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) Mus musculus
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Symbol: Skint2
Name: selection and upkeep of intraepithelial T cells 2
RGD ID: 1615548
MGI Page MGI
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 located in membrane. Predicted to be active in external side of plasma membrane. Is expressed in several structures, including genitourinary system; gut; integumental system; liver; and thymus.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: A430070M19; B7S; B7S3; RP23-170H12.1; selection and upkeep of intraepithelial T-cells protein 2; skint 2; Skint-2
RGD Orthologs
Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394112,470,917 - 112,509,447 (+)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
cM Map451.53NCBI
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

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:16141072   PMID:16141073   PMID:17339463   PMID:18408721   PMID:21267068   PMID:21300860  
PMID:21873635   PMID:32724083  


Genomics

Comparative Map Data
Skint2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394112,470,917 - 112,509,447 (+)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
cM Map451.53NCBI
Skint2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85132,107,274 - 132,115,231 (+)NCBIGRCr8
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

Variants

.
Variants in Skint2
3161 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:403
Count of miRNA genes:226
Interacting mature miRNAs:238
Transcripts:ENSMUST00000058791, ENSMUST00000106559, ENSMUST00000106560
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
13824982Svwq1_mseminal vesicle weight QTL 1 (mouse)489888237118857197Mouse
11532714Sluc43_msusceptibility to lung cancer 43 (mouse)446642108123127211Mouse
12904002Opfaq9_mopen field activity QTL 9 (mouse)492975790126975790Mouse
4141623W6q13_mweight 6 weeks QTL 13 (mouse)Not determined88982069140468203Mouse
12910797Pwgrq4_mpre-weaning growth rate QTL 4 (mouse)4105835310141433838Mouse
25314312Syncl2_msynaptonemal complex length 2 (mouse)465718237146584457Mouse
1357726Lnopy1_mlens opacity 1 (mouse)Not determined485428838119429037Mouse
12910794Pwbwq8_mpost-weaning body weight QTL 8 (mouse)4105835310141433838Mouse
14696689Gdq2_mgrooming duration QTL 2, females (mouse)4100857197124893793Mouse
1300743Skull6_mskull morphology 6 (mouse)Not determined4111009051145009280Mouse
1301382Arvm2_mautoimmune renal vasculitis 2 (mouse)Not determined4107791564141791756Mouse
12910813Pwbwq4_mpre-weaning body weight QTL 4 (mouse)4105835310141433838Mouse
4141093W3q17_mweight 3 weeks QTL 17 (mouse)Not determined88982069140468203Mouse
12910808Pwbwq9_mpost-weaning body weight QTL 9 (mouse)4105835310141433838Mouse
27095939Ulnl9_mulna length 9, 16 week (mouse)465318237118857197Mouse
11567249Elorr3_methanol induced loss of righting response 3 (mouse)43722677156268235Mouse
12904933Edlmmq3_mextensor digitorum longus muscle mass QTL 3 (mouse)481213991115213991Mouse
1301815Sles2_msystemic lupus erythmatosus suppressor 2 (mouse)Not determined494957579150676858Mouse
1300663Start2_mstartle response 2 (mouse)Not determined4107264957141265153Mouse
1300918Stheal4_msoft tissue heal 4 (mouse)Not determined489969627123969747Mouse
1301556Cd4vts1_mCD4 virgin T cell subset 1 (mouse)Not determined485428838119429037Mouse
1301823Bmd7_mbone mineral density 7 (mouse)Not determined488982069151654550Mouse
1302204Spm1_msplenomegaly modifier (mouse)Not determined482244395116244582Mouse
11039517Ltpr4_mLeishmania tropica response 4 (mouse)479365751113365867Mouse
10412072Ssen1_msuseptibility to Sendai virus 1 (mouse)Not determined4109658132133154782Mouse
11039504Ltpr4a_mLeishmania tropica response 4a (mouse)479365751113365867Mouse
11039505Ltpr4c_mLeishmania tropica response 4c (mouse)479365751113365867Mouse
1301930Papg1_mpulmonary adenoma progression 1 (mouse)Not determined485781167119781279Mouse
11039506Ltpr4b_mLeishmania tropica response 4b (mouse)479365751113365867Mouse
13208562Wght7_mweight 7 (mouse)490888237148084457Mouse
13208565Bmiq6_mbody mass index QTL 6 (mouse)4110857197125893793Mouse
1300781Lith8_mlithogenic gene 8 (mouse)Not determined4107264957141265153Mouse
39128212Lwq21_mliver weight QTL 21 (mouse)488982069140468203Mouse
1300689Dob1_mDietary obesity 1 (mouse)Body weight4101574601123127211Mouse
27226716Metcl2_mmetatarsal-calcaneal length 2, 5 week (mouse)488118237118557197Mouse
1301847Fecq2_mfecundity QTL 2 (mouse)Not determined4100071971134072206Mouse
26884445Sklq7_mskull length QTL 7, 10 week (mouse)468018237150884457Mouse
1301597Anxty_manxiety (mouse)Not determined474137574128009280Mouse
26884437Sklq13_mskull length QTL 13, 16 week (mouse)457700000155684457Mouse
4141549W10q10_mweight 10 weeks QTL 10 (mouse)Not determined88982069140468203Mouse
1357895Ctrcts_mcataract severity (mouse)Not determined445709925138342753Mouse
1300809Ccrs2_mcorpus callosum hemisphere surface size 2 (mouse)Not determined4107264957141265153Mouse
4142047Mvwf3_mmodifier of von Willebrand factor 3 (mouse)Not determined14010457117072206Mouse
1301106Skts7_mskin tumor susceptibility 7 (mouse)Not determined4100071971134072206Mouse
1301233Sbw2_msplenomegaly-NZB x NZW 2 (mouse)Not determined494957579128009280Mouse
10755520Rbc1_mred blood cell count 1 (mouse)4108477692142477692Mouse
10755521Hct1_mhematocrit 1 (mouse)4108477692142477692Mouse
10755522Hgb1_mhemoglobin 1 (mouse)4108477692142477692Mouse
27095924Pglq2_mpelvic girdle length QTL 2, 5 week (mouse)469118237130727311Mouse
1301118Bbaa23_mB.burgdorferi-associated arthritis 23 (mouse)Not determined485781167119781279Mouse
11532738Abd1_mautoimmune biliary disease 1 (mouse)488982069116271120Mouse
15039368Nmrs19_mNAFLD-associated magnetic resonance shift 19 (mouse)490882780124882780Mouse
27095917Scvln14_msacral vertebrae length 2, 16 week (mouse)468018237130277062Mouse
1301731Cafq2_mcaffeine metabolism QTL 2 (mouse)Not determined494732255128732454Mouse
4141900Skts-fp1_mskin tumor susceptibility in FVB and PWK 1 (mouse)Not determined453550839124055180Mouse
15039382Ltgq7_mliver triglyceride QTL 7 (mouse)4105705794139705794Mouse
15039377Bw45_mbody weight QTL 45 (mouse)4105705794139705794Mouse
1300839Dyscalc2_mdystrophic cardiac calcinosis 2 (mouse)Not determined4111009051145009280Mouse
12880433Fgf23lq1_mFGF23 serum level QTL 1 (mouse)4101157197135157197Mouse
1300580Lbw2_mlupus NZB x NZW 2 (mouse)Not determined498545539128009280Mouse
15039378Adip30_madiposity 30 (mouse)4105705794139705794Mouse
1301867Idd11_minsulin dependent diabetes susceptibility 11 (mouse)Not determined483604870117605006Mouse
26884449Sklq2_mskull length QTL 2, 5 week (mouse)436700000128993793Mouse
27095905Scvln3_msacral vertebrae length 2, 5 week (mouse)455600000128993793Mouse
1357800Tgq3_mtriglyceride QTL 3 (mouse)Not determined4107055093141055180Mouse
15039385Mvlq3_mmacrovesicular liver lesion QTL 3 (mouse)4112182386146182386Mouse
11553870Cmmm_mcarcinoma modifier of MSM (mouse)490590668124590781Mouse


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000058791   ⟹   ENSMUSP00000061011
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4112,470,794 - 112,483,900 (+)Ensembl
GRCm38.p6 Ensembl4112,613,597 - 112,626,703 (+)Ensembl
Ensembl Acc Id: ENSMUST00000106559
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4112,470,948 - 112,505,037 (+)Ensembl
GRCm38.p6 Ensembl4112,613,751 - 112,647,840 (+)Ensembl
Ensembl Acc Id: ENSMUST00000106560   ⟹   ENSMUSP00000102170
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4112,414,391 - 112,505,037 (+)Ensembl
GRCm38.p6 Ensembl4112,557,194 - 112,647,840 (+)Ensembl
Ensembl Acc Id: ENSMUST00000186969   ⟹   ENSMUSP00000139831
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4112,470,937 - 112,509,445 (+)Ensembl
GRCm38.p6 Ensembl4112,613,740 - 112,652,248 (+)Ensembl
RefSeq Acc Id: NM_001285963   ⟹   NP_001272892
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm394112,470,917 - 112,509,447 (+)NCBI
GRCm384112,613,740 - 112,652,248 (+)NCBI
Celera4110,443,090 - 110,484,501 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001285965   ⟹   NP_001272894
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm394112,470,917 - 112,509,447 (+)NCBI
GRCm384112,613,740 - 112,652,248 (+)NCBI
Celera4110,443,090 - 110,484,501 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001425821   ⟹   NP_001412750
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm394112,470,917 - 112,504,485 (+)NCBI
RefSeq Acc Id: NM_001425822   ⟹   NP_001412751
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm394112,470,917 - 112,483,900 (+)NCBI
RefSeq Acc Id: XM_017320265   ⟹   XP_017175754
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm394112,473,354 - 112,509,421 (+)NCBI
GRCm384112,616,157 - 112,652,224 (+)NCBI
Sequence:
RefSeq Acc Id: NP_001272894   ⟸   NM_001285965
- Peptide Label: isoform b precursor
- UniProtKB: A7XUX6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001272892   ⟸   NM_001285963
- Peptide Label: isoform a precursor
- UniProtKB: A7TZE9 (UniProtKB/Swiss-Prot),   A7TZE8 (UniProtKB/Swiss-Prot),   A7XUY1 (UniProtKB/Swiss-Prot),   A7XUX6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017175754   ⟸   XM_017320265
- Peptide Label: isoform X3
- Sequence:
Ensembl Acc Id: ENSMUSP00000139831   ⟸   ENSMUST00000186969
Ensembl Acc Id: ENSMUSP00000102170   ⟸   ENSMUST00000106560
Ensembl Acc Id: ENSMUSP00000061011   ⟸   ENSMUST00000058791
RefSeq Acc Id: NP_001412750   ⟸   NM_001425821
- Peptide Label: isoform 3 precursor
- UniProtKB: B2ZEZ5 (UniProtKB/TrEMBL),   E9Q127 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001412751   ⟸   NM_001425822
- Peptide Label: isoform 4 precursor
- UniProtKB: M9MMJ5 (UniProtKB/TrEMBL),   Q8CG82 (UniProtKB/TrEMBL)
Protein Domains
Ig-like   Ig-like C1-type   Ig-like V-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A7XUX6-F1-model_v2 AlphaFold A7XUX6 1-400 view protein structure

Promoters
RGD ID:6884202
Promoter ID:EPDNEW_M5552
Type:initiation region
Name:Skint2_1
Description:Mus musculus selection and upkeep of intraepithelial T cells2 , transcript variant 1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm384112,613,639 - 112,613,699EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:3649629 AgrOrtholog
Ensembl Genes ENSMUSG00000034359 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000058791 ENTREZGENE
  ENSMUST00000058791.14 UniProtKB/TrEMBL
  ENSMUST00000106560 ENTREZGENE
  ENSMUST00000106560.10 UniProtKB/TrEMBL
  ENSMUST00000186969 ENTREZGENE
  ENSMUST00000186969.2 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro BTN3A2-like_Ig-C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IgSF_BTN/MOG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:329919 UniProtKB/Swiss-Prot
MGD MGI:3649629 ENTREZGENE
NCBI Gene 329919 ENTREZGENE
PANTHER BUTYROPHILIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SELECTION AND UPKEEP OF INTRAEPITHELIAL T-CELLS PROTEIN 2-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam C2-set_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Skint2 PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART IGv UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A7TZE8 ENTREZGENE
  A7TZE9 ENTREZGENE
  A7XUX6 ENTREZGENE
  A7XUY1 ENTREZGENE
  B2ZEZ5 ENTREZGENE, UniProtKB/TrEMBL
  B2ZEZ6_MOUSE UniProtKB/TrEMBL
  E9Q127 ENTREZGENE
  M9MMJ5 ENTREZGENE, UniProtKB/TrEMBL
  Q8CG82 ENTREZGENE, UniProtKB/TrEMBL
  SKIT2_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary A7TZE8 UniProtKB/Swiss-Prot
  A7TZE9 UniProtKB/Swiss-Prot
  A7XUY1 UniProtKB/Swiss-Prot
  E9Q127 UniProtKB/TrEMBL