Shprh (SNF2 histone linker PHD RING helicase) - Rat Genome Database
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Gene: Shprh (SNF2 histone linker PHD RING helicase) Rattus norvegicus
Analyze
Symbol: Shprh
Name: SNF2 histone linker PHD RING helicase
RGD ID: 1310342
Description: Predicted to have ubiquitin protein ligase activity and ubiquitin protein ligase binding activity. Predicted to be involved in cellular response to DNA damage stimulus and protein polyubiquitination. Predicted to localize to nucleosome. Orthologous to human SHPRH (SNF2 histone linker PHD RING helicase); INTERACTS WITH acrylamide; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: E3 ubiquitin-protein ligase SHPRH; LOC308282; SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase
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
Rnor_6.015,240,139 - 5,313,064 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15,240,180 - 5,313,054 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.016,890,839 - 6,965,114 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415,846,062 - 5,922,176 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.115,848,348 - 5,920,472 (+)NCBI
Celera14,052,730 - 4,125,310 (+)NCBICelera
Cytogenetic Map1p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleosome  (IEA)

Molecular Function

References

Additional References at PubMed
PMID:17108083   PMID:17130289   PMID:18719106   PMID:25023518  


Genomics

Comparative Map Data
Shprh
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.015,240,139 - 5,313,064 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15,240,180 - 5,313,054 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.016,890,839 - 6,965,114 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415,846,062 - 5,922,176 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.115,848,348 - 5,920,472 (+)NCBI
Celera14,052,730 - 4,125,310 (+)NCBICelera
Cytogenetic Map1p13NCBI
SHPRH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6145,864,245 - 145,964,423 (-)EnsemblGRCh38hg38GRCh38
GRCh386145,857,838 - 145,964,358 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh376146,205,943 - 146,285,421 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366146,247,636 - 146,326,926 (-)NCBINCBI36hg18NCBI36
Build 346146,247,644 - 146,326,926NCBI
Celera6146,946,301 - 147,025,589 (-)NCBI
Cytogenetic Map6q24.3NCBI
HuRef6143,769,154 - 143,848,446 (-)NCBIHuRef
CHM1_16146,469,147 - 146,548,442 (-)NCBICHM1_1
Shprh
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391011,024,765 - 11,093,339 (+)NCBIGRCm39mm39
GRCm381011,149,272 - 11,217,595 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1011,149,427 - 11,217,595 (+)EnsemblGRCm38mm10GRCm38
MGSCv371010,869,228 - 10,935,072 (+)NCBIGRCm37mm9NCBIm37
MGSCv361010,839,714 - 10,899,742 (+)NCBImm8
Celera1011,042,359 - 11,108,579 (+)NCBICelera
Cytogenetic Map10A1NCBI
Shprh
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543614,698,187 - 14,779,814 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543614,698,210 - 14,779,231 (+)NCBIChiLan1.0ChiLan1.0
SHPRH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16148,386,451 - 148,466,127 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6148,388,329 - 148,457,023 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06143,628,076 - 143,751,370 (-)NCBIMhudiblu_PPA_v0panPan3
SHPRH
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl137,077,949 - 37,163,041 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1137,076,318 - 37,170,664 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Shprh
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936625533,870 - 617,936 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHPRH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl119,612,823 - 19,695,272 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1119,612,915 - 19,697,444 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2121,856,641 - 21,938,994 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SHPRH
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11325,878,354 - 25,959,922 (+)NCBI
ChlSab1.1 Ensembl1325,878,223 - 25,959,942 (+)Ensembl
Shprh
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247538,498,335 - 8,580,333 (+)NCBI

Position Markers
BE105044  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015,270,029 - 5,270,198NCBIRnor6.0
Rnor_5.016,921,102 - 6,921,271UniSTSRnor5.0
RGSC_v3.415,876,242 - 5,876,411UniSTSRGSC3.4
Celera14,082,671 - 4,082,840UniSTS
Cytogenetic Map1p13UniSTS
RH 3.4 Map1105.42UniSTS
RH127759  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015,238,249 - 5,238,420NCBIRnor6.0
Rnor_6.0558,098,979 - 58,099,158NCBIRnor6.0
Rnor_5.0562,623,090 - 62,623,269UniSTSRnor5.0
Rnor_5.016,889,322 - 6,889,493UniSTSRnor5.0
RGSC_v3.4559,139,697 - 59,139,876UniSTSRGSC3.4
RGSC_v3.415,844,131 - 5,844,302UniSTSRGSC3.4
Celera555,475,410 - 55,475,589UniSTS
Celera14,050,799 - 4,050,970UniSTS
Cytogenetic Map1p13UniSTS
Cytogenetic Map5q22UniSTS
RH135342  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015,312,523 - 5,312,714NCBIRnor6.0
Rnor_5.016,964,573 - 6,964,764UniSTSRnor5.0
RGSC_v3.415,921,636 - 5,921,827UniSTSRGSC3.4
Celera14,124,770 - 4,124,961UniSTS
Cytogenetic Map1p13UniSTS
RH 3.4 Map1103.52UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124368159Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128468970Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1134993530Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1134993530Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)1134993530Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1164407321Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)125439343579402Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)125439343579402Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)125439343579402Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)125439386904217Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1186804543724576Rat
1300170Rf6Renal function QTL 63.14renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)1383915911314658Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1457869349578693Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:149
Count of miRNA genes:121
Interacting mature miRNAs:130
Transcripts:ENSRNOT00000019893
Prediction methods:Miranda
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 8 20 4 18 4 1 1 74 28 35 11 1
Low 3 35 37 37 1 37 7 10 7 6 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019893   ⟹   ENSRNOP00000019893
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl15,240,180 - 5,313,054 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088292   ⟹   ENSRNOP00000071936
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl15,240,197 - 5,313,041 (+)Ensembl
RefSeq Acc Id: NM_001107470   ⟹   NP_001100940
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.015,240,180 - 5,313,063 (+)NCBI
Rnor_5.016,890,839 - 6,965,114 (+)NCBI
RGSC_v3.415,846,062 - 5,922,176 (+)RGD
Celera14,052,730 - 4,125,310 (+)RGD
Sequence:
RefSeq Acc Id: XM_006227639   ⟹   XP_006227701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.015,240,139 - 5,313,064 (+)NCBI
Rnor_5.016,890,839 - 6,965,114 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100940 (Get FASTA)   NCBI Sequence Viewer  
  XP_006227701 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93714 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100940   ⟸   NM_001107470
- UniProtKB: D4A9B2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006227701   ⟸   XM_006227639
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K1Q2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019893   ⟸   ENSRNOT00000019893
RefSeq Acc Id: ENSRNOP00000071936   ⟸   ENSRNOT00000088292
Transcriptome

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

Promoters
RGD ID:13689499
Promoter ID:EPDNEW_R13
Type:initiation region
Name:Shprh_1
Description:SNF2 histone linker PHD RING helicase
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_6.015,240,223 - 5,240,283EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
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
1 6930532 6930533 G A snv ACI/EurMcwi (MCW), ZFDM (KyushuU), GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MR/N (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), SBN/Ygl (KNAW), F344/NRrrc (Illumina) (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), M520/N (KNAW), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), F344/Jcl (KyushuU), ZF (KyushuU), COP/CrCrl (MCW & UW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 5279459 5279460 G A snv ACI/EurMcwi (MCW), SS/JrHsdMcwi (RGD), GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), CDR, CDS, ACI/N (MCW), F344/NRrrc (MCW), M520/N (MCW), MR/N (MCW), FHL/EurMcwi (RGD), ACI/EurMcwi (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), LE/Stm (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), SBN/Ygl (RGD), SR/JrHsd (RGD), SS/Jr (RGD), COP/CrCrl (MCW & UW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 5885673 5885674 G A snv FHH/EurMcwi (MDC), DA/BklArbNsi (ICAHN), ACI/N (KNAW), F344/NRrrc (KNAW), LE/Stm (KNAW), M520/N (KNAW), MR/N (KNAW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), F344/NCrl (ICL), LE/Stm (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), SBN/Ygl (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), F344/NHsd (ICAHN), SS/JrHsdMcwi (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310342 AgrOrtholog
Ensembl Genes ENSRNOG00000014450 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019893 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071936 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019893 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000088292 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
  3.40.50.10810 UniProtKB/TrEMBL
InterPro DEAD-like_N UniProtKB/TrEMBL
  DNA/RNA_helicase_C UniProtKB/TrEMBL
  Histone_H1/H5 UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  SNF2-like_sf UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:308282 UniProtKB/TrEMBL
NCBI Gene 308282 ENTREZGENE
Pfam Helicase_C UniProtKB/TrEMBL
  Linker_histone UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
PhenoGen Shprh PhenoGen
PROSITE H15 UniProtKB/TrEMBL
  HELICASE_ATP_BIND_1 UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/TrEMBL
SMART DEXDc UniProtKB/TrEMBL
  H15 UniProtKB/TrEMBL
  HELICc UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
Superfamily-SCOP FYVE_PHD_ZnF UniProtKB/TrEMBL
  SSF46785 UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt A0A0G2K1Q2 ENTREZGENE, UniProtKB/TrEMBL
  D4A9B2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-16 Shprh  SNF2 histone linker PHD RING helicase  Shprh  SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-16 Shprh  SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase  Shprh  SNF2 histone linker PHD RING helicase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Shprh  SNF2 histone linker PHD RING helicase   Shprh_predicted  SNF2 histone linker PHD RING helicase (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Shprh_predicted  SNF2 histone linker PHD RING helicase (predicted)      Symbol and Name status set to approved 70820 APPROVED