Skint4 (selection and upkeep of intraepithelial T cells 4) - Rat Genome Database

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Gene: Skint4 (selection and upkeep of intraepithelial T cells 4) Rattus norvegicus
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Symbol: Skint4
Name: selection and upkeep of intraepithelial T cells 4
RGD ID: 6490949
Description: Orthologous to human SKINT1L (Skint1 like (pseudogene)); INTERACTS WITH aflatoxin B1 (ortholog); benzo[a]pyrene (ortholog); folic acid (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC100911772; LOC689834; selection and upkeep of intraepithelial T-cells protein 2-like; selection and upkeep of intraepithelial T-cells protein 5-like; similar to Butyrophilin subfamily 1 member A1 precursor (BT)
RGD Orthologs
Human
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85132,549,296 - 132,750,557 (+)NCBIGRCr8
mRatBN7.25127,320,857 - 127,514,355 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.05132,577,383 - 132,636,782 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05136,404,174 - 136,414,187 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45134,149,336 - 134,206,433 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5125,976,364 - 126,034,941 (+)NCBICelera
Cytogenetic Map5q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Skint4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85132,549,296 - 132,750,557 (+)NCBIGRCr8
mRatBN7.25127,320,857 - 127,514,355 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.05132,577,383 - 132,636,782 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05136,404,174 - 136,414,187 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45134,149,336 - 134,206,433 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5125,976,364 - 126,034,941 (+)NCBICelera
Cytogenetic Map5q35NCBI
SKINT1L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38148,101,715 - 48,182,428 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl148,161,799 - 48,179,230 (-)EnsemblGRCh38hg38GRCh38
GRCh37148,567,387 - 48,648,100 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36148,399,270 - 48,445,685 (-)NCBINCBI36Build 36hg18NCBI36
Celera146,854,212 - 46,934,908 (-)NCBICelera
Cytogenetic Map1p33NCBI
HuRef146,684,001 - 46,764,876 (-)NCBIHuRef
CHM1_1148,684,336 - 48,765,042 (-)NCBICHM1_1
T2T-CHM13v2.0147,980,564 - 48,061,271 (-)NCBIT2T-CHM13v2.0
Skint4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394111,929,213 - 112,025,273 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4111,929,213 - 112,025,273 (+)EnsemblGRCm39 Ensembl
GRCm384112,072,016 - 112,168,076 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4112,072,016 - 112,168,076 (+)EnsemblGRCm38mm10GRCm38
MGSCv374111,754,075 - 111,840,681 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364111,579,402 - 111,666,008 (+)NCBIMGSCv36mm8
MGSCv364109,831,888 - 109,917,811 (+)NCBIMGSCv36mm8
Cytogenetic Map4D1NCBI
cM Map451.53NCBI

Variants

.
Variants in Skint4
1806 total Variants

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


Sequence


RefSeq Acc Id: XM_039111485   ⟹   XP_038967413
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85132,549,296 - 132,750,557 (+)NCBI
mRatBN7.25127,320,857 - 127,514,355 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038967413 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_038967413   ⟸   XM_039111485


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:6490949 AgrOrtholog
BioCyc Gene G2FUF-40330 BioCyc
NCBI Gene LOC100911772 ENTREZGENE
PhenoGen Skint4 PhenoGen


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-18 Skint4  selection and upkeep of intraepithelial T cells 4  LOC100911772  selection and upkeep of intraepithelial T-cells protein 5-like  Name and Symbol changed 629549 APPROVED
2015-07-29 LOC100911772  selection and upkeep of intraepithelial T-cells protein 5-like  LOC689834  similar to Butyrophilin subfamily 1 member A1 precursor (BT)  Data merged from RGD:1587546 737654 PROVISIONAL
2012-07-05 LOC100911772  selection and upkeep of intraepithelial T-cells protein 5-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-01-09 LOC689834  similar to Butyrophilin subfamily 1 member A1 precursor (BT)  LOC684069  similar to Butyrophilin subfamily 1 member A1 precursor (BT)  Data merged from RGD:1595177 1643240 APPROVED
2006-11-20 LOC684069  similar to Butyrophilin subfamily 1 member A1 precursor (BT)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC689834  similar to Butyrophilin subfamily 1 member A1 precursor (BT)      Symbol and Name status set to provisional 70820 PROVISIONAL