Skint1 (selection and upkeep of intraepithelial T cells 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Skint1 (selection and upkeep of intraepithelial T cells 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Skint1
Name: selection and upkeep of intraepithelial T cells 1
RGD ID: 1587579
Description: Predicted to enable signaling receptor binding activity. Predicted to be involved in T cell receptor signaling pathway and regulation of cytokine production. Predicted to be active in external side of plasma membrane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC689801; selection and upkeep of intraepithelial T-cells 1; selection and upkeep of intraepithelial T-cells protein 1; similar to butyrophilin-like 8
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85132,014,881 - 132,043,149 (+)NCBIGRCr8
mRatBN7.25126,786,469 - 126,814,599 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5126,786,469 - 126,814,720 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5129,444,807 - 129,479,644 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05131,167,891 - 131,202,726 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05131,196,091 - 131,230,924 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05131,915,266 - 131,944,842 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5131,915,382 - 131,943,132 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05135,739,813 - 135,767,455 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45133,518,934 - 133,546,575 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5125,490,170 - 125,517,817 (+)NCBICelera
Cytogenetic Map5q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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.

Genomics

Variants

.
Variants in Skint1
332 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:22
Count of miRNA genes:22
Interacting mature miRNAs:22
Transcripts:ENSRNOT00000064863
Prediction methods: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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1300122Wbc1White blood cell count QTL 12.75leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)5125392826139989768Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1582230Bw78Body weight QTL 783.20.0016epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)5119085612128034027Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)597570330136479578Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5120740824143608494Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
7394710Emca12Estrogen-induced mammary cancer QTL 12mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5124160767133749643Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5120740824151018848Rat
1358909Kidm25Kidney mass QTL 251.87kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)590067849128034027Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)584132602129132602Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
1358889Bp261Blood pressure QTL 2612.86arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)590067849128034027Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
4 1 17 20 19 1 23 1 6 38 30 4 2 12 18

Sequence


Ensembl Acc Id: ENSRNOT00000064863   ⟹   ENSRNOP00000060977
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5126,786,469 - 126,814,107 (+)Ensembl
Rnor_6.0 Ensembl5131,920,155 - 131,943,132 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000087012   ⟹   ENSRNOP00000075376
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5126,786,469 - 126,810,667 (+)Ensembl
Rnor_6.0 Ensembl5131,915,382 - 131,942,985 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000116511   ⟹   ENSRNOP00000081877
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5126,786,469 - 126,814,720 (+)Ensembl
RefSeq Acc Id: NM_001135916   ⟹   NP_001129388
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85132,014,905 - 132,042,544 (+)NCBI
mRatBN7.25126,786,469 - 126,814,108 (+)NCBI
Rnor_6.05131,915,491 - 131,943,133 (+)NCBI
Rnor_5.05135,739,813 - 135,767,455 (+)NCBI
RGSC_v3.45133,518,934 - 133,546,575 (+)RGD
Celera5125,490,170 - 125,517,817 (+)RGD
Sequence:
RefSeq Acc Id: XM_017593636   ⟹   XP_017449125
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85132,014,881 - 132,043,149 (+)NCBI
mRatBN7.25126,791,133 - 126,814,599 (+)NCBI
Rnor_6.05131,915,266 - 131,944,842 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001129388 (Get FASTA)   NCBI Sequence Viewer  
  NP_001417229 (Get FASTA)   NCBI Sequence Viewer  
  XP_017449125 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ACD02032 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000060977.1
  ENSRNOP00000075376.2
  ENSRNOP00000081877.1
RefSeq Acc Id: NP_001129388   ⟸   NM_001135916
- Peptide Label: precursor
- UniProtKB: B2ZEZ3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017449125   ⟸   XM_017593636
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000075376   ⟸   ENSRNOT00000087012
Ensembl Acc Id: ENSRNOP00000060977   ⟸   ENSRNOT00000064863
Ensembl Acc Id: ENSRNOP00000081877   ⟸   ENSRNOT00000116511
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B2ZEZ3-F1-model_v2 AlphaFold B2ZEZ3 1-377 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1587579 AgrOrtholog
BioCyc Gene G2FUF-40335 BioCyc
Ensembl Genes ENSRNOG00000043194 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064863.3 UniProtKB/TrEMBL
  ENSRNOT00000087012.2 UniProtKB/TrEMBL
  ENSRNOT00000116511.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro BTN3A2-like_Ig-C UniProtKB/TrEMBL
  Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
  IgSF_BTN/MOG UniProtKB/TrEMBL
KEGG Report rno:689801 UniProtKB/TrEMBL
NCBI Gene 689801 ENTREZGENE
PANTHER BUTYROPHILIN UniProtKB/TrEMBL
  SELECTION AND UPKEEP OF INTRAEPITHELIAL T-CELLS PROTEIN 1 UniProtKB/TrEMBL
Pfam C2-set_3 UniProtKB/TrEMBL
  V-set UniProtKB/TrEMBL
PhenoGen Skint1 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000043194 RatGTEx
SMART IGv UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt A0A0G2KAF2_RAT UniProtKB/TrEMBL
  A0A8I5ZVY8 ENTREZGENE, UniProtKB/TrEMBL
  B2ZEZ3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-12-01 Skint1  selection and upkeep of intraepithelial T-cells 1  LOC689801  similar to butyrophilin-like 8  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-12-01 Skint1  selection and upkeep of intraepithelial T cells 1  Skint1  selection and upkeep of intraepithelial T-cells 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC689801  similar to butyrophilin-like 8  LOC684034  similar to butyrophilin-like 8  Data merged from RGD:1595211 1643240 APPROVED
2006-11-20 LOC684034  similar to butyrophilin-like 8      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC689801  similar to butyrophilin-like 8      Symbol and Name status set to provisional 70820 PROVISIONAL