Arpc1b (actin related protein 2/3 complex, subunit 1B) - Rat Genome Database

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Gene: Arpc1b (actin related protein 2/3 complex, subunit 1B) Rattus norvegicus
Analyze
Symbol: Arpc1b
Name: actin related protein 2/3 complex, subunit 1B
RGD ID: 2155
Description: Predicted to have actin filament binding activity. Predicted to be a structural constituent of cytoskeleton. Involved in response to estradiol and response to estrogen. Localizes to tubulobulbar complex. Human ortholog(s) of this gene implicated in gastritis; immunodeficiency 71; and myelodysplastic syndrome. Orthologous to human ARPC1B (actin related protein 2/3 complex subunit 1B); PARTICIPATES IN insulin responsive facilitative sugar transporter mediated glucose transport pathway; platelet-derived growth factor signaling pathway; Rab family mediated signaling pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: actin-related protein 2/3 complex subunit 1B; Actin-related protein complex 1b; arp2/3 complex 41 kDa subunit; p41-ARC; p41Arc
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2129,482,176 - 9,495,772 (-)NCBI
Rnor_6.0 Ensembl1211,252,296 - 11,265,865 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01211,252,300 - 11,265,849 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01213,321,403 - 13,334,951 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4129,796,269 - 9,803,639 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1129,826,196 - 9,833,567 (-)NCBI
Celera1211,287,122 - 11,300,659 (-)NCBICelera
Cytogenetic Map12p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2,4-trimethylbenzene  (EXP)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-nitrofluorene  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
9-cis-retinoic acid  (EXP)
aconitine  (EXP)
acrolein  (ISO)
acrylamide  (EXP)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aripiprazole  (EXP)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bexarotene  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
bisphenol F  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
diethylstilbestrol  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
elemental selenium  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
genistein  (ISO)
glafenine  (EXP)
indometacin  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (EXP)
naphthalenes  (EXP)
nickel atom  (ISO)
ozone  (ISO)
p-toluidine  (EXP)
paracetamol  (ISO)
phenobarbital  (ISO)
pirinixic acid  (EXP)
resveratrol  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
sulindac sulfide  (ISO)
sunitinib  (ISO)
testosterone  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
1. Auzair LB, etal., Eur Arch Otorhinolaryngol. 2015 Jul 3.
2. Belickova M, etal., Clin Lymphoma Myeloma Leuk. 2012 Oct;12(5):375-83. doi: 10.1016/j.clml.2012.04.003. Epub 2012 May 18.
3. Cai L, etal., Cell. 2008 Sep 5;134(5):828-42. doi: 10.1016/j.cell.2008.06.054.
4. Chiu TT, etal., Mol Biol Cell. 2010 Oct 15;21(20):3529-39. doi: 10.1091/mbc.E10-04-0316. Epub 2010 Aug 25.
5. D'Souza R, etal., Endocrinology. 2009 Apr;150(4):1861-9. doi: 10.1210/en.2008-1232. Epub 2008 Dec 18.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. GOA data from the GO Consortium
8. Kaneda A, etal., Cancer Lett. 2004 Aug 30;212(2):203-10.
9. Kumar A, etal., Mol Cell Endocrinol. 2015 Mar 15;404:91-101. doi: 10.1016/j.mce.2014.12.029. Epub 2015 Jan 28.
10. MGD data from the GO Consortium
11. NCBI rat LocusLink and RefSeq merged data July 26, 2002
12. Pipeline to import KEGG annotations from KEGG into RGD
13. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
14. Prabakaran S, etal., Mol Psychiatry. 2004 Jul;9(7):684-97, 643.
15. RGD automated import pipeline for gene-chemical interactions
16. RGD comprehensive gene curation
17. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
18. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
19. Welch MD, etal., J Cell Biol 1997 Jul 28;138(2):375-84.
20. Yoshida T, etal., Gastric Cancer. 2013 Oct;16(4):488-97. doi: 10.1007/s10120-012-0230-x. Epub 2013 Jan 6.
Additional References at PubMed
PMID:11741539   PMID:15489334   PMID:20458337   PMID:21423176   PMID:23376485   PMID:27113856   PMID:28242260   PMID:28972183  


Genomics

Comparative Map Data
Arpc1b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2129,482,176 - 9,495,772 (-)NCBI
Rnor_6.0 Ensembl1211,252,296 - 11,265,865 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01211,252,300 - 11,265,849 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01213,321,403 - 13,334,951 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4129,796,269 - 9,803,639 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1129,826,196 - 9,833,567 (-)NCBI
Celera1211,287,122 - 11,300,659 (-)NCBICelera
Cytogenetic Map12p11NCBI
ARPC1B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl799,374,249 - 99,394,816 (+)EnsemblGRCh38hg38GRCh38
GRCh38799,374,254 - 99,394,816 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37798,972,353 - 98,992,439 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36798,810,265 - 98,830,360 (+)NCBINCBI36hg18NCBI36
Build 34798,616,979 - 98,637,053NCBI
Celera793,706,528 - 93,726,623 (+)NCBI
Cytogenetic Map7q22.1NCBI
HuRef793,608,035 - 93,628,135 (+)NCBIHuRef
CHM1_1798,902,377 - 98,922,501 (+)NCBICHM1_1
CRA_TCAGchr7v2798,332,071 - 98,352,197 (+)NCBI
Arpc1b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395145,051,066 - 145,064,996 (+)NCBIGRCm39mm39
GRCm39 Ensembl5145,051,025 - 145,067,515 (+)Ensembl
GRCm385145,114,256 - 145,128,186 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5145,114,215 - 145,130,705 (+)EnsemblGRCm38mm10GRCm38
MGSCv375145,875,125 - 145,889,055 (+)NCBIGRCm37mm9NCBIm37
MGSCv365145,367,857 - 145,381,713 (+)NCBImm8
Celera5142,106,218 - 142,120,149 (+)NCBICelera
Cytogenetic Map5G2NCBI
Arpc1b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546015,055,480 - 15,069,093 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495546015,055,753 - 15,069,093 (+)NCBIChiLan1.0ChiLan1.0
ARPC1B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17104,861,582 - 104,870,382 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7104,861,582 - 104,870,369 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0791,348,120 - 91,368,299 (+)NCBIMhudiblu_PPA_v0panPan3
ARPC1B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1610,192,299 - 10,198,383 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl610,178,462 - 10,198,309 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha611,819,059 - 11,832,117 (-)NCBI
ROS_Cfam_1.0610,192,483 - 10,205,575 (-)NCBI
UMICH_Zoey_3.1610,062,441 - 10,075,520 (-)NCBI
UNSW_CanFamBas_1.0610,040,965 - 10,054,042 (-)NCBI
UU_Cfam_GSD_1.0610,274,762 - 10,287,831 (-)NCBI
Arpc1b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344138,283,052 - 138,294,275 (-)NCBI
SpeTri2.0NW_0049367501,651,026 - 1,662,208 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ARPC1B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl36,220,939 - 6,342,637 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.136,329,737 - 6,342,641 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.236,520,442 - 6,527,677 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ARPC1B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12813,764,637 - 13,780,317 (-)NCBI
Vero_WHO_p1.0NW_0236660702,517,817 - 2,538,868 (+)NCBI
Arpc1b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474032,805,647 - 32,821,986 (+)NCBI

Position Markers
AW208418  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,482,384 - 9,482,495 (+)MAPPER
Rnor_6.01211,252,507 - 11,252,617NCBIRnor6.0
Rnor_5.01213,321,610 - 13,321,720UniSTSRnor5.0
RGSC_v3.4129,796,476 - 9,796,586UniSTSRGSC3.4
Celera1211,287,329 - 11,287,439UniSTS
Cytogenetic Map12p11UniSTS
RH127787  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,482,333 - 9,482,659 (+)MAPPER
mRatBN7.21531,903,244 - 31,903,431 (+)MAPPER
Rnor_6.01538,029,775 - 38,029,961NCBIRnor6.0
Rnor_6.01211,252,456 - 11,252,781NCBIRnor6.0
Rnor_5.01541,870,760 - 41,870,946UniSTSRnor5.0
Rnor_5.01213,321,559 - 13,321,884UniSTSRnor5.0
RGSC_v3.4129,796,425 - 9,796,750UniSTSRGSC3.4
RGSC_v3.41536,799,280 - 36,799,466UniSTSRGSC3.4
Celera1531,613,626 - 31,613,812UniSTS
Celera1211,287,278 - 11,287,603UniSTS
RH 3.4 Map15259.29UniSTS
Cytogenetic Map12p11UniSTS
Cytogenetic Map15p12UniSTS
RH129626  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21531,903,371 - 31,903,560 (+)MAPPER
mRatBN7.2129,482,210 - 9,482,393 (+)MAPPER
Rnor_6.01211,252,333 - 11,252,515NCBIRnor6.0
Rnor_6.01538,029,902 - 38,030,090NCBIRnor6.0
Rnor_5.01541,870,887 - 41,871,075UniSTSRnor5.0
Rnor_5.01213,321,436 - 13,321,618UniSTSRnor5.0
RGSC_v3.4129,796,302 - 9,796,484UniSTSRGSC3.4
RGSC_v3.41536,799,407 - 36,799,595UniSTSRGSC3.4
Celera1531,613,753 - 31,613,941UniSTS
Celera1211,287,155 - 11,287,337UniSTS
Cytogenetic Map15p12UniSTS
Cytogenetic Map12p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)1249257845492578Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12251344247513442Rat
724526Uae3Urinary albumin excretion QTL 34.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)12540609412355490Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12247568747475687Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12130749723Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12895459327911196Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12136919844Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12421005149210051Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12251344247513442Rat
1600391Edcs2Endometrial carcinoma susceptibility QTL23.50.01uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)12824960820590080Rat
1300174Bw15Body weight QTL 152.93body mass (VT:0001259)body weight loss (CMO:0001399)12111765163Rat
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12122650917Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121017588931975590Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)121025689031723732Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123758197Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6922362652716770Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922363052716770Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)1215081045150810Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1215081045150810Rat
7387292Kidm42Kidney mass QTL 423.030.0004kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)12138334225Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12978983452716770Rat
10450854Stl34Serum triglyceride level QTL 343.50.05blood LDL triglyceride amount (VT:0010699)blood lipoprotein triglyceride level (CMO:0002685)12122853017Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12123035872Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:49
Count of miRNA genes:35
Interacting mature miRNAs:42
Transcripts:ENSRNOT00000001315
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 43 57 41 19 41 8 11 74 35 40 11 8
Low 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001315   ⟹   ENSRNOP00000001315
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1211,252,296 - 11,265,865 (-)Ensembl
RefSeq Acc Id: NM_019289   ⟹   NP_062162
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,482,178 - 9,495,739 (-)NCBI
Rnor_6.01211,252,300 - 11,265,849 (-)NCBI
Rnor_5.01213,321,403 - 13,334,951 (-)NCBI
RGSC_v3.4129,796,269 - 9,803,639 (-)RGD
Celera1211,287,122 - 11,300,659 (-)RGD
Sequence:
RefSeq Acc Id: XM_039089713   ⟹   XP_038945641
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,482,176 - 9,495,772 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_062162   ⟸   NM_019289
- UniProtKB: O88656 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001315   ⟸   ENSRNOT00000001315
RefSeq Acc Id: XP_038945641   ⟸   XM_039089713
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13698419
Promoter ID:EPDNEW_R8943
Type:initiation region
Name:Arpc1b_1
Description:actin related protein 2/3 complex, subunit 1B
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_6.01211,265,834 - 11,265,894EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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:2155 AgrOrtholog
Ensembl Genes ENSRNOG00000000991 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000001315 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001315 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5622004 IMAGE-MGC_LOAD
InterPro ARC1B UniProtKB/Swiss-Prot
  ARPC1 UniProtKB/Swiss-Prot
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot
  WD40_repeat UniProtKB/Swiss-Prot
  WD40_repeat_dom UniProtKB/Swiss-Prot
  WD40_repeat_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:54227 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72489 IMAGE-MGC_LOAD
NCBI Gene 54227 ENTREZGENE
PANTHER PTHR10709 UniProtKB/Swiss-Prot
  PTHR10709:SF10 UniProtKB/Swiss-Prot
Pfam WD40 UniProtKB/Swiss-Prot
PhenoGen Arpc1b PhenoGen
PIRSF ARP2/3_su1 UniProtKB/Swiss-Prot
PROSITE WD_REPEATS_2 UniProtKB/Swiss-Prot
  WD_REPEATS_REGION UniProtKB/Swiss-Prot
SMART WD40 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50978 UniProtKB/Swiss-Prot
TIGR TC217626
UniProt ARC1B_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2003-04-09 Arpc1b  actin related protein 2/3 complex, subunit 1B    Actin-related protein complex 1b  Name updated 629478 APPROVED
2002-06-10 Arpc1b  Actin-related protein complex 1b      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function human homolog is a subunit of the Arp2/3 protein complex 631743
gene_process human homolog is involved in control of actin polymerization 631743