan1.0
CYTH4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12236,030,112 - 36,063,113 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2236,040,326 - 36,061,264 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02218,197,307 - 18,230,274 (+)NCBIMhudiblu_PPA_v0panPan3
CYTH4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1027,239,405 - 27,268,823 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11027,238,028 - 27,268,759 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cyth4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364923,678,299 - 3,703,787 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CYTH4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl510,489,286 - 10,521,736 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1510,491,202 - 10,521,583 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.258,074,091 - 8,104,464 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CYTH4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11919,989,081 - 20,021,545 (+)NCBI
ChlSab1.1 Ensembl1920,001,934 - 20,021,539 (+)Ensembl
Cyth4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475210,536,539 - 10,559,090 (-)NCBI

Position Markers
BE107924  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07119,836,987 - 119,837,145NCBIRnor6.0
Rnor_5.07119,825,925 - 119,826,083UniSTSRnor5.0
RGSC_v3.47116,574,199 - 116,574,357UniSTSRGSC3.4
Celera7106,506,226 - 106,506,384UniSTS
RH 3.4 Map7818.3UniSTS
Cytogenetic Map7q34UniSTS
AA893106  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07119,819,616 - 119,819,707NCBIRnor6.0
Rnor_5.07119,808,554 - 119,808,645UniSTSRnor5.0
RGSC_v3.47116,556,873 - 116,556,964UniSTSRGSC3.4
Celera7106,488,855 - 106,488,946UniSTS
RH 3.4 Map7817.2UniSTS
Cytogenetic Map7q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)755072862123602998Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)755072862123602998Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)755072862123602998Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)777428105127748511Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)777428234122421148Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)788365265121986709Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)788365265133365265Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)788365265134673427Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)791018361136018361Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)793726906138726906Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)793726906138726906Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)796630946141630946Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)7100160423140335001Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)7103815550126525386Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)7103867802126080176Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7112429186126525386Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:151
Count of miRNA genes:127
Interacting mature miRNAs:134
Transcripts:ENSRNOT00000056221
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 2 10 2 18 2 10 6 11
Low 1 43 47 39 1 39 8 11 74 25 34 8
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000056221   ⟹   ENSRNOP00000053065
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7119,820,540 - 119,845,003 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077256   ⟹   ENSRNOP00000071361
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7119,820,537 - 119,844,668 (+)Ensembl
RefSeq Acc Id: NM_001130577   ⟹   NP_001124049
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27110,152,276 - 110,176,741 (+)NCBI
Rnor_6.07119,820,540 - 119,845,003 (+)NCBI
Rnor_5.07119,809,471 - 119,833,941 (+)NCBI
RGSC_v3.47116,557,797 - 116,582,215 (+)RGD
Celera7106,489,779 - 106,514,242 (+)RGD
Sequence:
RefSeq Acc Id: XM_006242031   ⟹   XP_006242093
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27110,152,233 - 110,176,726 (+)NCBI
Rnor_6.07119,820,521 - 119,844,988 (+)NCBI
Rnor_5.07119,809,471 - 119,833,941 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006242033   ⟹   XP_006242095
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07119,820,534 - 119,844,988 (+)NCBI
Rnor_5.07119,809,471 - 119,833,941 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595057   ⟹   XP_017450546
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27110,152,274 - 110,176,726 (+)NCBI
Rnor_6.07119,820,534 - 119,844,988 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595058   ⟹   XP_017450547
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07119,828,029 - 119,844,988 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039079763   ⟹   XP_038935691
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27110,152,232 - 110,176,726 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001124049   ⟸   NM_001130577
- UniProtKB: D3ZHR6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242095   ⟸   XM_006242033
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006242093   ⟸   XM_006242031
- Peptide Label: isoform X3
- UniProtKB: A0A0G2K0A0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017450546   ⟸   XM_017595057
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017450547   ⟸   XM_017595058
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000071361   ⟸   ENSRNOT00000077256
RefSeq Acc Id: ENSRNOP00000053065   ⟸   ENSRNOT00000056221
RefSeq Acc Id: XP_038935691   ⟸   XM_039079763
- Peptide Label: isoform X2
Protein Domains
PH   SEC7

Transcriptome

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

Promoters
RGD ID:13695467
Promoter ID:EPDNEW_R5991
Type:single initiation site
Name:Cyth4_1
Description:cytohesin 4
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_6.07119,820,566 - 119,820,626EPDNEW

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)
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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_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 119826110 119826111 T A snv MR/N (MCW), M520/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564842 AgrOrtholog
Ensembl Genes ENSRNOG00000007679 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000053065 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071361 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000056221 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000077256 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1000.11 UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/TrEMBL
InterPro PH_type UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
  Sec7 UniProtKB/TrEMBL
  SEC7_alpha_orthog UniProtKB/TrEMBL
  Sec7_sf UniProtKB/TrEMBL
KEGG Report rno:500906 UniProtKB/TrEMBL
NCBI Gene 500906 ENTREZGENE
Pfam PF00169 UniProtKB/TrEMBL
  Sec7 UniProtKB/TrEMBL
PhenoGen Cyth4 PhenoGen
PROSITE PH_DOMAIN UniProtKB/TrEMBL
  SEC7 UniProtKB/TrEMBL
SMART Sec7 UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
Superfamily-SCOP Sec7 UniProtKB/TrEMBL
UniProt A0A0G2K0A0 ENTREZGENE, UniProtKB/TrEMBL
  D3ZHR6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-11-04 Cyth4  cytohesin 4  Pscd4  pleckstrin homology, Sec7 and coiled/coil domains 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Pscd4  pleckstrin homology, Sec7 and coiled/coil domains 4  RGD1564842_predicted  similar to cytohesin-4 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564842_predicted  similar to cytohesin-4 (predicted)  LOC500906  similar to cytohesin-4  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC500906  similar to cytohesin-4      Symbol and Name status set to provisional 70820 PROVISIONAL