Uvssa (UV-stimulated scaffold protein A) - Rat Genome Database
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Gene: Uvssa (UV-stimulated scaffold protein A) Rattus norvegicus
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Symbol: Uvssa
Name: UV-stimulated scaffold protein A
RGD ID: 1306371
Description: Predicted to have RNA polymerase II complex binding activity. Predicted to be involved in protein ubiquitination; response to UV; and transcription-coupled nucleotide-excision repair. Predicted to localize to chromosome and nucleoplasm. Human ortholog(s) of this gene implicated in UV-sensitive syndrome. Orthologous to human UVSSA (UV stimulated scaffold protein A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: hypothetical protein LOC314061; LOC314061; RGD1306371; similar to putative nuclear protein, with 2 coiled coil-4 domains, of eukaryotic origin (5I282); uncharacterized protein LOC314061
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
mRatBN7.21477,309,188 - 77,351,922 (-)NCBI
Rnor_6.0 Ensembl1482,623,050 - 82,658,891 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01482,621,028 - 82,658,912 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01483,306,349 - 83,344,222 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41483,163,555 - 83,199,401 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11483,172,596 - 83,201,792 (+)NCBI
Celera1476,235,354 - 76,271,195 (-)NCBICelera
Cytogenetic Map14q21NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromosome  (IBA,ISO,ISS)
nucleoplasm  (ISO)

Molecular Function

References

Additional References at PubMed
PMID:22466610   PMID:22466611   PMID:22466612  


Genomics

Comparative Map Data
Uvssa
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21477,309,188 - 77,351,922 (-)NCBI
Rnor_6.0 Ensembl1482,623,050 - 82,658,891 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01482,621,028 - 82,658,912 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01483,306,349 - 83,344,222 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41483,163,555 - 83,199,401 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11483,172,596 - 83,201,792 (+)NCBI
Celera1476,235,354 - 76,271,195 (-)NCBICelera
Cytogenetic Map14q21NCBI
UVSSA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl41,345,691 - 1,395,989 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl41,347,208 - 1,388,049 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl41,347,208 - 1,395,989 (+)EnsemblGRCh38hg38GRCh38
GRCh3841,341,998 - 1,388,049 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3741,340,996 - 1,381,837 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3641,331,104 - 1,371,732 (+)NCBINCBI36hg18NCBI36
Cytogenetic Map4p16.3NCBI
HuRef41,308,628 - 1,349,495 (+)NCBIHuRef
CHM1_141,340,867 - 1,381,652 (+)NCBICHM1_1
Uvssa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39533,535,868 - 33,578,243 (+)NCBIGRCm39mm39
GRCm39 Ensembl533,535,893 - 33,577,098 (+)Ensembl
GRCm38533,378,523 - 33,420,899 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl533,378,549 - 33,419,754 (+)EnsemblGRCm38mm10GRCm38
MGSCv37533,721,345 - 33,762,403 (+)NCBIGRCm37mm9NCBIm37
MGSCv36533,695,553 - 33,739,362 (+)NCBImm8
Celera530,857,971 - 30,898,922 (+)NCBICelera
Cytogenetic Map5B1NCBI
Uvssa
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955514728,522 - 756,348 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955514725,257 - 754,274 (+)NCBIChiLan1.0ChiLan1.0
UVSSA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.141,373,342 - 1,414,370 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl41,373,562 - 1,413,982 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v041,492,716 - 1,532,114 (+)NCBIMhudiblu_PPA_v0panPan3
UVSSA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl362,649,207 - 62,674,884 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1362,647,992 - 62,674,830 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Uvssa
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647721,918,091 - 21,950,895 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UVSSA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8573,421 - 601,944 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18573,299 - 602,617 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
UVSSA
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12747,378,310 - 47,418,861 (-)NCBI
ChlSab1.1 Ensembl2747,378,770 - 47,417,559 (-)Ensembl
Uvssa
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475525,904,273 - 25,930,564 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)144031561085315610Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)144031561085315610Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)144031561085315610Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)144031561085315610Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1443910761105074364Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1451818462105074364Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1460980905105980905Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1460980905105980905Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)146187332388870994Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1461993178106993178Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1463548095108548095Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)147339146788870994Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)1478172765102549388Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1478172765102549388Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765106641756Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1478446303110402569Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1480049285115493446Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1480049285115493446Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:118
Count of miRNA genes:105
Interacting mature miRNAs:108
Transcripts:ENSRNOT00000006841
Prediction methods:Microtar, 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
Low 3 41 57 41 19 41 8 10 74 35 41 11 8
Below cutoff 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006841   ⟹   ENSRNOP00000006841
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1482,623,050 - 82,658,891 (-)Ensembl
RefSeq Acc Id: NM_001134558   ⟹   NP_001128030
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,316,060 - 77,351,903 (-)NCBI
Rnor_6.01482,623,050 - 82,658,891 (-)NCBI
Rnor_5.01483,306,349 - 83,344,222 (-)NCBI
RGSC_v3.41483,163,555 - 83,199,401 (+)RGD
Celera1476,235,354 - 76,271,195 (-)RGD
Sequence:
RefSeq Acc Id: XM_006251321   ⟹   XP_006251383
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,309,188 - 77,351,922 (-)NCBI
Rnor_6.01482,621,028 - 82,658,912 (-)NCBI
Rnor_5.01483,306,349 - 83,344,222 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251323   ⟹   XP_006251385
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,309,188 - 77,351,922 (-)NCBI
Rnor_6.01482,621,028 - 82,658,912 (-)NCBI
Rnor_5.01483,306,349 - 83,344,222 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251324   ⟹   XP_006251386
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,309,188 - 77,351,724 (-)NCBI
Rnor_6.01482,621,028 - 82,658,722 (-)NCBI
Rnor_5.01483,306,349 - 83,344,222 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251325   ⟹   XP_006251387
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,309,188 - 77,351,922 (-)NCBI
Rnor_6.01482,621,028 - 82,658,912 (-)NCBI
Rnor_5.01483,306,349 - 83,344,222 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039092133   ⟹   XP_038948061
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,309,188 - 77,351,734 (-)NCBI
RefSeq Acc Id: XM_039092134   ⟹   XP_038948062
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,309,188 - 77,351,734 (-)NCBI
RefSeq Acc Id: XM_039092135   ⟹   XP_038948063
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,309,188 - 77,351,922 (-)NCBI
RefSeq Acc Id: XM_039092136   ⟹   XP_038948064
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,309,188 - 77,351,702 (-)NCBI
RefSeq Acc Id: XM_039092137   ⟹   XP_038948065
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,309,188 - 77,351,921 (-)NCBI
RefSeq Acc Id: XM_039092138   ⟹   XP_038948066
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,320,114 - 77,351,734 (-)NCBI
RefSeq Acc Id: XM_039092140   ⟹   XP_038948068
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,320,058 - 77,351,734 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001128030   ⟸   NM_001134558
- UniProtKB: D3ZND0 (UniProtKB/Swiss-Prot),   A0A096P6L4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251383   ⟸   XM_006251321
- Peptide Label: isoform X1
- UniProtKB: D3ZND0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006251385   ⟸   XM_006251323
- Peptide Label: isoform X1
- UniProtKB: D3ZND0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006251386   ⟸   XM_006251324
- Peptide Label: isoform X1
- UniProtKB: D3ZND0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006251387   ⟸   XM_006251325
- Peptide Label: isoform X1
- UniProtKB: D3ZND0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006841   ⟸   ENSRNOT00000006841
RefSeq Acc Id: XP_038948063   ⟸   XM_039092135
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038948065   ⟸   XM_039092137
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038948061   ⟸   XM_039092133
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948062   ⟸   XM_039092134
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038948064   ⟸   XM_039092136
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038948068   ⟸   XM_039092140
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038948066   ⟸   XM_039092138
- Peptide Label: isoform X4

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 83309371 83309372 G A snv COP/CrCrl (MCW & UW), BBDP/WorN (KNAW), F344/Jcl (KyushuU), F344/Stm (KyushuU), F344/NSlc (KyushuU), LE/Stm (KyushuU), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), BUF/N (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), M520/N (KNAW), F344/DuCrlCrlj (KyushuU)
14 83311744 83311745 G A snv BDIX/NemOda (KyushuU), LEC/Tj (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU)
14 83313978 83313979 G A snv IS-Tlk/Kyo (KyushuU), IS/Kyo (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 82624048 82624049 C T snv F344/NRrrc (MCW), Buf/N (MCW), WKY/N (MCW), M520/N (MCW)
14 82624050 82624051 G A snv SHRSP/Gcrc (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), SHR/NHsd (RGD), LE/Stm (RGD), WKY/NHsd (RGD), COP/CrCrl (MCW & UW), BBDP/Wor (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 83196028 83196029 C T snv LCR/1Mco (UMich)
14 83198401 83198402 C T snv LCR/2Mco (UMich), BUF/N (KNAW), F344/NRrrc (KNAW), LE/Stm (KNAW), M520/N (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), COP/CrCrl (MCW & UW), BBDP/WorN (ICL), F344/NCrl (ICL), LE/Stm (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), SHR/OlaIpcv (ICL), SHRSP/Gcrc (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306371 AgrOrtholog
Ensembl Genes ENSRNOG00000005122 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006841 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006841 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.90 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ENTH_VHS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UVSSA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:314061 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 314061 ENTREZGENE
PANTHER PTHR28670 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF2043 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Uvssa PhenoGen
Superfamily-SCOP SSF48464 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A096P6L4 ENTREZGENE, UniProtKB/TrEMBL
  D3ZND0 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-10 Uvssa  UV-stimulated scaffold protein A  RGD1306371  similar to putative nuclear protein, with 2 coiled coil-4 domains, of eukaryotic origin (5I282)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1306371  similar to putative nuclear protein, with 2 coiled coil-4 domains, of eukaryotic origin (5I282)   RGD1306371_predicted  similar to putative nuclear protein, with 2 coiled coil-4 domains, of eukaryotic origin (5I282) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1306371_predicted  similar to putative nuclear protein, with 2 coiled coil-4 domains, of eukaryotic origin (5I282) (predicted)  LOC314061_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC314061_predicted  similar to putative nuclear protein, with 2 coiled coil-4 domains, of eukaryotic origin (5I282) (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL