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SNX20 sorting nexin 20 [ Homo sapiens (human) ]

Gene ID: 124460, updated on 17-Jun-2019

Summary

Official Symbol
SNX20provided by HGNC
Official Full Name
sorting nexin 20provided by HGNC
Primary source
HGNC:HGNC:30390
See related
Ensembl:ENSG00000167208 MIM:613281
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SLIC1
Summary
SNX20 interacts with the cytoplasmic domain of PSGL1 (SELPLG; MIM 600738) and cycles PSGL1 into endosomes.[supplied by OMIM, Feb 2010]
Expression
Biased expression in lymph node (RPKM 7.6), appendix (RPKM 6.3) and 12 other tissues See more
Orthologs

Genomic context

See SNX20 in Genome Data Viewer
Location:
16q12.1
Exon count:
5
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (50666300..50681312, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (50700211..50715264, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2178 Neighboring gene NKD inhibitor of WNT signaling pathway 1 Neighboring gene uncharacterized LOC101927272 Neighboring gene uncharacterized LOC102724907 Neighboring gene nucleotide binding oligomerization domain containing 2 Neighboring gene microRNA 3181 Neighboring gene CYLD lysine 63 deubiquitinase

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
NHGRI GWA Catalog
Discovery of six new susceptibility loci and analysis of pleiotropic effects in leprosy.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC35578

Gene Ontology Provided by GOA

Function Evidence Code Pubs
phosphatidylinositol-3-phosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
 
phosphatidylinositol-4,5-bisphosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
protein transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
early endosome membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
sorting nexin-20
Names
selectin ligand-interactor cytoplasmic 1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001144972.2NP_001138444.1  sorting nexin-20 isoform 3

    See identical proteins and their annotated locations for NP_001138444.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternative 3' exon, compared to variant 1. The resulting isoform (3) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK055837, AK292650, BC063423, D20065
    Consensus CDS
    CCDS45481.1
    UniProtKB/Swiss-Prot
    Q7Z614
    Related
    ENSP00000388875.2, ENST00000423026.6
    Conserved Domains (1) summary
    cl02563
    Location:7694
    PX_domain; The Phox Homology domain, a phosphoinositide binding module
  2. NM_153337.3NP_699168.1  sorting nexin-20 isoform 2

    See identical proteins and their annotated locations for NP_699168.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternative 3' exon, compared to variant 1. The resulting isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AA278249, AK055837, BC063423, D20065
    Consensus CDS
    CCDS10744.1
    UniProtKB/Swiss-Prot
    Q7Z614
    Related
    ENSP00000300590.3, ENST00000300590.7
    Conserved Domains (1) summary
    cl02563
    Location:7695
    PX_domain; The Phox Homology domain, a phosphoinositide binding module
  3. NM_182854.4NP_878274.1  sorting nexin-20 isoform 1

    See identical proteins and their annotated locations for NP_878274.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AA278249, AC007608, AY302441, BF446287
    Consensus CDS
    CCDS10745.1
    UniProtKB/Swiss-Prot
    Q7Z614
    Related
    ENSP00000332062.4, ENST00000330943.9
    Conserved Domains (1) summary
    cd07300
    Location:76189
    PX_SNX20; The phosphoinositide binding Phox Homology domain of Sorting Nexin 20

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    50666300..50681312 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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