Washc3 (WASH complex subunit 3) - Rat Genome Database

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Gene: Washc3 (WASH complex subunit 3) Rattus norvegicus
Analyze
Symbol: Washc3
Name: WASH complex subunit 3
RGD ID: 1563761
Description: Predicted to be involved in actin filament polymerization and exocytosis. Predicted to be part of WASH complex. Orthologous to human WASHC3 (WASH complex subunit 3); PARTICIPATES IN retromer-mediated pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Ccdc53; coiled-coil domain containing 53; LOC299707; RGD1563761; similar to RIKEN cDNA 2900091E11; WASH complex subunit CCDC53
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8724,508,544 - 24,553,012 (+)NCBIGRCr8
mRatBN7.2722,621,078 - 22,665,550 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl722,621,078 - 22,690,696 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx724,615,718 - 24,660,180 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0726,778,427 - 26,822,893 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0726,555,458 - 26,599,927 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0728,762,417 - 28,809,286 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl728,762,417 - 28,809,280 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0728,872,399 - 28,917,934 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4724,894,880 - 24,942,581 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera719,784,271 - 19,828,542 (+)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
WASH complex  (IBA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Retromer and sorting nexins in endosomal sorting. Gallon M and Cullen PJ, Biochem Soc Trans. 2015 Feb;43(1):33-47. doi: 10.1042/BST20140290.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:19922875   PMID:27390154  


Genomics

Comparative Map Data
Washc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8724,508,544 - 24,553,012 (+)NCBIGRCr8
mRatBN7.2722,621,078 - 22,665,550 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl722,621,078 - 22,690,696 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx724,615,718 - 24,660,180 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0726,778,427 - 26,822,893 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0726,555,458 - 26,599,927 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0728,762,417 - 28,809,286 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl728,762,417 - 28,809,280 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0728,872,399 - 28,917,934 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4724,894,880 - 24,942,581 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera719,784,271 - 19,828,542 (+)NCBICelera
Cytogenetic Map7q13NCBI
WASHC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812102,012,840 - 102,062,124 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12102,012,840 - 102,062,149 (-)EnsemblGRCh38hg38GRCh38
GRCh3712102,406,618 - 102,455,902 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612100,930,848 - 100,980,029 (-)NCBINCBI36Build 36hg18NCBI36
Celera12102,070,738 - 102,119,920 (-)NCBICelera
Cytogenetic Map12q23.2NCBI
HuRef1299,466,365 - 99,515,550 (-)NCBIHuRef
CHM1_112102,373,375 - 102,422,566 (-)NCBICHM1_1
T2T-CHM13v2.012101,973,971 - 102,023,257 (-)NCBIT2T-CHM13v2.0
Washc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391088,036,954 - 88,160,001 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1088,036,955 - 88,082,020 (+)EnsemblGRCm39 Ensembl
GRCm381088,201,097 - 88,324,139 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1088,201,093 - 88,246,158 (+)EnsemblGRCm38mm10GRCm38
MGSCv371087,663,842 - 87,708,903 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361087,630,892 - 87,675,957 (+)NCBIMGSCv36mm8
Celera1090,178,752 - 90,223,621 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1043.7NCBI
WASHC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v210110,086,154 - 110,135,621 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan112110,082,554 - 110,132,019 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01299,600,287 - 99,649,731 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.112102,997,783 - 103,047,199 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12103,010,829 - 103,047,037 (-)Ensemblpanpan1.1panPan2
WASHC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11540,871,793 - 40,916,534 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1541,239,757 - 41,284,516 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01541,526,088 - 41,570,837 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1541,521,613 - 41,570,760 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11540,786,842 - 40,831,541 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01540,889,125 - 40,933,841 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01541,163,711 - 41,208,455 (-)NCBIUU_Cfam_GSD_1.0
Washc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494519,043,347 - 19,090,135 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649212,053,730 - 12,101,273 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649212,053,730 - 12,098,660 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
WASHC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl582,155,256 - 82,217,300 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1582,155,253 - 82,259,552 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
WASHC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11197,261,193 - 97,307,960 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1197,261,088 - 97,307,914 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037147,696,359 - 147,743,098 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Washc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247506,215,971 - 6,251,634 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247506,216,242 - 6,248,526 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Washc3
225 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:163
Count of miRNA genes:125
Interacting mature miRNAs:142
Transcripts:ENSRNOT00000006903
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)72055570529891047Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)71903280735526300Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
70207Niddm31Non-insulin dependent diabetes mellitus QTL 313.9blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)71816950526029351Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000006903   ⟹   ENSRNOP00000006903
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl722,621,078 - 22,665,544 (+)Ensembl
Rnor_6.0 Ensembl728,762,417 - 28,809,280 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000100629   ⟹   ENSRNOP00000090249
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl722,621,078 - 22,644,307 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000107294   ⟹   ENSRNOP00000096775
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl722,621,078 - 22,690,696 (+)Ensembl
RefSeq Acc Id: NM_001106776   ⟹   NP_001100246
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8724,508,544 - 24,553,012 (+)NCBI
mRatBN7.2722,621,078 - 22,665,550 (+)NCBI
Rnor_6.0728,762,417 - 28,809,286 (+)NCBI
Rnor_5.0728,872,399 - 28,917,934 (+)NCBI
RGSC_v3.4724,894,880 - 24,942,581 (+)RGD
Celera719,784,271 - 19,828,542 (+)RGD
Sequence:
RefSeq Acc Id: XM_006241199   ⟹   XP_006241261
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8724,508,549 - 24,552,859 (+)NCBI
mRatBN7.2722,621,110 - 22,665,397 (+)NCBI
Rnor_6.0728,762,448 - 28,809,133 (+)NCBI
Rnor_5.0728,872,399 - 28,917,934 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078687   ⟹   XP_038934615
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8724,508,572 - 24,542,557 (+)NCBI
mRatBN7.2722,621,109 - 22,655,104 (+)NCBI
RefSeq Acc Id: XM_063263195   ⟹   XP_063119265
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8724,508,560 - 24,542,557 (+)NCBI
RefSeq Acc Id: NP_001100246   ⟸   NM_001106776
- UniProtKB: D3ZKX1 (UniProtKB/TrEMBL),   A6IFN5 (UniProtKB/TrEMBL),   A0A8I6ATX8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241261   ⟸   XM_006241199
- Peptide Label: isoform X1
- UniProtKB: A0A8I6ATX8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000006903   ⟸   ENSRNOT00000006903
RefSeq Acc Id: XP_038934615   ⟸   XM_039078687
- Peptide Label: isoform X3
- UniProtKB: A0A8I6GIR0 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000096775   ⟸   ENSRNOT00000107294
Ensembl Acc Id: ENSRNOP00000090249   ⟸   ENSRNOT00000100629
RefSeq Acc Id: XP_063119265   ⟸   XM_063263195
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZKX1-F1-model_v2 AlphaFold D3ZKX1 1-194 view protein structure

Transcriptome

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

Promoters
RGD ID:13695124
Promoter ID:EPDNEW_R5649
Type:initiation region
Name:Washc3_1
Description:WASH complex subunit 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_6.0728,762,504 - 28,762,564EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563761 AgrOrtholog
BioCyc Gene G2FUF-34516 BioCyc
Ensembl Genes ENSRNOG00000005102 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006903.6 UniProtKB/TrEMBL
  ENSRNOT00000100629.1 UniProtKB/TrEMBL
  ENSRNOT00000107294.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.110 UniProtKB/TrEMBL
InterPro DUF2360_coiled-coil UniProtKB/TrEMBL
KEGG Report rno:299707 UniProtKB/TrEMBL
NCBI Gene 299707 ENTREZGENE
PANTHER PTHR13015 UniProtKB/TrEMBL
  WASH COMPLEX SUBUNIT 3 UniProtKB/TrEMBL
Pfam DUF2360 UniProtKB/TrEMBL
PhenoGen Washc3 PhenoGen
RatGTEx ENSRNOG00000005102 RatGTEx
UniProt A0A8I6ATX8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GIR0 ENTREZGENE, UniProtKB/TrEMBL
  A6IFN5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZKX1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-10-26 Washc3  WASH complex subunit 3  Ccdc53  coiled-coil domain containing 53  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Ccdc53  coiled-coil domain containing 53   Ccdc53_predicted  coiled-coil domain containing 53 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Ccdc53_predicted  coiled-coil domain containing 53 (predicted)  RGD1563761_predicted  similar to RIKEN cDNA 2900091E11 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1563761_predicted  similar to RIKEN cDNA 2900091E11 (predicted)  LOC299707  similar to RIKEN cDNA 2900091E11  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC299707  similar to RIKEN cDNA 2900091E11      Symbol and Name status set to provisional 70820 PROVISIONAL