Clvs1 (clavesin 1) - Rat Genome Database

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Gene: Clvs1 (clavesin 1) Rattus norvegicus
Analyze
Symbol: Clvs1
Name: clavesin 1
RGD ID: 1564200
Description: Predicted to have phosphatidylinositol-3,5-bisphosphate binding activity. Involved in lysosome organization. Localizes to clathrin-coated vesicle and trans-Golgi network. Orthologous to human CLVS1 (clavesin 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: clavesin-1; hypothetical protein LOC366311; LOC366311; retinaldehyde-binding protein 1-like 1; Retinaldehyde-binding protein 1-like protein 1; RGD1564200; Rlbp1l1; similar to hypothetical protein MGC34646
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
mRatBN7.2522,408,384 - 22,604,281 (+)NCBI
Rnor_6.0 Ensembl522,380,334 - 22,578,297 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0522,380,318 - 22,580,391 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0527,115,709 - 27,312,485 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4523,135,749 - 23,336,357 (+)NCBIRGSC3.4rn4RGSC3.4
Celera521,664,843 - 21,859,477 (+)NCBICelera
Cytogenetic Map5q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
lysosome organization  (IBA,IEA,IMP)

Cellular Component
clathrin-coated vesicle  (IBA,IDA,IEA)
early endosome membrane  (IEA)
endosome  (IBA,ISO,ISS)
trans-Golgi network  (IBA,IDA,IEA)

Molecular Function

References


Genomics

Comparative Map Data
Clvs1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2522,408,384 - 22,604,281 (+)NCBI
Rnor_6.0 Ensembl522,380,334 - 22,578,297 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0522,380,318 - 22,580,391 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0527,115,709 - 27,312,485 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4523,135,749 - 23,336,357 (+)NCBIRGSC3.4rn4RGSC3.4
Celera521,664,843 - 21,859,477 (+)NCBICelera
Cytogenetic Map5q13NCBI
CLVS1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl861,057,158 - 61,501,645 (+)EnsemblGRCh38hg38GRCh38
GRCh38860,964,833 - 61,501,629 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37862,200,529 - 62,414,188 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36862,363,104 - 62,576,758 (+)NCBINCBI36hg18NCBI36
Celera858,190,369 - 58,404,047 (+)NCBI
Cytogenetic Map8q12.2-q12.3NCBI
HuRef857,688,952 - 57,902,676 (+)NCBIHuRef
CHM1_1862,252,500 - 62,466,191 (+)NCBICHM1_1
Clvs1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3949,144,753 - 9,451,691 (+)NCBIGRCm39mm39
GRCm39 Ensembl49,269,293 - 9,451,691 (+)Ensembl
GRCm3849,144,745 - 9,451,691 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl49,269,293 - 9,451,691 (+)EnsemblGRCm38mm10GRCm38
MGSCv3749,196,464 - 9,378,838 (+)NCBIGRCm37mm9NCBIm37
MGSCv3649,196,509 - 9,378,838 (+)NCBImm8
Celera49,108,545 - 9,292,342 (+)NCBICelera
Cytogenetic Map4A1NCBI
Clvs1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544417,319,905 - 17,515,421 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544417,319,905 - 17,515,397 (-)NCBIChiLan1.0ChiLan1.0
CLVS1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1859,414,746 - 59,630,784 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl859,252,291 - 59,630,784 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0857,703,459 - 57,921,997 (+)NCBIMhudiblu_PPA_v0panPan3
CLVS1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12911,638,550 - 11,811,853 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2911,638,024 - 11,812,396 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2911,953,510 - 12,128,291 (+)NCBI
ROS_Cfam_1.02911,734,430 - 11,909,539 (+)NCBI
UMICH_Zoey_3.12911,726,549 - 11,901,504 (+)NCBI
UNSW_CanFamBas_1.02911,863,231 - 12,037,919 (+)NCBI
UU_Cfam_GSD_1.02912,133,085 - 12,308,297 (+)NCBI
Clvs1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530362,777,239 - 62,970,859 (+)NCBI
SpeTri2.0NW_00493649611,814,627 - 12,008,233 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLVS1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl472,082,685 - 72,257,226 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1472,104,521 - 72,257,259 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2478,504,691 - 78,655,974 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLVS1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1857,174,083 - 57,378,424 (+)NCBI
ChlSab1.1 Ensembl857,174,291 - 57,380,412 (+)Ensembl
Vero_WHO_p1.0NW_02366603984,271,844 - 84,482,024 (-)NCBI
Clvs1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474430,423,605 - 30,680,264 (-)NCBI

Position Markers
D5Rat209  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2522,509,722 - 22,510,074 (+)MAPPER
mRatBN7.2522,509,847 - 22,510,074 (+)MAPPER
Rnor_6.0522,481,610 - 22,482,014NCBIRnor6.0
Rnor_6.0522,481,786 - 22,482,014NCBIRnor6.0
Rnor_5.0527,215,662 - 27,215,890UniSTSRnor5.0
Rnor_5.0527,215,486 - 27,215,890UniSTSRnor5.0
RGSC_v3.4523,240,869 - 23,241,097UniSTSRGSC3.4
RGSC_v3.4523,240,868 - 23,241,097RGDRGSC3.4
RGSC_v3.1523,240,850 - 23,241,219RGD
Celera521,766,907 - 21,767,135UniSTS
FHH x ACI Map56.59RGD
FHH x ACI Map56.59UniSTS
Cytogenetic Map5q13UniSTS
RH134214  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2522,603,238 - 22,603,419 (+)MAPPER
Rnor_6.0522,579,349 - 22,579,529NCBIRnor6.0
Rnor_5.0527,311,454 - 27,311,634UniSTSRnor5.0
RGSC_v3.4523,335,326 - 23,335,506UniSTSRGSC3.4
Celera521,858,446 - 21,858,626UniSTS
RH 3.4 Map5130.4UniSTS
Cytogenetic Map5q13UniSTS
RH133813  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2522,604,000 - 22,604,192 (+)MAPPER
Rnor_6.0522,580,111 - 22,580,302NCBIRnor6.0
Rnor_5.0527,312,216 - 27,312,407UniSTSRnor5.0
RGSC_v3.4523,336,088 - 23,336,279UniSTSRGSC3.4
Celera521,859,208 - 21,859,399UniSTS
RH 3.4 Map5119.4UniSTS
Cytogenetic Map5q13UniSTS
RH142849  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2522,508,169 - 22,508,329 (+)MAPPER
Rnor_6.0522,479,932 - 22,480,091NCBIRnor6.0
Rnor_5.0527,213,808 - 27,213,967UniSTSRnor5.0
RGSC_v3.4523,239,191 - 23,239,350UniSTSRGSC3.4
Celera521,765,229 - 21,765,388UniSTS
RH 3.4 Map5131.2UniSTS
Cytogenetic Map5q13UniSTS
RH139730  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2522,604,139 - 22,604,344 (+)MAPPER
Rnor_6.0522,580,250 - 22,580,454NCBIRnor6.0
Rnor_5.0527,312,355 - 27,312,559UniSTSRnor5.0
RGSC_v3.4523,336,227 - 23,336,431UniSTSRGSC3.4
Celera521,859,347 - 21,859,551UniSTS
RH 3.4 Map5130.8UniSTS
Cytogenetic Map5q13UniSTS
RH141951  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2522,505,861 - 22,506,074 (+)MAPPER
Rnor_6.0522,477,626 - 22,477,838NCBIRnor6.0
Rnor_5.0527,211,502 - 27,211,714UniSTSRnor5.0
RGSC_v3.4523,236,884 - 23,237,096UniSTSRGSC3.4
Celera521,762,922 - 21,763,134UniSTS
RH 3.4 Map5115.0UniSTS
Cytogenetic Map5q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5152509833001026Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5152509878720537Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5166658771552720Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5325132926252076Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5325132948722188Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5452573847978104Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5863228553632285Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)59514842103580403Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512651967117554267Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51328888858288888Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51884791363847913Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51884791376608178Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52190436366904363Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:893
Count of miRNA genes:317
Interacting mature miRNAs:405
Transcripts:ENSRNOT00000009744
Prediction methods:Microtar, 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 68
Low 1 10 6 1 14
Below cutoff 2 33 15 10 7 10 4 4 22 23 10 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009744   ⟹   ENSRNOP00000009744
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl522,380,334 - 22,578,297 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087182   ⟹   ENSRNOP00000073425
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl522,392,732 - 22,578,101 (+)Ensembl
RefSeq Acc Id: NM_001108969   ⟹   NP_001102439
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,408,384 - 22,604,270 (+)NCBI
Rnor_6.0522,380,368 - 22,580,380 (+)NCBI
Rnor_5.0527,115,709 - 27,312,485 (+)NCBI
RGSC_v3.4523,135,749 - 23,336,357 (+)RGD
Celera521,664,843 - 21,859,477 (+)RGD
Sequence:
RefSeq Acc Id: XM_017593530   ⟹   XP_017449019
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,408,397 - 22,604,281 (+)NCBI
Rnor_6.0522,380,318 - 22,580,391 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593531   ⟹   XP_017449020
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,408,677 - 22,603,731 (+)NCBI
Rnor_6.0522,380,721 - 22,578,946 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001102439   ⟸   NM_001108969
- UniProtKB: A6JFQ6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017449019   ⟸   XM_017593530
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017449020   ⟸   XM_017593531
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000073425   ⟸   ENSRNOT00000087182
RefSeq Acc Id: ENSRNOP00000009744   ⟸   ENSRNOT00000009744
Protein Domains
CRAL-TRIO

Transcriptome

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

Promoters
RGD ID:13693557
Promoter ID:EPDNEW_R4081
Type:initiation region
Name:Clvs1_1
Description:clavesin 1
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_6.0522,380,400 - 22,380,460EPDNEW

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564200 AgrOrtholog
Ensembl Genes ENSRNOG00000006919 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009744 UniProtKB/TrEMBL
  ENSRNOP00000073425 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009744 UniProtKB/TrEMBL
  ENSRNOT00000087182 UniProtKB/TrEMBL
Gene3D-CATH 3.40.525.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Clavesin-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CRAL-TRIO_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CRAL-TRIO_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CRAL/TRIO_N_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CRAL/TRIO_N_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:366311 UniProtKB/Swiss-Prot
NCBI Gene 366311 ENTREZGENE
PANTHER PTHR10174:SF72 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CRAL_TRIO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CRAL_TRIO_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Clvs1 PhenoGen
PROSITE CRAL_TRIO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CRAL_TRIO_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SEC14 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46938 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52087 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K5H2_RAT UniProtKB/TrEMBL
  A6JFQ6 ENTREZGENE, UniProtKB/Swiss-Prot
  F1LRF3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 RGD1564200  similar to hypothetical protein MGC34646   RGD1564200_predicted  similar to hypothetical protein MGC34646 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1564200_predicted  similar to hypothetical protein MGC34646 (predicted)  LOC366311  similar to hypothetical protein MGC34646  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC366311  similar to hypothetical protein MGC34646      Symbol and Name status set to provisional 70820 PROVISIONAL