SNX4 (sorting nexin 4) - Rat Genome Database
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Gene: SNX4 (sorting nexin 4) Homo sapiens
Analyze
Symbol: SNX4
Name: sorting nexin 4
RGD ID: 1320273
HGNC Page HGNC
Description: Exhibits phosphatidylinositol binding activity and signaling receptor binding activity. Involved in endocytic recycling; positive regulation of histamine secretion by mast cell; and protein transport. Localizes to several cellular components, including SNARE complex; cytoplasmic dynein complex; and early endosome membrane.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: ATG24B; sorting nexin-4
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3125,446,650 - 125,520,202 (-)EnsemblGRCh38hg38GRCh38
GRCh383125,446,644 - 125,520,202 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh373125,165,494 - 125,239,046 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh373125,165,488 - 125,239,058 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363126,648,184 - 126,721,748 (-)NCBINCBI36hg18NCBI36
Build 343126,648,184 - 126,721,748NCBI
Celera3123,575,104 - 123,648,748 (-)NCBI
Cytogenetic Map3q21.2NCBI
HuRef3122,541,455 - 122,614,640 (-)NCBIHuRef
CHM1_13125,128,503 - 125,202,079 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
1. GOA_HUMAN data from the GO Consortium
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9819414   PMID:11278302   PMID:11279102   PMID:12477932   PMID:12668730   PMID:14702039   PMID:15489334   PMID:16169070   PMID:16344560   PMID:17110338   PMID:17319803   PMID:17994011  
PMID:18253931   PMID:19529763   PMID:20301317   PMID:20379614   PMID:21145461   PMID:21973056   PMID:21988832   PMID:22939629   PMID:23085988   PMID:24690921   PMID:25416956   PMID:25544563  
PMID:26186194   PMID:26638075   PMID:27880917   PMID:28109317   PMID:28514442   PMID:28712724   PMID:28718761   PMID:29568061   PMID:31073040   PMID:31413325   PMID:32296183  


Genomics

Comparative Map Data
SNX4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3125,446,650 - 125,520,202 (-)EnsemblGRCh38hg38GRCh38
GRCh383125,446,644 - 125,520,202 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh373125,165,494 - 125,239,046 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh373125,165,488 - 125,239,058 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363126,648,184 - 126,721,748 (-)NCBINCBI36hg18NCBI36
Build 343126,648,184 - 126,721,748NCBI
Celera3123,575,104 - 123,648,748 (-)NCBI
Cytogenetic Map3q21.2NCBI
HuRef3122,541,455 - 122,614,640 (-)NCBIHuRef
CHM1_13125,128,503 - 125,202,079 (-)NCBICHM1_1
Snx4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391633,071,826 - 33,119,932 (+)NCBIGRCm39mm39
GRCm381633,251,456 - 33,299,562 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1633,251,442 - 33,300,269 (+)EnsemblGRCm38mm10GRCm38
MGSCv371633,251,542 - 33,299,648 (+)NCBIGRCm37mm9NCBIm37
MGSCv361633,171,203 - 33,219,309 (+)NCBImm8
Celera1633,735,288 - 33,783,365 (+)NCBICelera
Cytogenetic Map16B3NCBI
Snx4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21167,460,872 - 67,518,143 (-)NCBI
Rnor_6.0 Ensembl1170,693,366 - 70,753,632 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01170,693,381 - 70,753,620 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01173,779,997 - 73,836,594 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41169,283,047 - 69,340,448 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11169,340,633 - 69,398,051 (-)NCBI
Celera1166,908,596 - 66,965,885 (-)NCBICelera
Cytogenetic Map11q22NCBI
Snx4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542724,520,125 - 24,579,589 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542724,520,125 - 24,579,589 (-)NCBIChiLan1.0ChiLan1.0
SNX4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13129,443,369 - 129,515,917 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3129,443,369 - 129,515,917 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03122,578,527 - 122,652,007 (-)NCBIMhudiblu_PPA_v0panPan3
SNX4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3328,419,128 - 28,469,488 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13328,413,586 - 28,468,546 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Snx4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004937215127,074 - 137,281 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNX4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13134,824,043 - 134,905,359 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113134,824,028 - 134,903,765 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SNX4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12255,311,896 - 55,389,174 (+)NCBI
ChlSab1.1 Ensembl2255,311,933 - 55,389,349 (+)Ensembl
Snx4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247311,522,467 - 1,585,793 (-)NCBI

Position Markers
SHGC-77294  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh373125,165,524 - 125,165,598UniSTSGRCh37
Build 363126,648,214 - 126,648,288RGDNCBI36
Celera3123,575,134 - 123,575,208RGD
Cytogenetic Map3q21.2UniSTS
HuRef3122,541,491 - 122,541,565UniSTS
TNG Radiation Hybrid Map311120.0UniSTS
GeneMap99-GB4 RH Map3447.29UniSTS
Whitehead-RH Map3546.0UniSTS
NCBI RH Map31078.0UniSTS
RH103376  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh373125,165,526 - 125,165,681UniSTSGRCh37
Build 363126,648,216 - 126,648,371RGDNCBI36
Celera3123,575,136 - 123,575,291RGD
Cytogenetic Map3q21.2UniSTS
HuRef3122,541,493 - 122,541,648UniSTS
GeneMap99-GB4 RH Map3446.51UniSTS
D3S4226  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh373125,165,526 - 125,165,673UniSTSGRCh37
Build 363126,648,216 - 126,648,363RGDNCBI36
Celera3123,575,136 - 123,575,283RGD
Cytogenetic Map3q21.2UniSTS
HuRef3122,541,493 - 122,541,640UniSTS
SNX4  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh373125,165,667 - 125,165,895UniSTSGRCh37
Celera3123,575,277 - 123,575,505UniSTS
HuRef3122,541,634 - 122,541,862UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1306
Count of miRNA genes:755
Interacting mature miRNAs:847
Transcripts:ENST00000251775, ENST00000465505, ENST00000471751, ENST00000473417, ENST00000482965, ENST00000536067
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.


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 sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 2380 1619 1680 603 1209 445 4078 1721 3105 397 1451 1607 174 1 1200 2623 6 2
Low 59 1362 46 21 730 20 279 475 629 22 9 6 1 4 165
Below cutoff 10 9 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000251775   ⟹   ENSP00000251775
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl3125,446,650 - 125,520,202 (-)Ensembl
RefSeq Acc Id: ENST00000465505   ⟹   ENSP00000420175
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl3125,476,695 - 125,504,744 (-)Ensembl
RefSeq Acc Id: ENST00000471751   ⟹   ENSP00000420526
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl3125,447,711 - 125,520,181 (-)Ensembl
RefSeq Acc Id: ENST00000473417
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl3125,469,444 - 125,520,191 (-)Ensembl
RefSeq Acc Id: ENST00000482965
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl3125,449,070 - 125,460,801 (-)Ensembl
RefSeq Acc Id: NM_003794   ⟹   NP_003785
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383125,446,650 - 125,520,202 (-)NCBI
GRCh373125,165,488 - 125,239,058 (-)NCBI
Build 363126,648,184 - 126,721,748 (-)NCBI Archive
Celera3123,575,104 - 123,648,748 (-)RGD
HuRef3122,541,455 - 122,614,640 (-)NCBI
CHM1_13125,128,503 - 125,202,079 (-)NCBI
Sequence:
RefSeq Acc Id: NR_073435
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383125,446,650 - 125,520,202 (-)NCBI
HuRef3122,541,455 - 122,614,640 (-)NCBI
CHM1_13125,128,503 - 125,202,079 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017007414   ⟹   XP_016862903
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383125,446,644 - 125,520,202 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_003785   ⟸   NM_003794
- UniProtKB: O95219 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_016862903   ⟸   XM_017007414
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSP00000420175   ⟸   ENST00000465505
RefSeq Acc Id: ENSP00000420526   ⟸   ENST00000471751
RefSeq Acc Id: ENSP00000251775   ⟸   ENST00000251775
Protein Domains
PX

Promoters
RGD ID:6865516
Promoter ID:EPDNEW_H5923
Type:initiation region
Name:SNX4_1
Description:sorting nexin 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh383125,520,202 - 125,520,262EPDNEW
RGD ID:6801712
Promoter ID:HG_KWN:46054
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_003794
Position:
Human AssemblyChrPosition (strand)Source
Build 363126,721,291 - 126,721,837 (-)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q13.33-21.2(chr3:121644209-125676353)x1 copy number loss See cases [RCV000051569] Chr3:121644209..125676353 [GRCh38]
Chr3:121363056..125395197 [GRCh37]
Chr3:122845746..126877887 [NCBI36]
Chr3:3q13.33-21.2		 pathogenic
GRCh38/hg38 3q13.32-21.2(chr3:119117166-125920734)x1 copy number loss See cases [RCV000051546] Chr3:119117166..125920734 [GRCh38]
Chr3:118836013..125639577 [GRCh37]
Chr3:120318703..127122267 [NCBI36]
Chr3:3q13.32-21.2		 pathogenic
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29		 pathogenic
GRCh38/hg38 3q13.2-21.3(chr3:112620977-128734134)x1 copy number loss See cases [RCV000139033] Chr3:112620977..128734134 [GRCh38]
Chr3:112339824..128452977 [GRCh37]
Chr3:113822514..129935667 [NCBI36]
Chr3:3q13.2-21.3		 pathogenic
GRCh38/hg38 3q13.33-21.3(chr3:121925147-126782249)x1 copy number loss See cases [RCV000140814] Chr3:121925147..126782249 [GRCh38]
Chr3:121643994..126501092 [GRCh37]
Chr3:123126684..127983782 [NCBI36]
Chr3:3q13.33-21.3		 pathogenic
GRCh38/hg38 3q11.1-24(chr3:93800620-145695381)x3 copy number gain See cases [RCV000142340] Chr3:93800620..145695381 [GRCh38]
Chr3:93519464..145413168 [GRCh37]
Chr3:95002154..146895858 [NCBI36]
Chr3:3q11.1-24		 pathogenic
GRCh38/hg38 3q13.32-21.3(chr3:118673898-126540730)x1 copy number loss See cases [RCV000143695] Chr3:118673898..126540730 [GRCh38]
Chr3:118392745..126259573 [GRCh37]
Chr3:119875435..127742263 [NCBI36]
Chr3:3q13.32-21.3		 pathogenic
GRCh37/hg19 3q21.2-21.3(chr3:124806350-126567150)x4 copy number gain See cases [RCV000448957] Chr3:124806350..126567150 [GRCh37]
Chr3:3q21.2-21.3		 uncertain significance
GRCh37/hg19 3q21.2-21.3(chr3:124990032-126088215)x3 copy number gain See cases [RCV000510692] Chr3:124990032..126088215 [GRCh37]
Chr3:3q21.2-21.3		 uncertain significance
GRCh37/hg19 3q21.2-21.3(chr3:124981934-126087100)x3 copy number gain See cases [RCV000511803] Chr3:124981934..126087100 [GRCh37]
Chr3:3q21.2-21.3		 uncertain significance
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986) copy number gain See cases [RCV000512358] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986)x3 copy number gain See cases [RCV000511055] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61495-197838262)x3 copy number gain not provided [RCV000742138] Chr3:61495..197838262 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:60174-197948027)x3 copy number gain not provided [RCV000742133] Chr3:60174..197948027 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3q21.2-21.3(chr3:124369671-126423192) copy number loss not provided [RCV000767706] Chr3:124369671..126423192 [GRCh37]
Chr3:3q21.2-21.3		 likely pathogenic
GRCh37/hg19 3q21.2-21.3(chr3:124981934-126088215)x3 copy number gain not provided [RCV000846647] Chr3:124981934..126088215 [GRCh37]
Chr3:3q21.2-21.3		 uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:11175 AgrOrtholog
COSMIC SNX4 COSMIC
Ensembl Genes ENSG00000114520 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000251775 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000420175 UniProtKB/TrEMBL
  ENSP00000420526 UniProtKB/TrEMBL
Ensembl Transcript ENST00000251775 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000465505 UniProtKB/TrEMBL
  ENST00000471751 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1270.60 UniProtKB/Swiss-Prot
  3.30.1520.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000114520 GTEx
HGNC ID HGNC:11175 ENTREZGENE
Human Proteome Map SNX4 Human Proteome Map
InterPro AH/BAR_dom_sf UniProtKB/Swiss-Prot
  Phox UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PX_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PX_SNX4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNX4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNX4_BAR UniProtKB/Swiss-Prot
KEGG Report hsa:8723 UniProtKB/Swiss-Prot
NCBI Gene 8723 ENTREZGENE
OMIM 605931 OMIM
PANTHER PTHR46596 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PF00787 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA36014 PharmGKB
PROSITE PS50195 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00312 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF64268 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F8W9T3_HUMAN UniProtKB/TrEMBL
  F8WDD4_HUMAN UniProtKB/TrEMBL
  O95219 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary B3KMH0 UniProtKB/Swiss-Prot
  B4DQV4 UniProtKB/Swiss-Prot
  D3DNA3 UniProtKB/Swiss-Prot