Itga1 (integrin subunit alpha 1) - Rat Genome Database

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Gene: Itga1 (integrin subunit alpha 1) Rattus norvegicus
Analyze
Symbol: Itga1
Name: integrin subunit alpha 1
RGD ID: 2923
Description: Enables collagen binding activity and signaling receptor binding activity. Involved in several processes, including positive regulation of MAPK cascade; positive regulation of neuron apoptotic process; and vasodilation. Located in several cellular components, including acrosomal vesicle; external side of plasma membrane; and perikaryon. Orthologous to human ITGA1 (integrin subunit alpha 1); PARTICIPATES IN altered integrin mediated signaling pathway; myocardial infarction pathway; integrin mediated signaling pathway; INTERACTS WITH (+)-pilocarpine; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: CD49 antigen-like family member A; integrin alpha 1; integrin alpha-1; integrin, alpha 1; laminin and collagen receptor; VLA-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2246,646,125 - 46,812,237 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl246,653,193 - 46,812,238 (-)Ensembl
Rnor_6.0247,127,403 - 47,281,387 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl247,127,219 - 47,281,421 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0271,666,601 - 71,823,120 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4247,107,849 - 47,206,261 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1247,036,084 - 47,134,488 (-)NCBI
Celera242,407,780 - 42,559,904 (-)NCBICelera
Cytogenetic Map2q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-dichloroaniline  (EXP)
3,4-methylenedioxymethamphetamine  (EXP)
3-Nitrobenzanthrone  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
Allylamine  (EXP)
aluminium oxide  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
berberine  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
colforsin daropate hydrochloride  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
corticosterone  (EXP)
crocidolite asbestos  (ISO)
dibutyl phthalate  (ISO)
dichlorine  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
geldanamycin  (ISO)
genistein  (ISO)
indometacin  (EXP)
ivermectin  (ISO)
leflunomide  (ISO)
medroxyprogesterone acetate  (ISO)
methamphetamine  (ISO)
methotrexate  (ISO)
Methylazoxymethanol acetate  (EXP)
oxaliplatin  (EXP)
ozone  (EXP)
paclitaxel  (ISO)
perfluorobutanesulfonic acid  (ISO)
perfluorodecanoic acid  (ISO)
perfluorododecanoic acid  (ISO)
perfluoroheptanoic acid  (ISO)
perfluorooctanesulfonamide  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
titanium dioxide  (ISO)
toluene  (EXP)
topotecan  (EXP,ISO)
trichostatin A  (ISO)
triclosan  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vincristine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

References

References - curated
1. Anderson KL and Ferreira A, J Neurosci Res. 2004 Mar 1;75(5):688-97.
2. Bamdad M, etal., Cell Tissue Res. 2004 Jan;315(1):15-25. Epub 2003 Oct 16.
3. Damjanovich L, etal., Acta Chir Hung. 1997;36(1-4):69-71.
4. Dina OA, etal., Eur J Neurosci. 2004 Feb;19(3):634-42.
5. Dina OA, etal., Pain. 2005 May;115(1-2):191-203.
6. Fujimura T, etal., J Dermatol Sci. 2007 Jan;45(1):45-53. Epub 2006 Nov 21.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Giebel J, etal., Int J Androl. 1997 Feb;20(1):3-9.
9. Gindraux F, etal., Cell Tissue Res. 2007 Mar;327(3):471-83. Epub 2006 Nov 16.
10. Ignatius MJ, etal., J Cell Biol 1990 Aug;111(2):709-20.
11. Kitamura A, etal., Biochem Biophys Res Commun 2002 Dec 13;299(4):555-61.
12. Loufrani L, etal., Am J Physiol Heart Circ Physiol. 2008 Apr;294(4):H1906-13. Epub 2008 Feb 1.
13. MGD data from the GO Consortium
14. Nawata J, etal., Cardiovasc Res 1999 Aug 1;43(2):371-81.
15. NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. Olfa KZ, etal., Lab Invest. 2005 Dec;85(12):1507-16.
17. Pipeline to import KEGG annotations from KEGG into RGD
18. RGD automated data pipeline
19. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. RGD automated import pipeline for gene-chemical interactions
21. Schapira K, etal., Arterioscler Thromb Vasc Biol. 2005 Sep;25(9):1917-24. Epub 2005 Jun 23.
22. Szpirer C, etal., Mamm Genome 1998 Sep;9(9):721-34
23. Takada Y, etal., Genome Biol. 2007;8(5):215.
24. Tharmalingam S, etal., J Biol Chem. 2011 Nov 25;286(47):40922-33. doi: 10.1074/jbc.M111.265454. Epub 2011 Oct 3.
Additional References at PubMed
PMID:9553049   PMID:10386626   PMID:10528208   PMID:11518510   PMID:11767049   PMID:15592458   PMID:16271045   PMID:16973387   PMID:17161391   PMID:19056867   PMID:19581412   PMID:19933311  
PMID:19946888   PMID:20563599   PMID:21423176   PMID:22847004   PMID:23023225   PMID:23658023   PMID:24823363   PMID:26520903   PMID:27108411   PMID:27484337  


Genomics

Comparative Map Data
Itga1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2246,646,125 - 46,812,237 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl246,653,193 - 46,812,238 (-)Ensembl
Rnor_6.0247,127,403 - 47,281,387 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl247,127,219 - 47,281,421 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0271,666,601 - 71,823,120 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4247,107,849 - 47,206,261 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1247,036,084 - 47,134,488 (-)NCBI
Celera242,407,780 - 42,559,904 (-)NCBICelera
Cytogenetic Map2q14NCBI
ITGA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38552,787,916 - 52,959,209 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl552,787,916 - 52,959,209 (+)EnsemblGRCh38hg38GRCh38
GRCh37552,083,750 - 52,255,039 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36552,119,893 - 52,285,242 (+)NCBINCBI36hg18NCBI36
Build 34552,119,892 - 52,285,241NCBI
Celera549,037,686 - 49,203,085 (+)NCBI
Cytogenetic Map5q11.2NCBI
HuRef549,055,982 - 49,221,542 (+)NCBIHuRef
CHM1_1552,086,786 - 52,252,111 (+)NCBICHM1_1
Itga1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3913115,094,615 - 115,238,500 (-)NCBIGRCm39mm39
GRCm39 Ensembl13115,089,632 - 115,238,500 (-)Ensembl
GRCm3813114,958,079 - 115,101,964 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl13114,953,096 - 115,101,964 (-)EnsemblGRCm38mm10GRCm38
MGSCv3713115,748,287 - 115,892,172 (-)NCBIGRCm37mm9NCBIm37
MGSCv3613116,080,957 - 116,222,842 (-)NCBImm8
Celera13119,308,615 - 119,462,806 (-)NCBICelera
Cytogenetic Map13D2.2NCBI
cM Map1364.61NCBI
Itga1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544614,446,300 - 14,577,605 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544614,439,571 - 14,582,236 (-)NCBIChiLan1.0ChiLan1.0
ITGA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1562,692,673 - 62,865,771 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl562,692,673 - 62,865,769 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0561,073,507 - 61,247,565 (-)NCBIMhudiblu_PPA_v0panPan3
ITGA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1462,287,823 - 62,455,940 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl462,293,082 - 62,455,650 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha462,062,740 - 62,230,868 (-)NCBI
ROS_Cfam_1.0462,785,836 - 62,953,966 (-)NCBI
ROS_Cfam_1.0 Ensembl462,791,553 - 62,953,332 (-)Ensembl
UMICH_Zoey_3.1462,561,013 - 62,729,609 (-)NCBI
UNSW_CanFamBas_1.0462,685,631 - 62,847,651 (-)NCBI
UU_Cfam_GSD_1.0463,212,383 - 63,380,850 (-)NCBI
Itga1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213205,502,947 - 205,654,957 (-)NCBI
SpeTri2.0NW_00493648014,442,481 - 14,591,574 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ITGA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1632,130,235 - 32,304,592 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11632,130,265 - 32,309,917 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21633,940,969 - 34,132,541 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ITGA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1449,081,687 - 49,248,321 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl449,082,787 - 49,246,186 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660821,876,808 - 2,052,640 (-)NCBIVero_WHO_p1.0
Itga1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247596,397,743 - 6,543,652 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH130277  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2246,797,854 - 46,798,034 (+)MAPPERmRatBN7.2
Rnor_6.0247,266,760 - 47,266,939NCBIRnor6.0
Rnor_5.0271,808,493 - 71,808,672UniSTSRnor5.0
RGSC_v3.4245,900,725 - 45,900,904UniSTSRGSC3.4
Celera242,545,598 - 42,545,777UniSTS
RH 3.4 Map2307.3UniSTS
Cytogenetic Map2q14UniSTS
Cytogenetic Map2q16-q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1643006Pain1Pain QTL 13.630.005mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)22699957148268661Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22715716072157160Rat
1300160Hrtrt3Heart rate QTL 33.62heart pumping trait (VT:2000009)absolute change in heart rate (CMO:0000534)22997159351729300Rat
10755434Coatc7Coat color QTL 70.04794coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23064806575648065Rat
10755436Coatc8Coat color QTL 80.02431coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23502311780023117Rat
61371Edpm1Estrogen-dependent pituitary mass QTL 140.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)23513484188029593Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)240067944102785628Rat
12879863Bp402Blood pressure QTL 4020.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)24112578956532139Rat
1300155Bp174Blood pressure QTL 1744.09arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)24280460760653831Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607157142209Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
2293676Bmd19Bone mineral density QTL 1910.70.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)243162366111362592Rat
2293682Bmd24Bone mineral density QTL 248.90.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)243162366111362592Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243162366148478373Rat
631208Bw1Body weight QTL15.09mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)24317101783575226Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:76
Count of miRNA genes:68
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000016353
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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.


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 40 20 10 13 10 3 3 35 10 11 3
Low 3 3 37 31 6 31 5 8 74 31 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000086114   ⟹   ENSRNOP00000074337
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl246,657,201 - 46,812,238 (-)Ensembl
Rnor_6.0 Ensembl247,127,219 - 47,281,421 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106157   ⟹   ENSRNOP00000086956
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl246,653,193 - 46,812,238 (-)Ensembl
RefSeq Acc Id: NM_030994   ⟹   NP_112256
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2246,653,188 - 46,812,237 (-)NCBI
Rnor_6.0247,127,403 - 47,281,387 (-)NCBI
Rnor_5.0271,666,601 - 71,823,120 (-)NCBI
RGSC_v3.4247,107,849 - 47,206,261 (-)RGD
Celera242,407,780 - 42,559,904 (-)RGD
Sequence:
RefSeq Acc Id: XM_039101763   ⟹   XP_038957691
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2246,646,125 - 46,811,914 (-)NCBI
Protein Sequences
Protein RefSeqs NP_112256 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957691 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA36384 (Get FASTA)   NCBI Sequence Viewer  
  EDM10391 (Get FASTA)   NCBI Sequence Viewer  
  EDM10392 (Get FASTA)   NCBI Sequence Viewer  
  P18614 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_112256   ⟸   NM_030994
- Peptide Label: precursor
- UniProtKB: P18614 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074337   ⟸   ENSRNOT00000086114
RefSeq Acc Id: XP_038957691   ⟸   XM_039101763
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000086956   ⟸   ENSRNOT00000106157
Protein Domains
VWFA

Protein Structures
Name Modeller Protein Id AA Range Protein Structure Video
AF-P18614-F1-model_v2 AlphaFold P18614 1-1180 view protein structure  

Transcriptome

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

Promoters
RGD ID:13691151
Promoter ID:EPDNEW_R1675
Type:multiple initiation site
Name:Itga1_2
Description:integrin subunit alpha 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R1676  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0247,281,160 - 47,281,220EPDNEW
RGD ID:13691152
Promoter ID:EPDNEW_R1676
Type:multiple initiation site
Name:Itga1_1
Description:integrin subunit alpha 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R1675  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0247,281,392 - 47,281,452EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 71809978 71809979 T G snv SR/JrHsd (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2923 AgrOrtholog
BioCyc Gene G2FUF-54324 BioCyc
Ensembl Genes ENSRNOG00000053550 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000074337 UniProtKB/Swiss-Prot
  ENSRNOP00000086956 ENTREZGENE
Ensembl Transcript ENSRNOT00000086114 UniProtKB/Swiss-Prot
  ENSRNOT00000106157 ENTREZGENE
Gene3D-CATH 2.130.10.130 UniProtKB/Swiss-Prot
  3.40.50.410 UniProtKB/Swiss-Prot
InterPro FG-GAP UniProtKB/Swiss-Prot
  Int_alpha_beta-p UniProtKB/Swiss-Prot
  Integrin_alpha UniProtKB/Swiss-Prot
  Integrin_alpha-2 UniProtKB/Swiss-Prot
  Integrin_alpha_C_CS UniProtKB/Swiss-Prot
  Integrin_alpha_N UniProtKB/Swiss-Prot
  Integrin_dom_sf UniProtKB/Swiss-Prot
  VWF_A UniProtKB/Swiss-Prot
  vWFA_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:25118 UniProtKB/Swiss-Prot
NCBI Gene 25118 ENTREZGENE
Pfam FG-GAP UniProtKB/Swiss-Prot
  Integrin_alpha2 UniProtKB/Swiss-Prot
  VWA UniProtKB/Swiss-Prot
PhenoGen Itga1 PhenoGen
PRINTS INTEGRINA UniProtKB/Swiss-Prot
PROSITE FG_GAP UniProtKB/Swiss-Prot
  INTEGRIN_ALPHA UniProtKB/Swiss-Prot
  VWFA UniProtKB/Swiss-Prot
SMART Int_alpha UniProtKB/Swiss-Prot
  VWA UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53300 UniProtKB/Swiss-Prot
  SSF69179 UniProtKB/Swiss-Prot
  SSF69318 UniProtKB/Swiss-Prot
UniProt ITA1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-23 Itga1  integrin subunit alpha 1  Itga1  integrin, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-02-09 Itga1  integrin, alpha 1  Itga1  integrin alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Itga1  integrin alpha 1    integrin, alpha 1  Name updated 629478 APPROVED
2002-06-10 Itga1  integrin, alpha 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function associates with the beta-1 chain to form a dual laminin/collagen receptor 729264
gene_process has a role in cell attachment and neurite outgrowth on laminin and collagen as well as in peripheral nerve regeneration  
gene_process involved in mesangial cell (MC) migration 727474
gene_regulation activity stimulated by Endothelin-1 (ET) in mesangial cells 727474