Ap4s1 (adaptor-related protein complex AP-4, sigma 1) - Rat Genome Database

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Gene: Ap4s1 (adaptor-related protein complex AP-4, sigma 1) Mus musculus
Analyze
Symbol: Ap4s1
Name: adaptor-related protein complex AP-4, sigma 1
RGD ID: 1323737
MGI Page MGI
Description: Predicted to be involved in vesicle-mediated transport. Predicted to act upstream of or within intracellular protein transport. Predicted to be located in trans-Golgi network. Predicted to be part of AP-4 adaptor complex. Predicted to be active in intracellular membrane-bounded organelle. Is expressed in embryo. Human ortholog(s) of this gene implicated in hereditary spastic paraplegia 52. Orthologous to human AP4S1 (adaptor related protein complex 4 subunit sigma 1).
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: adapter-related protein complex 4 subunit sigma-1; adaptor-related protein complex 4 subunit sigma-1; AI314282; AP-4 adapter complex subunit sigma-1; AP-4 adaptor complex subunit sigma-1; AP-4 complex subunit sigma-1; sigma-1 subunit of AP-4; sigma-4-adaptin; sigma4-adaptin
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391251,708,545 - 51,785,716 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1251,737,816 - 51,791,569 (+)EnsemblGRCm39 Ensembl
GRCm381251,680,481 - 51,738,933 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1251,691,033 - 51,744,786 (+)EnsemblGRCm38mm10GRCm38
MGSCv371252,791,953 - 52,839,926 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361252,612,657 - 52,660,551 (+)NCBIMGSCv36mm8
Celera1252,994,302 - 53,043,215 (+)NCBICelera
Cytogenetic Map12B3NCBI
cM Map1222.11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
2. MGDs mouse GO annotations MGD data from the GO Consortium
3. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:9714600   PMID:10066790   PMID:10349636   PMID:10436028   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11544199   PMID:12477932   PMID:14610273   PMID:15489334  
PMID:15782199   PMID:16141072   PMID:16141073   PMID:17062627   PMID:17967808   PMID:18799693   PMID:18973680   PMID:21267068   PMID:21620353   PMID:21677750   PMID:21873635   PMID:23897027  
PMID:24065543   PMID:24975939   PMID:25552650   PMID:28413018   PMID:32968282  


Genomics

Comparative Map Data
Ap4s1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391251,708,545 - 51,785,716 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1251,737,816 - 51,791,569 (+)EnsemblGRCm39 Ensembl
GRCm381251,680,481 - 51,738,933 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1251,691,033 - 51,744,786 (+)EnsemblGRCm38mm10GRCm38
MGSCv371252,791,953 - 52,839,926 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361252,612,657 - 52,660,551 (+)NCBIMGSCv36mm8
Celera1252,994,302 - 53,043,215 (+)NCBICelera
Cytogenetic Map12B3NCBI
cM Map1222.11NCBI
AP4S1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381431,025,106 - 31,096,450 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1431,025,106 - 31,130,996 (+)EnsemblGRCh38hg38GRCh38
GRCh371431,494,312 - 31,565,656 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361430,564,644 - 30,624,759 (+)NCBINCBI36Build 36hg18NCBI36
Build 341430,564,643 - 30,624,758NCBI
Celera1411,360,171 - 11,428,127 (+)NCBICelera
Cytogenetic Map14q12NCBI
HuRef1411,612,000 - 11,683,212 (+)NCBIHuRef
CHM1_11431,493,514 - 31,564,822 (+)NCBICHM1_1
T2T-CHM13v2.01425,222,939 - 25,294,259 (+)NCBIT2T-CHM13v2.0
Ap4s1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8674,863,742 - 74,916,907 (+)NCBIGRCr8
mRatBN7.2669,133,403 - 69,174,488 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl669,133,373 - 69,175,496 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx669,553,612 - 69,594,561 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0669,860,250 - 69,901,198 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0669,299,772 - 69,340,706 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0672,461,977 - 72,502,717 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl672,461,977 - 72,503,847 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0682,026,136 - 82,066,642 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4671,794,606 - 71,835,640 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1671,819,503 - 71,838,512 (+)NCBI
Celera668,009,030 - 68,050,287 (+)NCBICelera
Cytogenetic Map6q23NCBI
Ap4s1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540929,482,820 - 29,530,691 (-)NCBIChiLan1.0ChiLan1.0
AP4S1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21532,350,416 - 32,420,582 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11431,566,902 - 31,634,057 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01411,797,778 - 11,868,127 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11429,996,524 - 30,066,666 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1429,996,877 - 30,063,239 (+)Ensemblpanpan1.1panPan2
AP4S1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1810,342,988 - 10,397,171 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl810,343,510 - 10,397,175 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha810,269,299 - 10,323,907 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0810,444,018 - 10,498,667 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl810,445,703 - 10,527,220 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1810,127,733 - 10,182,039 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0810,204,122 - 10,258,401 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0810,488,466 - 10,543,254 (+)NCBIUU_Cfam_GSD_1.0
Ap4s1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864042,215,118 - 42,254,579 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049364945,720,474 - 5,758,888 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AP4S1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl768,393,285 - 68,471,722 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1768,420,286 - 68,475,643 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2773,306,594 - 73,328,725 (-)NCBISscrofa10.2Sscrofa10.2susScr3
AP4S1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11313,825,831 - 13,826,957 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666040190,142,419 - 190,143,441 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ap4s1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248201,214,662 - 1,265,243 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248201,214,991 - 1,265,051 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ap4s1
2648 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:100
Count of miRNA genes:87
Interacting mature miRNAs:99
Transcripts:ENSMUST00000021338
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142234Tmc1m3_mTmc1 modifier 3 (mouse)Not determined12541844077031203Mouse
27226753Femd7_mfemur midshaft diameter 7, 10 week (mouse)12955000084146774Mouse
13207568Tcq14_mtotal cholesterol QTL 14 (mouse)121166000197176774Mouse
13524839Ppiq10_mprepulse inhibition QTL 10 (mouse)121304319554945798Mouse
1558978Cplaq10_mcircadian period of locomotor activity 10 (mouse)Not determined121534102679040364Mouse
1301574Lmblgq5_mlimb length QTL 5 (mouse)Not determined121759644780956883Mouse
15039339Nmrs29_mNAFLD-associated magnetic resonance shift 29 (mouse)121782585251825852Mouse
10043848Hdlq90_mHDL QTL 90 (mouse)Not determined121783993951840081Mouse
1300870Ath18_matherosclerosis 18 (mouse)Not determined121825996652260067Mouse
12904956Edlmmq10_mextensor digitorum longus muscle mass QTL 10 (mouse)121973983353739833Mouse
1302172Skts5_mskin tumor susceptibility 5 (mouse)Not determined122214886656149016Mouse
1301989Hdlq18_mHDL QTL 18 (mouse)Not determined122916068563160884Mouse
1300636Gct2_mgranulosa cell tumorigenesis 2 (mouse)Not determined122916068563160884Mouse
4141843Moen3_mmodifier of engrailed QTL 3 (mouse)Not determined122980158463801733Mouse
14747008Mancz10_mmandible centroid size 10 (mouse)122986352263863522Mouse
10402492Dipa8_mdrug induced psychomotor activation 8 (mouse)Not determined123493387268934019Mouse
1300818Bbaa10_mB.burgdorferi-associated arthritis 10 (mouse)Not determined123509100465511019Mouse
4142002Tbqt3_mtibia bone quality traits 3 (mouse)Not determined1235285496109936243Mouse
1357479Splwt1_mspleen weight 1 (mouse)Not determined124169317590887526Mouse

Markers in Region
D12Mit237  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381251,738,999 - 51,739,298UniSTSGRCm38
MGSCv371252,839,986 - 52,840,285UniSTSGRCm37
Celera1253,043,275 - 53,043,574UniSTS
Cytogenetic Map12C1UniSTS
cM Map1222.0UniSTS
Whitehead Genetic1217.5UniSTS
Whitehead_YAC12 UniSTS
AI314282  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381251,738,600 - 51,738,701UniSTSGRCm38
MGSCv371252,839,587 - 52,839,688UniSTSGRCm37
Celera1253,042,876 - 53,042,977UniSTS
Cytogenetic Map12C1UniSTS
Whitehead/MRC_RH12427.3UniSTS


Expression


Sequence


RefSeq Acc Id: ENSMUST00000021338   ⟹   ENSMUSP00000021338
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1251,737,820 - 51,785,715 (+)Ensembl
GRCm38.p6 Ensembl1251,691,037 - 51,738,932 (+)Ensembl
RefSeq Acc Id: ENSMUST00000218820   ⟹   ENSMUSP00000151472
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1251,737,816 - 51,791,569 (+)Ensembl
GRCm38.p6 Ensembl1251,691,033 - 51,744,786 (+)Ensembl
RefSeq Acc Id: NM_001329698   ⟹   NP_001316627
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391251,737,749 - 51,785,716 (+)NCBI
GRCm381251,690,966 - 51,738,933 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001329699   ⟹   NP_001316628
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391251,737,749 - 51,785,716 (+)NCBI
GRCm381251,690,966 - 51,738,933 (+)NCBI
Sequence:
RefSeq Acc Id: NM_021710   ⟹   NP_068356
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391251,737,749 - 51,785,716 (+)NCBI
GRCm381251,690,966 - 51,738,933 (+)NCBI
MGSCv371252,791,953 - 52,839,926 (+)RGD
Celera1252,994,302 - 53,043,215 (+)RGD
cM Map12 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006515433   ⟹   XP_006515496
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391251,708,545 - 51,785,716 (+)NCBI
GRCm381251,680,481 - 51,738,933 (+)NCBI
Sequence:
RefSeq Acc Id: XM_036157170   ⟹   XP_036013063
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391251,748,145 - 51,785,716 (+)NCBI
Sequence:
RefSeq Acc Id: NP_068356   ⟸   NM_021710
- Peptide Label: isoform 2
- UniProtKB: Q9WVL1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006515496   ⟸   XM_006515433
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001316627   ⟸   NM_001329698
- Peptide Label: isoform 1
RefSeq Acc Id: NP_001316628   ⟸   NM_001329699
- Peptide Label: isoform 3
- UniProtKB: A0A1W2P708 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSMUSP00000151472   ⟸   ENSMUST00000218820
RefSeq Acc Id: ENSMUSP00000021338   ⟸   ENSMUST00000021338
RefSeq Acc Id: XP_036013063   ⟸   XM_036157170
- Peptide Label: isoform X1
Protein Domains
AP complex mu/sigma subunit

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9WVL1-F1-model_v2 AlphaFold Q9WVL1 1-144 view protein structure

Promoters
RGD ID:8678242
Promoter ID:EPDNEW_M17152
Type:initiation region
Name:Ap4s1_2
Description:Mus musculus adaptor-related protein complex AP-4, sigma 1 ,transcript variant 2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M17153  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381251,691,015 - 51,691,075EPDNEW
RGD ID:8678244
Promoter ID:EPDNEW_M17153
Type:single initiation site
Name:Ap4s1_1
Description:Mus musculus adaptor-related protein complex AP-4, sigma 1 ,transcript variant 2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M17152  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381251,691,133 - 51,691,193EPDNEW
RGD ID:6822725
Promoter ID:MM_KWN:11612
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day3,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   ES_Cell,   Kidney,   Lung,   MEF_B4,   Spleen
Transcripts:NM_021710,   UC007NMW.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361252,791,826 - 52,792,326 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1337065 AgrOrtholog
Ensembl Genes ENSMUSG00000020955 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000021338 ENTREZGENE
  ENSMUST00000021338.10 UniProtKB/Swiss-Prot
  ENSMUST00000218820 ENTREZGENE
  ENSMUST00000218820.2 UniProtKB/TrEMBL
Gene3D-CATH 3.30.450.60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro AP_complex_ssu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AP_mu_sigma_su UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Longin-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:11782 UniProtKB/Swiss-Prot
MGD MGI:1337065 ENTREZGENE
NCBI Gene 11782 ENTREZGENE
PANTHER ADAPTOR RELATED PROTEIN COMPLEX 4 SUBUNIT SIGMA 1 UniProtKB/TrEMBL
  AP-4 COMPLEX SUBUNIT SIGMA-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11753 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Clat_adaptor_s UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ap4s1 PhenoGen
PIRSF AP_complex_sigma UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF64356 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A1W2P708 ENTREZGENE, UniProtKB/TrEMBL
  AP4S1_MOUSE UniProtKB/Swiss-Prot
  Q99M60_MOUSE UniProtKB/TrEMBL
  Q9WVL1 ENTREZGENE