Acap3 (ArfGAP with coiled-coil, ankyrin repeat and PH domains 3) - Rat Genome Database

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Gene: Acap3 (ArfGAP with coiled-coil, ankyrin repeat and PH domains 3) Rattus norvegicus
Analyze
Symbol: Acap3
Name: ArfGAP with coiled-coil, ankyrin repeat and PH domains 3
RGD ID: 1310711
Description: Predicted to enable GTPase activator activity. Predicted to act upstream of or within neuron migration and regulation of neuron projection development. Predicted to be located in growth cone. Orthologous to human ACAP3 (ArfGAP with coiled-coil, ankyrin repeat and PH domains 3); PARTICIPATES IN endocytosis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol; bis(2-ethylhexyl) phthalate.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3; centaurin, beta 5; Centb5; LOC313772
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
GRCr85171,783,382 - 171,797,709 (+)NCBIGRCr8
mRatBN7.25166,501,150 - 166,515,477 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5166,500,781 - 166,515,481 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5169,205,960 - 169,220,285 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05171,027,381 - 171,041,706 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05170,989,913 - 171,004,239 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05173,340,060 - 173,354,756 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,340,060 - 173,354,755 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05176,815,678 - 176,830,374 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45172,749,741 - 172,764,436 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15172,760,695 - 172,773,599 (+)NCBI
Celera5164,701,505 - 164,716,200 (+)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
2. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:27330119   PMID:28919417  


Genomics

Comparative Map Data
Acap3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85171,783,382 - 171,797,709 (+)NCBIGRCr8
mRatBN7.25166,501,150 - 166,515,477 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5166,500,781 - 166,515,481 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5169,205,960 - 169,220,285 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05171,027,381 - 171,041,706 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05170,989,913 - 171,004,239 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05173,340,060 - 173,354,756 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,340,060 - 173,354,755 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05176,815,678 - 176,830,374 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45172,749,741 - 172,764,436 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15172,760,695 - 172,773,599 (+)NCBI
Celera5164,701,505 - 164,716,200 (+)NCBICelera
Cytogenetic Map5q36NCBI
ACAP3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811,292,391 - 1,307,930 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11,292,390 - 1,309,609 (-)EnsemblGRCh38hg38GRCh38
GRCh3711,227,771 - 1,243,310 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611,218,807 - 1,228,503 (-)NCBINCBI36Build 36hg18NCBI36
Build 3411,268,866 - 1,278,563NCBI
Celera11,337,872 - 1,353,397 (+)NCBICelera
Cytogenetic Map1p36.33NCBI
HuRef1498,970 - 514,519 (-)NCBIHuRef
CHM1_111,213,463 - 1,228,970 (-)NCBICHM1_1
T2T-CHM13v2.01723,917 - 739,479 (-)NCBIT2T-CHM13v2.0
Acap3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394155,976,332 - 155,991,708 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4155,976,279 - 155,991,708 (+)EnsemblGRCm39 Ensembl
GRCm384155,891,875 - 155,907,251 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4155,891,822 - 155,907,251 (+)EnsemblGRCm38mm10GRCm38
MGSCv374155,265,984 - 155,281,360 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364154,735,675 - 154,751,051 (+)NCBIMGSCv36mm8
Celera4158,162,838 - 158,177,746 (+)NCBICelera
Cytogenetic Map4E2NCBI
cM Map487.66NCBI
Acap3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554869,495,186 - 9,508,214 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554869,495,087 - 9,508,047 (+)NCBIChiLan1.0ChiLan1.0
ACAP3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21226,919,234 - 226,934,998 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11225,615,917 - 225,631,674 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0146,883 - 62,642 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.111,248,155 - 1,263,111 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11,249,719 - 1,259,645 (-)Ensemblpanpan1.1panPan2
ACAP3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1556,466,833 - 56,482,023 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl556,468,164 - 56,481,913 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha556,543,733 - 56,558,335 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0556,669,651 - 56,684,257 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl556,669,651 - 56,684,280 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1556,660,374 - 56,674,973 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0556,552,661 - 56,567,265 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0556,942,661 - 56,957,269 (-)NCBIUU_Cfam_GSD_1.0
Acap3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505827,615,667 - 27,629,099 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367371,836,897 - 1,848,989 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367371,836,851 - 1,850,279 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ACAP3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl663,579,304 - 63,593,435 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1663,579,291 - 63,593,429 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2658,048,113 - 58,091,501 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ACAP3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120130,143,085 - 130,157,716 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20130,143,520 - 130,157,730 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605434,709,327 - 34,724,115 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Acap3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248188,302,957 - 8,314,590 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248188,302,409 - 8,315,878 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Acap3
39 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:216
Count of miRNA genes:129
Interacting mature miRNAs:166
Transcripts:ENSRNOT00000067841
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5154828214166875058Rat

Markers in Region
RH134239  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25166,515,245 - 166,515,446 (+)MAPPERmRatBN7.2
Rnor_6.05173,354,525 - 173,354,725NCBIRnor6.0
Rnor_5.05176,830,143 - 176,830,343UniSTSRnor5.0
RGSC_v3.45172,764,206 - 172,764,406UniSTSRGSC3.4
Celera5164,715,970 - 164,716,170UniSTS
RH 3.4 Map51173.8UniSTS
Cytogenetic Map5q36UniSTS


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 2 6 13 72 18 34 11
Low 3 41 51 41 6 41 8 11 2 17 7 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067841   ⟹   ENSRNOP00000061938
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5166,500,781 - 166,515,476 (+)Ensembl
Rnor_6.0 Ensembl5173,340,060 - 173,354,755 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078306   ⟹   ENSRNOP00000073498
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5166,501,212 - 166,515,469 (+)Ensembl
Rnor_6.0 Ensembl5173,340,487 - 173,354,753 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101434   ⟹   ENSRNOP00000091826
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5166,501,221 - 166,514,981 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114207   ⟹   ENSRNOP00000086578
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5166,501,181 - 166,515,481 (+)Ensembl
RefSeq Acc Id: NM_001395748   ⟹   NP_001382677
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85171,783,382 - 171,797,709 (+)NCBI
mRatBN7.25166,501,150 - 166,515,477 (+)NCBI
RefSeq Acc Id: XM_063287838   ⟹   XP_063143908
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85171,783,382 - 171,797,709 (+)NCBI
RefSeq Acc Id: XM_063287839   ⟹   XP_063143909
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85171,783,643 - 171,797,709 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000061938   ⟸   ENSRNOT00000067841
RefSeq Acc Id: ENSRNOP00000073498   ⟸   ENSRNOT00000078306
RefSeq Acc Id: ENSRNOP00000086578   ⟸   ENSRNOT00000114207
RefSeq Acc Id: ENSRNOP00000091826   ⟸   ENSRNOT00000101434
RefSeq Acc Id: NP_001382677   ⟸   NM_001395748
- UniProtKB: A0A8I6GJX2 (UniProtKB/TrEMBL),   A0A8I6A5L6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063143908   ⟸   XM_063287838
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K5N8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063143909   ⟸   XM_063287839
- Peptide Label: isoform X2
Protein Domains
Arf-GAP   PH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K5N8-F1-model_v2 AlphaFold A0A0G2K5N8 1-833 view protein structure

Transcriptome

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

Promoters
RGD ID:13694357
Promoter ID:EPDNEW_R4862
Type:initiation region
Name:Acap3_1
Description:ArfGAP with coiled-coil, ankyrin repeat and PH domains 3
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_6.05173,340,455 - 173,340,515EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310711 AgrOrtholog
BioCyc Gene G2FUF-38888 BioCyc
Ensembl Genes ENSRNOG00000022307 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067841.3 UniProtKB/TrEMBL
  ENSRNOT00000078306.2 UniProtKB/TrEMBL
  ENSRNOT00000101434 ENTREZGENE
  ENSRNOT00000101434.1 UniProtKB/TrEMBL
  ENSRNOT00000114207.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.220.150 UniProtKB/TrEMBL
  1.20.1270.60 UniProtKB/TrEMBL
  1.25.40.20 UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/TrEMBL
InterPro ACAP1/2/3-like UniProtKB/TrEMBL
  ACAP3_BAR UniProtKB/TrEMBL
  AH/BAR-dom UniProtKB/TrEMBL
  Ankyrin_rpt UniProtKB/TrEMBL
  Ankyrin_rpt-contain_sf UniProtKB/TrEMBL
  ArfGAP UniProtKB/TrEMBL
  ARFGAP/RecO UniProtKB/TrEMBL
  ArfGAP_dom_sf UniProtKB/TrEMBL
  BAR_dom UniProtKB/TrEMBL
  PH_type UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
KEGG Report rno:313772 UniProtKB/TrEMBL
NCBI Gene 313772 ENTREZGENE
PANTHER ARF-GAP WITH COILED-COIL, ANK REPEAT AND PH DOMAIN-CONTAINING PROTEIN 3 UniProtKB/TrEMBL
  PTHR23180 UniProtKB/TrEMBL
Pfam Ank_2 UniProtKB/TrEMBL
  ArfGap UniProtKB/TrEMBL
  BAR_3 UniProtKB/TrEMBL
  PF00169 UniProtKB/TrEMBL
PhenoGen Acap3 PhenoGen
PRINTS REVINTRACTNG UniProtKB/TrEMBL
PROSITE ANK_REP_REGION UniProtKB/TrEMBL
  ANK_REPEAT UniProtKB/TrEMBL
  ARFGAP UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000022307 RatGTEx
SMART ANK UniProtKB/TrEMBL
  ArfGap UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
Superfamily-SCOP ANK UniProtKB/TrEMBL
  PH domain-like UniProtKB/TrEMBL
  SSF103657 UniProtKB/TrEMBL
  SSF57863 UniProtKB/TrEMBL
UniProt A0A0G2K5N8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A5L6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GJX2 ENTREZGENE, UniProtKB/TrEMBL
  D4A346_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-15 Acap3  ArfGAP with coiled-coil, ankyrin repeat and PH domains 3  Centb5  centaurin, beta 5   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Centb5  centaurin, beta 5   Centb5_predicted  centaurin, beta 5 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Centb5_predicted  centaurin, beta 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED