Skint2 (selection and upkeep of intraepithelial T cells 2) - Rat Genome Database

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Gene: Skint2 (selection and upkeep of intraepithelial T cells 2) Rattus norvegicus
Analyze
Symbol: Skint2 (Ensembl: AABR07049648.1)
Name: selection and upkeep of intraepithelial T cells 2 (Ensembl:selection and upkeep of intraepithelial T cells 4)
RGD ID: 1566327
Description: ENCODES a protein that exhibits signaling receptor binding (ortholog); T cell receptor binding (ortholog); INVOLVED IN CD4-positive, alpha-beta T cell activation (ortholog); CD8-positive, alpha-beta T cell activation (ortholog); negative regulation of CD4-positive, alpha-beta T cell activation (ortholog); FOUND IN plasma membrane (ortholog); INTERACTS WITH 1,2-dichloroethane (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: AABR07049648.1; LOC313485; RGD1566327; selection and upkeep of intraepithelial T cells 4; selection and upkeep of intraepithelial T-cells protein 2-like; similar to hypothetical protein A430070M19; Skint4
RGD Orthologs
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25126,878,834 - 126,909,044 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5126,875,682 - 126,913,167 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.05132,005,656 - 132,043,655 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5132,005,738 - 132,016,885 (+)NCBIRnor6.0rn6Rnor6.0
Rnor_5.05135,830,324 - 135,860,355 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45133,611,316 - 133,641,536 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5125,571,009 - 125,608,744 (+)NCBICelera
Cytogenetic Map5q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

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.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Skint2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25126,878,834 - 126,909,044 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5126,875,682 - 126,913,167 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.05132,005,656 - 132,043,655 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5132,005,738 - 132,016,885 (+)NCBIRnor6.0rn6Rnor6.0
Rnor_5.05135,830,324 - 135,860,355 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45133,611,316 - 133,641,536 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5125,571,009 - 125,608,744 (+)NCBICelera
Cytogenetic Map5q35NCBI
Skint2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394112,470,795 - 112,509,445 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4112,414,391 - 112,509,445 (+)EnsemblGRCm39 Ensembl
GRCm384112,613,598 - 112,652,248 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4112,557,194 - 112,652,248 (+)EnsemblGRCm38mm10GRCm38
MGSCv374112,286,357 - 112,320,445 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364112,111,684 - 112,145,772 (+)NCBIMGSCv36mm8
Celera4110,445,935 - 110,480,122 (+)NCBICelera
Cytogenetic Map4D1NCBI

Variants

.
Variants in Skint2
469 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:81
Interacting mature miRNAs:82
Transcripts:ENSRNOT00000041421
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
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
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
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)584132602129132602Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
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
1358909Kidm25Kidney mass QTL 251.87kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)590067849128034027Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)597570330136479578Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
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
1582230Bw78Body weight QTL 783.20.0016epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)5119085612128034027Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5120740824143608494Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5120740824151018848Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
7394710Emca12Estrogen-induced mammary cancer QTL 12mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5124160767133749643Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
1300122Wbc1White blood cell count QTL 12.75leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)5125392826139989768Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041421   ⟹   ENSRNOP00000043233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5126,875,682 - 126,913,167 (+)Ensembl
RefSeq Acc Id: XM_006238600   ⟹   XP_006238662
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25126,878,834 - 126,909,044 (+)NCBI
Rnor_6.05132,005,656 - 132,043,655 (+)NCBI
Rnor_5.05135,830,324 - 135,860,355 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_006238662 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006238662   ⟸   XM_006238600
- Sequence:
RefSeq Acc Id: ENSRNOP00000043233   ⟸   ENSRNOT00000041421
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZBR5-F1-model_v2 AlphaFold D3ZBR5 1-252 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:1566327 AgrOrtholog
BioCyc Gene G2FUF-40333 BioCyc
Ensembl Genes ENSRNOG00000042047 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000043233 ENTREZGENE
  ENSRNOP00000043233.6 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041421 ENTREZGENE
  ENSRNOT00000041421.6 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro CD80_C2-set UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
KEGG Report rno:313485 UniProtKB/TrEMBL
NCBI Gene 313485 ENTREZGENE
PANTHER BUTYROPHILIN UniProtKB/TrEMBL
  SELECTION AND UPKEEP OF INTRAEPITHELIAL T-CELLS PROTEIN 2-RELATED UniProtKB/TrEMBL
Pfam C2-set_2 UniProtKB/TrEMBL
  V-set UniProtKB/TrEMBL
PhenoGen Skint2 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
SMART IGv UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt D3ZBR5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-05-01 Skint2  selection and upkeep of intraepithelial T cells 2  Skint4  selection and upkeep of intraepithelial T cells 4  Name and Symbol changed 629549 APPROVED
2022-06-02 Skint4  selection and upkeep of intraepithelial T cells 4  AABR07049648.1    Data Merged 737654 PROVISIONAL
2019-11-08 AABR07049648.1        Symbol and Name status set to provisional 45752 PROVISIONAL
2008-11-20 Skint4  selection and upkeep of intraepithelial T cells 4  RGD1566327  similar to hypothetical protein A430070M19   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1566327  similar to hypothetical protein A430070M19   RGD1566327_predicted  similar to hypothetical protein A430070M19 (predicted)  'predicted' is removed 2292626 APPROVED
2008-01-09 RGD1566327_predicted  similar to hypothetical protein A430070M19 (predicted)  LOC684061  similar to Butyrophilin subfamily 1 member A1 precursor (BT)  Data Merged 1643240 APPROVED
2006-11-20 LOC684061  similar to Butyrophilin subfamily 1 member A1 precursor (BT)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-07 RGD1566327_predicted  similar to hypothetical protein A430070M19 (predicted)  LOC313485  similar to hypothetical protein A430070M19  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC313485  similar to hypothetical protein A430070M19      Symbol and Name status set to provisional 70820 PROVISIONAL