Ap5s1 (adaptor related protein complex 5 subunit sigma 1) - Rat Genome Database

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Gene: Ap5s1 (adaptor related protein complex 5 subunit sigma 1) Rattus norvegicus
Analyze
Symbol: Ap5s1
Name: adaptor related protein complex 5 subunit sigma 1
RGD ID: 1561852
Description: Predicted to be involved in double-strand break repair via homologous recombination and endosomal transport. Predicted to be located in nucleoplasm. Predicted to be part of AP-type membrane coat adaptor complex. Predicted to be active in cytosol; late endosome; and lysosome. Orthologous to human AP5S1 (adaptor related protein complex 5 subunit sigma 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: adaptor-related protein complex 5, sigma 1 subunit; AP-5 complex subunit sigma-1; hypothetical protein LOC499893; LOC499893; RGD1561852; similar to Protein C20orf29
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83138,882,634 - 138,885,940 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3138,882,634 - 138,888,899 (+)EnsemblGRCr8
mRatBN7.23118,429,618 - 118,432,929 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3118,429,637 - 118,432,926 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3122,323,931 - 122,327,243 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03130,923,309 - 130,926,616 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03128,580,032 - 128,583,344 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03123,754,035 - 123,757,349 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3123,754,057 - 123,757,359 (+)Ensemblrn6Rnor6.0
Rnor_5.03130,251,640 - 130,255,035 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43118,916,234 - 118,919,526 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3117,237,741 - 117,241,033 (+)NCBICelera
Cytogenetic Map3q36NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
AP-type membrane coat adaptor complex  (IBA,IEA,ISO)
cytosol  (IBA,IEA,ISO)
late endosome  (IBA,IEA,ISO)
lysosome  (IBA,IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:20613862   PMID:22022230  


Genomics

Comparative Map Data
Ap5s1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83138,882,634 - 138,885,940 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3138,882,634 - 138,888,899 (+)EnsemblGRCr8
mRatBN7.23118,429,618 - 118,432,929 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3118,429,637 - 118,432,926 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3122,323,931 - 122,327,243 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03130,923,309 - 130,926,616 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03128,580,032 - 128,583,344 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03123,754,035 - 123,757,349 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3123,754,057 - 123,757,359 (+)Ensemblrn6Rnor6.0
Rnor_5.03130,251,640 - 130,255,035 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43118,916,234 - 118,919,526 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3117,237,741 - 117,241,033 (+)NCBICelera
Cytogenetic Map3q36NCBI
AP5S1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38203,820,547 - 3,828,838 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl203,811,384 - 3,828,838 (+)Ensemblhg38GRCh38
GRCh37203,801,194 - 3,809,485 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36203,749,203 - 3,753,954 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34203,749,202 - 3,753,954NCBI
Celera203,863,077 - 3,867,828 (+)NCBICelera
Cytogenetic Map20p13NCBI
HuRef203,749,721 - 3,754,504 (+)NCBIHuRef
CHM1_1203,801,016 - 3,805,802 (+)NCBICHM1_1
T2T-CHM13v2.0203,851,488 - 3,859,779 (+)NCBIT2T-CHM13v2.0
Ap5s1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392131,052,280 - 131,055,434 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2131,048,998 - 131,055,434 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm382131,210,360 - 131,213,514 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2131,207,078 - 131,213,514 (+)Ensemblmm10GRCm38
MGSCv372131,036,176 - 131,039,250 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv362130,901,881 - 130,904,955 (+)NCBIMGSCv36mm8
Celera2132,436,277 - 132,439,341 (+)NCBICelera
Cytogenetic Map2F1NCBI
cM Map263.29NCBI
Ap5s1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541514,664,849 - 14,672,478 (+)Ensembl
ChiLan1.0NW_00495541514,665,450 - 14,669,456 (+)NCBIChiLan1.0ChiLan1.0
AP5S1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2214,785,611 - 4,790,772 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1204,782,442 - 4,796,080 (+)NCBINHGRI_mPanPan1
PanPan1.1 Ensembl203,659,526 - 3,664,347 (+)EnsemblpanPan2panpan1.1
AP5S1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12417,537,539 - 17,543,834 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2417,537,544 - 17,543,901 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2417,367,232 - 17,373,467 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02417,956,524 - 17,962,765 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2417,959,357 - 17,961,616 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12417,551,445 - 17,557,683 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02417,662,233 - 17,668,466 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02417,990,130 - 17,996,377 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ap5s1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640166,447,004 - 166,453,021 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648514,877,206 - 14,884,369 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493648514,880,338 - 14,884,383 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AP5S1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1731,894,391 - 31,902,166 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11731,896,117 - 31,906,833 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21736,230,496 - 36,236,088 (-)NCBISscrofa10.2Sscrofa10.2susScr3
AP5S1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1234,494,318 - 34,514,074 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl234,508,315 - 34,514,299 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660719,938,385 - 9,956,754 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ap5s1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247414,903,492 - 4,910,923 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247414,903,219 - 4,930,021 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Ap5s1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v15110,937,109 - 110,940,081 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ap5s1
33 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:36
Count of miRNA genes:34
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000034201
Prediction methods:Miranda, Rnahybrid
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1582233Insul10Insulin level QTL 105.40.0015blood insulin amount (VT:0001560)serum insulin level times blood glucose level (CMO:0002040)3133259579178259579Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)396509147141509147Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3129154923182114333Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)367641776167835660Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)358601291153936591Rat
7387306Bw124Body weight QTL 1243.20.0003body mass (VT:0001259)body weight (CMO:0000012)3104545086149545086Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3133134628178134628Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)381425008141509147Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)3112250810157250810Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)379649560177741895Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)396509147141509147Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3117537367162537367Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3125116475170116475Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3110225882155225882Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3136091420155634702Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)390755164141509147Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3122395989167395989Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)3131036586176036586Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3137114333182114333Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)3131036586176036586Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)398651826167012663Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)3125814931139636791Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3110634702155634702Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3116188400161188400Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 92 59 6 356 192 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000034201   ⟹   ENSRNOP00000031548
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3138,882,634 - 138,885,655 (+)Ensembl
mRatBN7.2 Ensembl3118,429,637 - 118,432,644 (+)Ensembl
Rnor_6.0 Ensembl3123,754,057 - 123,757,349 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000084671   ⟹   ENSRNOP00000072616
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3138,882,649 - 138,885,937 (+)Ensembl
mRatBN7.2 Ensembl3118,429,657 - 118,432,744 (+)Ensembl
Rnor_6.0 Ensembl3123,754,064 - 123,757,359 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000093861   ⟹   ENSRNOP00000091363
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3118,429,640 - 118,432,926 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000164731   ⟹   ENSRNOP00000099228
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3138,882,681 - 138,888,899 (+)Ensembl
RefSeq Acc Id: NM_001398912   ⟹   NP_001385841
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83138,882,634 - 138,885,940 (+)NCBI
mRatBN7.23118,429,623 - 118,432,929 (+)NCBI
RefSeq Acc Id: XM_039105699   ⟹   XP_038961627
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83138,882,635 - 138,885,066 (+)NCBI
mRatBN7.23118,429,618 - 118,432,055 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001385841 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961627 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL80233 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000031548.4
  ENSRNOP00000072616.2
  ENSRNOP00000099228
  ENSRNOP00000099228.1
Ensembl Acc Id: ENSRNOP00000072616   ⟸   ENSRNOT00000084671
Ensembl Acc Id: ENSRNOP00000031548   ⟸   ENSRNOT00000034201
RefSeq Acc Id: XP_038961627   ⟸   XM_039105699
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000091363   ⟸   ENSRNOT00000093861
RefSeq Acc Id: NP_001385841   ⟸   NM_001398912
- UniProtKB: A0A0G2K3F6 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000099228   ⟸   ENSRNOT00000164731

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K3F6-F1-model_v2 AlphaFold A0A0G2K3F6 1-200 view protein structure

Transcriptome

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

Promoters
RGD ID:13692447
Promoter ID:EPDNEW_R2972
Type:initiation region
Name:Ap5s1_1
Description:adaptor-related protein complex 5, sigma 1 subunit
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_6.03123,754,055 - 123,754,115EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561852 AgrOrtholog
BioCyc Gene G2FUF-47819 BioCyc
Ensembl Genes ENSRNOG00000021249 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034201.5 UniProtKB/TrEMBL
  ENSRNOT00000084671.3 UniProtKB/TrEMBL
  ENSRNOT00000164731 ENTREZGENE
  ENSRNOT00000164731.1 UniProtKB/TrEMBL
InterPro AP-5_subunit_s1 UniProtKB/TrEMBL
NCBI Gene 499893 ENTREZGENE
PANTHER AP-5 COMPLEX SUBUNIT SIGMA-1 UniProtKB/TrEMBL
  PTHR16120 UniProtKB/TrEMBL
Pfam AP-5_subunit_s1 UniProtKB/TrEMBL
PhenoGen Ap5s1 PhenoGen
RatGTEx ENSRNOG00000021249 RatGTEx
UniProt A0A0G2K3F6 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LBV3_RAT UniProtKB/TrEMBL
  D3ZGQ9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-03 Ap5s1  adaptor related protein complex 5 subunit sigma 1  Ap5s1  adaptor-related protein complex 5, sigma 1 subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-11 Ap5s1  adaptor-related protein complex 5, sigma 1 subunit  RGD1561852  similar to Protein C20orf29  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1561852  similar to Protein C20orf29   RGD1561852_predicted  similar to Protein C20orf29 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1561852_predicted  similar to Protein C20orf29 (predicted)  LOC499893  similar to Protein C20orf29  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499893  similar to Protein C20orf29      Symbol and Name status set to provisional 70820 PROVISIONAL