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 enable 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 be located in nuclear speck. Predicted to be part of chromatin. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Ruijs-Aalfs syndrome. Orthologous to human SPRTN (SprT-like N-terminal domain); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously 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 Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81969,754,989 - 69,762,240 (+)NCBIGRCr8
mRatBN7.21952,857,612 - 52,864,864 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1952,857,866 - 52,864,864 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1959,642,389 - 59,649,644 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01960,493,441 - 60,500,696 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01962,568,856 - 62,576,111 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01957,649,901 - 57,657,158 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1957,650,163 - 57,654,864 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01968,363,163 - 68,370,397 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41955,069,130 - 55,073,670 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1952,225,035 - 52,229,575 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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,IEA,ISO,ISS)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
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
GRCr81969,754,989 - 69,762,240 (+)NCBIGRCr8
mRatBN7.21952,857,612 - 52,864,864 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1952,857,866 - 52,864,864 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1959,642,389 - 59,649,644 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01960,493,441 - 60,500,696 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01962,568,856 - 62,576,111 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01957,649,901 - 57,657,158 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1957,650,163 - 57,654,864 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01968,363,163 - 68,370,397 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41955,069,130 - 55,073,670 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1952,225,035 - 52,229,575 (+)NCBICelera
Cytogenetic Map19q12NCBI
SPRTN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381231,338,293 - 231,355,023 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1231,337,104 - 231,355,023 (+)EnsemblGRCh38hg38GRCh38
GRCh371231,474,039 - 231,490,769 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361229,540,305 - 229,556,612 (+)NCBINCBI36Build 36hg18NCBI36
Celera1204,738,552 - 204,754,859 (+)NCBICelera
Cytogenetic Map1q42.2NCBI
HuRef1201,957,001 - 201,974,087 (+)NCBIHuRef
CHM1_11232,747,331 - 232,764,412 (+)NCBICHM1_1
T2T-CHM13v2.01230,721,543 - 230,738,274 (+)NCBIT2T-CHM13v2.0
Sprtn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398125,624,612 - 125,632,903 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8125,624,625 - 125,632,900 (+)EnsemblGRCm39 Ensembl
GRCm388124,897,771 - 124,906,161 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8124,897,886 - 124,906,161 (+)EnsemblGRCm38mm10GRCm38
MGSCv378127,421,786 - 127,427,713 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368127,783,757 - 127,789,903 (+)NCBIMGSCv36mm8
Celera8129,206,579 - 129,212,500 (+)NCBICelera
Cytogenetic Map8E2NCBI
cM Map872.83NCBI
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
NHGRI_mPanPan1-v2117,849,113 - 17,866,630 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1118,045,564 - 18,062,262 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01206,889,897 - 206,906,047 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11211,914,100 - 211,931,093 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1211,914,082 - 211,931,093 (+)Ensemblpanpan1.1panPan2
SPRTN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.148,120,151 - 8,133,402 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl48,120,351 - 8,133,191 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha48,103,760 - 8,125,780 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.048,136,875 - 8,158,889 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl48,145,629 - 8,158,778 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.148,140,254 - 8,162,248 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.048,262,219 - 8,284,247 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.048,490,636 - 8,512,645 (-)NCBIUU_Cfam_GSD_1.0
Sprtn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934443,226,459 - 43,237,640 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648419,391,420 - 19,402,944 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648419,391,685 - 19,402,938 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPRTN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1459,171,192 - 59,192,269 (-)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12568,599,377 - 68,620,568 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2568,599,780 - 68,620,621 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605570,507,407 - 70,524,424 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sprtn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477518,384,276 - 18,397,399 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477518,382,718 - 18,397,411 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sprtn
20 total Variants
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.


QTLs in Region (mRatBN7.2)
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)19218792756457239Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194997648153225766Rat


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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1952,857,868 - 52,862,409 (+)Ensembl
Rnor_6.0 Ensembl1957,650,163 - 57,654,703 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000083572   ⟹   ENSRNOP00000075544
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1952,857,866 - 52,864,864 (+)Ensembl
Rnor_6.0 Ensembl1957,650,233 - 57,654,864 (+)Ensembl
RefSeq Acc Id: NM_001399182   ⟹   NP_001386111
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81969,754,989 - 69,762,240 (+)NCBI
mRatBN7.21952,857,612 - 52,864,864 (+)NCBI
RefSeq Acc Id: XM_006255810   ⟹   XP_006255872
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81969,755,484 - 69,762,240 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81969,755,337 - 69,762,240 (+)NCBI
mRatBN7.21952,857,960 - 52,864,864 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_006255872   ⟸   XM_006255810
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KAV7 (UniProtKB/TrEMBL),   A6KJ26 (UniProtKB/TrEMBL),   D4AB73 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000033080   ⟸   ENSRNOT00000038257
RefSeq Acc Id: ENSRNOP00000075544   ⟸   ENSRNOT00000083572
RefSeq Acc Id: XP_038953600   ⟸   XM_039097672
- Peptide Label: isoform X2
RefSeq Acc Id: NP_001386111   ⟸   NM_001399182
- UniProtKB: D3ZVU1 (UniProtKB/Swiss-Prot)
Protein Domains
SprT-like   UBZ4-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZVU1-F1-model_v2 AlphaFold D3ZVU1 1-496 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559496 AgrOrtholog
BioCyc Gene G2FUF-5226 BioCyc
Ensembl Genes ENSRNOG00000021330 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038257.6 UniProtKB/TrEMBL
  ENSRNOT00000083572 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000083572.2 UniProtKB/Swiss-Prot
Gene3D-CATH Classic Zinc Finger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Spartan UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  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
PANTHER DNA-DEPENDENT METALLOPROTEASE SPRTN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR21220 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SprT-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sprtn PhenoGen
PROSITE ZF_UBZ4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZINC_PROTEASE UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000021330 RatGTEx
SMART SprT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_Rad18 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2KAV7 ENTREZGENE, UniProtKB/TrEMBL
  A6KJ26 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