Actn1 (actinin, alpha 1) - Rat Genome Database

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Gene: Actn1 (actinin, alpha 1) Rattus norvegicus
Analyze
Symbol: Actn1
Name: actinin, alpha 1
RGD ID: 70907
Description: Exhibits cytoskeletal regulatory protein binding activity and protein domain specific binding activity. Predicted to be involved in several processes, including actin cytoskeleton organization; focal adhesion assembly; and platelet formation. Localizes to several cellular components, including cytoskeleton; dendritic spine; and nucleus. Colocalizes with cortical actin cytoskeleton and stress fiber. Human ortholog(s) of this gene implicated in platelet-type bleeding disorder 15. Orthologous to human ACTN1 (actinin alpha 1); PARTICIPATES IN E-cadherin signaling pathway; syndecan signaling pathway; arrhythmogenic right ventricular cardiomyopathy pathway; INTERACTS WITH (R)-adrenaline; 1-naphthyl isothiocyanate; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: alpha-actinin cytoskeletal isoform; alpha-actinin-1; F-actin cross-linking protein; non-muscle alpha-actinin 1; non-muscle alpha-actinin-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Actn1_v3   Actn1_v2   Actn1_v1  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2698,998,553 - 99,093,334 (-)NCBI
Rnor_6.0 Ensembl6103,375,799 - 103,470,555 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06103,376,557 - 103,470,497 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06116,056,248 - 116,149,471 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46103,188,593 - 103,282,873 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16103,192,048 - 103,286,329NCBI
Celera697,355,796 - 97,450,012 (-)NCBICelera
Cytogenetic Map6q24NCBI
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
(R)-adrenaline  (EXP)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,3',4,4',5,5'-Heptachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-dinitrotoluene  (EXP)
2-nitrotoluene  (EXP)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
7,12-dimethyltetraphene  (EXP)
acetamide  (EXP)
acrolein  (ISO)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
androgen antagonist  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP)
bromochloroacetic acid  (EXP)
buspirone  (EXP)
Butylparaben  (EXP)
cadmium dichloride  (EXP)
cannabidiol  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
chloropicrin  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cyproconazole  (ISO)
DDE  (EXP)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diazinon  (ISO)
dibutyl phthalate  (EXP,ISO)
diclofenac  (EXP)
dicrotophos  (ISO)
dieldrin  (EXP)
dimethylarsinic acid  (EXP)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
entinostat  (ISO)
enzacamene  (EXP)
enzyme inhibitor  (ISO)
epoxiconazole  (EXP)
ethanol  (ISO)
fenamidone  (ISO)
folic acid  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
indometacin  (ISO)
ionomycin  (EXP)
isoflavones  (EXP)
leflunomide  (ISO)
linuron  (EXP)
metformin  (EXP)
methylmercury chloride  (ISO)
methylmercury(1+)  (ISO)
N-nitrosodimethylamine  (EXP)
ochratoxin A  (ISO)
oxycodone  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
phenylmercury acetate  (ISO)
potassium dichromate  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
progesterone  (ISO)
prostaglandin A1  (ISO)
quercitrin  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP)
sodium fluoride  (ISO)
Soman  (EXP)
starch  (EXP)
sulindac sulfide  (ISO)
tauroursodeoxycholic acid  (EXP)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
triadimefon  (ISO)
tributylstannane  (ISO)
Tributyltin oxide  (ISO)
troglitazone  (EXP)
ursodeoxycholic acid  (EXP)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Bunn RC, etal., Mol Biol Cell 1999 Apr;10(4):819-32.
2. Dhavan R, etal., J Neurosci. 2002 Sep 15;22(18):7879-91.
3. GOA data from the GO Consortium
4. Kremerskothen J, etal., Biochem Biophys Res Commun 2002 Jul 19;295(3):678-81.
5. Kremerskothen J, etal., J Neurochem. 2006 Mar;96(6):1659-66. doi: 10.1111/j.1471-4159.2006.03679.x. Epub 2006 Feb 8.
6. Kurklinsky S, etal., J Neurochem. 2011 Apr;117(1):48-60. doi: 10.1111/j.1471-4159.2011.07169.x. Epub 2011 Feb 9.
7. Li Q, etal., Hum Mol Genet. 2005 Jun 15;14(12):1587-603. Epub 2005 Apr 20.
8. MGD data from the GO Consortium
9. Miyazaki K, etal., Exp Cell Res. 2012 Aug 15;318(14):1716-25. doi: 10.1016/j.yexcr.2012.05.006. Epub 2012 May 30.
10. NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. OMIM Disease Annotation Pipeline
12. Ooshio T, etal., J Biol Chem 2004 Jul 23;279(30):31365-73. Epub 2004 May 12.
13. Pipeline to import KEGG annotations from KEGG into RGD
14. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
15. RGD automated data pipeline
16. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. RGD automated import pipeline for gene-chemical interactions
18. Ridinger H, etal., Exp Mol Pathol. 2009 Feb;86(1):23-31. Epub 2008 Nov 27.
19. Sherniakov MA Voen Med Zh 1978 Nov;(11):20-2.
20. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
21. Torrado M, etal., Invest Ophthalmol Vis Sci 2004 Nov;45(11):3955-63.
22. Vallenius T, etal., Exp Cell Res 2004 Feb 1;293(1):117-28.
Additional References at PubMed
PMID:7750553   PMID:7983147   PMID:11223950   PMID:11274145   PMID:11732910   PMID:12493766   PMID:12837758   PMID:15465019   PMID:15665106   PMID:15988023   PMID:16025302   PMID:16043482  
PMID:16170337   PMID:16502470   PMID:16807302   PMID:16820411   PMID:17298598   PMID:17311919   PMID:17854826   PMID:17944866   PMID:18332105   PMID:18519573   PMID:19056867   PMID:19160484  
PMID:19199708   PMID:19943616   PMID:20124353   PMID:20215401   PMID:20368620   PMID:21266579   PMID:21362503   PMID:21423176   PMID:21784188   PMID:22114352   PMID:22351778   PMID:22772996  
PMID:22871113   PMID:23434115   PMID:23533145   PMID:23890175   PMID:24069336   PMID:24364879   PMID:24625528   PMID:24780915   PMID:25931508   PMID:26316108   PMID:29429936   PMID:29476059  
PMID:30039887  


Genomics

Candidate Gene Status
Actn1 is a candidate Gene for QTL Uae22
Comparative Map Data
Actn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2698,998,553 - 99,093,334 (-)NCBI
Rnor_6.0 Ensembl6103,375,799 - 103,470,555 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06103,376,557 - 103,470,497 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06116,056,248 - 116,149,471 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46103,188,593 - 103,282,873 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16103,192,048 - 103,286,329NCBI
Celera697,355,796 - 97,450,012 (-)NCBICelera
Cytogenetic Map6q24NCBI
ACTN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1468,874,128 - 68,979,440 (-)EnsemblGRCh38hg38GRCh38
GRCh381468,874,123 - 68,979,302 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371469,340,845 - 69,446,019 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361468,410,793 - 68,515,709 (-)NCBINCBI36hg18NCBI36
Build 341468,410,792 - 68,515,709NCBI
Celera1449,401,716 - 49,506,993 (-)NCBI
Cytogenetic Map14q24.1NCBI
HuRef1449,510,917 - 49,616,121 (-)NCBIHuRef
CHM1_11469,279,215 - 69,384,488 (-)NCBICHM1_1
Actn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391280,214,316 - 80,307,165 (-)NCBIGRCm39mm39
GRCm39 Ensembl1280,214,321 - 80,307,145 (-)Ensembl
GRCm381280,167,542 - 80,260,420 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1280,167,547 - 80,260,371 (-)EnsemblGRCm38mm10GRCm38
MGSCv371281,268,529 - 81,361,358 (-)NCBIGRCm37mm9NCBIm37
MGSCv361281,086,387 - 81,179,156 (-)NCBImm8
Celera1281,632,311 - 81,725,181 (-)NCBICelera
Cytogenetic Map12C3NCBI
cM Map1236.49NCBI
Actn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554661,388,507 - 1,480,282 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554661,388,507 - 1,480,990 (+)NCBIChiLan1.0ChiLan1.0
ACTN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11468,335,694 - 68,440,836 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1468,335,694 - 68,440,836 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01449,460,390 - 49,565,986 (-)NCBIMhudiblu_PPA_v0panPan3
ACTN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1842,714,806 - 42,808,318 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl842,712,142 - 42,808,323 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha842,404,474 - 42,497,710 (-)NCBI
ROS_Cfam_1.0842,945,028 - 43,038,491 (-)NCBI
UMICH_Zoey_3.1842,559,338 - 42,652,710 (-)NCBI
UNSW_CanFamBas_1.0842,634,268 - 42,727,356 (-)NCBI
UU_Cfam_GSD_1.0842,993,500 - 43,086,762 (-)NCBI
Actn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864061,974,520 - 62,067,210 (+)NCBI
SpeTri2.0NW_00493649512,124,489 - 12,217,223 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ACTN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl792,550,007 - 92,644,842 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1792,550,132 - 92,644,842 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2798,863,871 - 98,874,025 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ACTN1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12446,089,989 - 46,196,897 (-)NCBI
ChlSab1.1 Ensembl2446,085,751 - 46,196,886 (-)Ensembl
Vero_WHO_p1.0NW_02366605334,323,625 - 34,430,616 (-)NCBI
Actn1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473432,097,364 - 32,190,162 (+)NCBI

Position Markers
C77473  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2698,998,858 - 98,998,992 (+)MAPPER
Rnor_6.06103,376,175 - 103,376,308NCBIRnor6.0
Rnor_5.06116,055,867 - 116,055,999UniSTSRnor5.0
RGSC_v3.46103,188,211 - 103,188,344UniSTSRGSC3.4
Celera697,355,417 - 97,355,550UniSTS
Cytogenetic Map6q24UniSTS
RH142024  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2699,000,729 - 99,000,918 (+)MAPPER
Rnor_6.06103,378,046 - 103,378,234NCBIRnor6.0
Rnor_5.06116,057,737 - 116,057,925UniSTSRnor5.0
RGSC_v3.46103,190,082 - 103,190,270UniSTSRGSC3.4
Celera697,357,285 - 97,357,473UniSTS
RH 3.4 Map6692.1UniSTS
Cytogenetic Map6q24UniSTS
BE119221  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2699,091,243 - 99,091,419 (+)MAPPER
Rnor_6.06103,468,554 - 103,468,729NCBIRnor6.0
Rnor_5.06116,147,528 - 116,147,703UniSTSRnor5.0
RGSC_v3.46103,280,930 - 103,281,105UniSTSRGSC3.4
Celera697,448,069 - 97,448,244UniSTS
RH 3.4 Map6690.0UniSTS
Cytogenetic Map6q24UniSTS
BE098731  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2699,094,236 - 99,094,390 (+)MAPPER
Rnor_6.06103,471,547 - 103,471,700NCBIRnor6.0
Rnor_5.06116,150,521 - 116,150,674UniSTSRnor5.0
RGSC_v3.46103,283,923 - 103,284,076UniSTSRGSC3.4
Celera697,451,062 - 97,451,215UniSTS
RH 3.4 Map6711.3UniSTS
Cytogenetic Map6q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)648432758108268790Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)660606431108154445Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)660606431108154445Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)662263348107263348Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)666129520111129520Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)671206251116206251Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)675449871120449871Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)675623277120276465Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)675623277120623277Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)676902247114203334Rat
2293837Kiddil1Kidney dilation QTL 13.7kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)684763275108464097Rat
2293842Kiddil3Kidney dilation QTL 34.3kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)684763275108464097Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)686422697115379601Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)687418448111129520Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)688507712133507712Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)689631358134631358Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)689631358134631358Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)692879510137879510Rat
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)693706176111134673Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)697949772133849286Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:64
Count of miRNA genes:58
Interacting mature miRNAs:63
Transcripts:ENSRNOT00000068522
Prediction methods: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 3 32 45 30 19 30 74 33 33 11
Low 11 12 11 11 8 11 2 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000079824   ⟹   ENSRNOP00000074946
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6103,375,873 - 103,470,555 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088795   ⟹   ENSRNOP00000069598
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6103,376,557 - 103,470,501 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091560   ⟹   ENSRNOP00000068851
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6103,375,799 - 103,470,427 (-)Ensembl
RefSeq Acc Id: NM_031005   ⟹   NP_112267
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2698,998,553 - 99,093,245 (-)NCBI
Rnor_6.06103,376,557 - 103,470,497 (-)NCBI
Rnor_5.06116,056,248 - 116,149,471 (-)NCBI
RGSC_v3.46103,188,593 - 103,282,873 (-)RGD
Celera697,355,796 - 97,450,012 (-)RGD
Sequence:
RefSeq Acc Id: XM_039112992   ⟹   XP_038968920
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2698,998,556 - 99,093,334 (-)NCBI
RefSeq Acc Id: XM_039112993   ⟹   XP_038968921
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2698,998,556 - 99,093,332 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_112267   ⟸   NM_031005
- UniProtKB: Q9Z1P2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074946   ⟸   ENSRNOT00000079824
RefSeq Acc Id: ENSRNOP00000068851   ⟸   ENSRNOT00000091560
RefSeq Acc Id: ENSRNOP00000069598   ⟸   ENSRNOT00000088795
RefSeq Acc Id: XP_038968920   ⟸   XM_039112992
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968921   ⟸   XM_039112993
- Peptide Label: isoform X2
Protein Domains
Calponin-homology (CH)   EF-hand

Transcriptome

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

Promoters
RGD ID:13694699
Promoter ID:EPDNEW_R5221
Type:initiation region
Name:Actn1_1
Description:actinin, alpha 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06103,470,564 - 103,470,624EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70907 AgrOrtholog
Ensembl Genes ENSRNOG00000056756 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000068851 UniProtKB/TrEMBL
  ENSRNOP00000069598 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000074946 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000079824 UniProtKB/TrEMBL
  ENSRNOT00000088795 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000091560 UniProtKB/TrEMBL
Gene3D-CATH 1.10.418.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7099133 IMAGE-MGC_LOAD
InterPro Actinin_actin-bd_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CH-domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CH_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand-dom_pair UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand_Ca_insen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Spectrin/alpha-actinin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Spectrin_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:81634 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91658 IMAGE-MGC_LOAD
NCBI Gene 81634 ENTREZGENE
Pfam EF-hand_8 UniProtKB/TrEMBL
  EFhand_Ca_insen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00307 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Spectrin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Actn1 PhenoGen
PROSITE ACTININ_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ACTININ_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PS50021 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART EFh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00033 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SPEC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF47576 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt ACTN1_RAT UniProtKB/Swiss-Prot
  Q6GMN8_RAT UniProtKB/TrEMBL
  Q6T487_RAT UniProtKB/TrEMBL
  Q9Z1P2 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-07-09 Actn1  actinin, alpha 1      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains has an N-terminal region containing two actin-binding motifs, a central four spectrin-like domain with the dimer forming sequence and a C-terminal domain with two EF hand motifs 625419
gene_expression expressed in the adult brain, with highest in neurons of the hippocampus, cortex, and caudate putamen while the cerebellum and other subcortical structures showed low expression 625419
gene_expression expressed in the adult rat brain 625419