Sprtn (SprT-like N-terminal domain) - Rat Genome Database
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Gene: Sprtn (SprT-like N-terminal domain) Rattus norvegicus
Analyze
Symbol: Sprtn
Name: SprT-like N-terminal domain
RGD ID: 1559496
Description: Predicted to have several functions, including DNA binding activity; K63-linked polyubiquitin modification-dependent protein binding activity; and metalloendopeptidase activity. Predicted to be involved in several processes, including DNA repair; positive regulation of protein ubiquitination; and protein autoprocessing. Predicted to localize to chromatin and nuclear speck. Human ortholog(s) of this gene implicated in Ruijs-Aalfs syndrome. Orthologous to human SPRTN (SprT-like N-terminal domain); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; furan.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DNA-dependent metalloprotease SPRTN; hypothetical protein LOC292101; LOC292101; protein with SprT-like domain at the N terminus; RGD1559496; similar to hypothetical protein; spartan; sprT-like domain-containing protein Spartan; uncharacterized protein LOC292101
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
mRatBN7.21952,857,599 - 52,864,864 (+)NCBI
Rnor_6.0 Ensembl1957,650,163 - 57,654,864 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01957,649,901 - 57,657,158 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01968,363,163 - 68,370,397 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41955,069,130 - 55,073,670 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1952,225,035 - 52,229,575 (+)NCBICelera
Cytogenetic Map19q12NCBI
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
chromatin  (IEA,ISO,ISS)
chromosome  (IEA)
nuclear speck  (IEA,ISO)
nucleoplasm  (ISO)
nucleus  (IBA,ISO,ISS)

References

Additional References at PubMed
PMID:22681887   PMID:22894931   PMID:22902628   PMID:23042605   PMID:23042607  


Genomics

Comparative Map Data
Sprtn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21952,857,599 - 52,864,864 (+)NCBI
Rnor_6.0 Ensembl1957,650,163 - 57,654,864 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01957,649,901 - 57,657,158 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01968,363,163 - 68,370,397 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41955,069,130 - 55,073,670 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1952,225,035 - 52,229,575 (+)NCBICelera
Cytogenetic Map19q12NCBI
SPRTN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1231,337,104 - 231,355,023 (+)EnsemblGRCh38hg38GRCh38
GRCh381231,337,980 - 231,355,023 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371231,474,039 - 231,490,769 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361229,540,305 - 229,556,612 (+)NCBINCBI36hg18NCBI36
Celera1204,738,552 - 204,754,859 (+)NCBI
Cytogenetic Map1q42.2NCBI
HuRef1201,957,001 - 201,974,087 (+)NCBIHuRef
CHM1_11232,747,331 - 232,764,418 (+)NCBICHM1_1
Sprtn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398125,624,612 - 125,632,903 (+)NCBIGRCm39mm39
GRCm39 Ensembl8125,624,625 - 125,632,900 (+)Ensembl
GRCm388124,897,771 - 124,906,161 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8124,897,886 - 124,906,161 (+)EnsemblGRCm38mm10GRCm38
MGSCv378127,421,786 - 127,427,713 (+)NCBIGRCm37mm9NCBIm37
MGSCv368127,783,757 - 127,789,903 (+)NCBImm8
Celera8129,206,579 - 129,212,500 (+)NCBICelera
Cytogenetic Map8E2NCBI
Sprtn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554927,464,959 - 7,476,458 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554927,463,228 - 7,476,683 (-)NCBIChiLan1.0ChiLan1.0
SPRTN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11211,914,100 - 211,931,093 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1211,914,082 - 211,931,093 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01206,889,897 - 206,906,047 (+)NCBIMhudiblu_PPA_v0panPan3
SPRTN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl48,120,351 - 8,133,191 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.148,120,151 - 8,133,402 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Sprtn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493648419,391,685 - 19,402,938 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPRTN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1459,171,170 - 59,192,270 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11459,177,801 - 59,192,221 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21463,849,792 - 63,860,814 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SPRTN
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12568,599,377 - 68,620,568 (+)NCBI
ChlSab1.1 Ensembl2568,599,780 - 68,620,621 (+)Ensembl
Sprtn
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477518,382,718 - 18,397,411 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194883071260220581Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)195473521758072143Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:79
Count of miRNA genes:68
Interacting mature miRNAs:70
Transcripts:ENSRNOT00000038257
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 1 24 16 6 19 6 66 21 40 11
Low 2 19 41 35 35 8 11 8 14 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000038257   ⟹   ENSRNOP00000033080
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1957,650,163 - 57,654,703 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000083572   ⟹   ENSRNOP00000075544
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1957,650,233 - 57,654,864 (+)Ensembl
RefSeq Acc Id: NM_001106199   ⟹   NP_001099669
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,857,868 - 52,862,409 (+)NCBI
Rnor_6.01957,650,163 - 57,654,703 (+)NCBI
Rnor_5.01968,363,163 - 68,370,397 (+)NCBI
RGSC_v3.41955,069,130 - 55,073,670 (+)RGD
Celera1952,225,035 - 52,229,575 (+)RGD
Sequence:
RefSeq Acc Id: XM_006255808   ⟹   XP_006255870
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,857,599 - 52,864,864 (+)NCBI
Rnor_6.01957,649,901 - 57,657,158 (+)NCBI
Rnor_5.01968,363,163 - 68,370,397 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006255809   ⟹   XP_006255871
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,858,180 - 52,864,864 (+)NCBI
Rnor_6.01957,650,398 - 57,657,158 (+)NCBI
Rnor_5.01968,363,163 - 68,370,397 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006255810   ⟹   XP_006255872
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,858,179 - 52,864,864 (+)NCBI
Rnor_6.01957,650,398 - 57,657,158 (+)NCBI
Rnor_5.01968,363,163 - 68,370,397 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039097672   ⟹   XP_038953600
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,857,960 - 52,864,864 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001099669   ⟸   NM_001106199
- UniProtKB: D4AB73 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255870   ⟸   XM_006255808
- Peptide Label: isoform X1
- UniProtKB: D3ZVU1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006255872   ⟸   XM_006255810
- Peptide Label: isoform X2
- UniProtKB: A0A0G2KAV7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255871   ⟸   XM_006255809
- Peptide Label: isoform X2
- UniProtKB: A0A0G2KAV7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000033080   ⟸   ENSRNOT00000038257
RefSeq Acc Id: ENSRNOP00000075544   ⟸   ENSRNOT00000083572
RefSeq Acc Id: XP_038953600   ⟸   XM_039097672
- Peptide Label: isoform X3
Protein Domains
SprT-like   UBZ4-type

Transcriptome

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

Promoters
RGD ID:13701245
Promoter ID:EPDNEW_R11767
Type:multiple initiation site
Name:Sprtn_2
Description:SprT-like N-terminal domain
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11769  EPDNEW_R11768  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01957,650,159 - 57,650,219EPDNEW
RGD ID:13701252
Promoter ID:EPDNEW_R11768
Type:initiation region
Name:Sprtn_3
Description:SprT-like N-terminal domain
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11767  EPDNEW_R11769  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01957,650,295 - 57,650,355EPDNEW
RGD ID:13701246
Promoter ID:EPDNEW_R11769
Type:multiple initiation site
Name:Sprtn_1
Description:SprT-like N-terminal domain
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11767  EPDNEW_R11768  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01957,650,468 - 57,650,528EPDNEW

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)
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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:1559496 AgrOrtholog
Ensembl Genes ENSRNOG00000021330 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000033080 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075544 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038257 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000083572 UniProtKB/TrEMBL
InterPro SprT-like_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_Rad18_put UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:292101 UniProtKB/TrEMBL
NCBI Gene 292101 ENTREZGENE
Pfam SprT-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sprtn PhenoGen
PROSITE ZF_UBZ4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZINC_PROTEASE UniProtKB/Swiss-Prot
SMART SprT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_Rad18 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2KAV7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZVU1 ENTREZGENE
  D4AB73 ENTREZGENE, UniProtKB/TrEMBL
  SPRTN_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-11 Sprtn  SprT-like N-terminal domain  RGD1559496  similar to hypothetical protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1559496  similar to hypothetical protein   RGD1559496_predicted  similar to hypothetical protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1559496_predicted  similar to hypothetical protein (predicted)  LOC292101  similar to hypothetical protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC292101  similar to hypothetical protein      Symbol and Name status set to provisional 70820 PROVISIONAL