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SNX25 sorting nexin 25 [ Homo sapiens (human) ]

Gene ID: 83891, updated on 5-Mar-2024

Summary

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Official Symbol
SNX25provided by HGNC
Official Full Name
sorting nexin 25provided by HGNC
Primary source
HGNC:HGNC:21883
See related
Ensembl:ENSG00000109762 AllianceGenome:HGNC:21883
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
SBBI31; MSTP043
Summary
Predicted to enable type I transforming growth factor beta receptor binding activity. Involved in negative regulation of pathway-restricted SMAD protein phosphorylation; negative regulation of transforming growth factor beta receptor signaling pathway; and receptor catabolic process. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in lung (RPKM 10.3), thyroid (RPKM 5.9) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
4q35.1
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (185204237..185378642)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (188547948..188721939)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (186125391..186285120)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2436 Neighboring gene uncharacterized LOC105377588 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:186030634-186031272 Neighboring gene Sharpr-MPRA regulatory region 4736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22247 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:186049861-186050404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15847 Neighboring gene solute carrier family 25 member 4 Neighboring gene cilia and flagella associated protein 97 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:186125066-186125237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22249 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15849 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22250 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:186160877-186161869 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:186161870-186162861 Neighboring gene NANOG hESC enhancer GRCh37_chr4:186187032-186187533 Neighboring gene Sharpr-MPRA regulatory region 940 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:186223282-186223782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22253 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:186227325-186227825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22256 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:186239748-186240413 Neighboring gene uncharacterized LOC124900827 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22258 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15855 Neighboring gene LRP2 binding protein Neighboring gene ankyrin repeat domain 37 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22261 Neighboring gene UFM1 specific peptidase 2 Neighboring gene cilia and flagella associated protein 96 Neighboring gene coiled-coil domain containing 110

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Expression pattern of sorting Nexin 25 in temporal lobe epilepsy: a study on patients and pilocarpine-induced rats. Du Y, et al. Brain Res, 2013 May 6. PMID 23518199
  2. Genetic Modifiers of Age at Onset in Carriers of the G206A Mutation in PSEN1 With Familial Alzheimer Disease Among Caribbean Hispanics. Lee JH, et al. JAMA Neurol, 2015 Sep. PMID 26214276, Free PMC Article
  3. SNX25 regulates TGF-β signaling by enhancing the receptor degradation. Hao X, et al. Cell Signal, 2011 May. PMID 21266196
  4. Snazarus and its human ortholog SNX25 modulate autophagic flux. Lauzier A, et al. J Cell Sci, 2022 Mar 1. PMID 34821359
  5. Sorting out the cellular functions of sorting nexins. Worby CA, et al. Nat Rev Mol Cell Biol, 2002 Dec. PMID 12461558

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. This study confirmed that SNX25 as genetic modifiers of age at onset of Alzheimer disease.
    Title: Genetic Modifiers of Age at Onset in Carriers of the G206A Mutation in PSEN1 With Familial Alzheimer Disease Among Caribbean Hispanics.
  2. upregulation of SNX25 might be involved in the development of temporal lobe epilepsy.
    Title: Expression pattern of sorting Nexin 25 in temporal lobe epilepsy: a study on patients and pilocarpine-induced rats.
  3. SNX25 negatively regulates TGF-beta signaling by enhancing the receptor degradation through lysosome pathway.
    Title: SNX25 regulates TGF-β signaling by enhancing the receptor degradation.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ23161

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
enables phosphatidylinositol binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in negative regulation of transforming growth factor beta receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in receptor catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
sorting nexin-25

NCBI Reference Sequences (RefSeq)

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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_001317781.2 → NP_001304710.1  sorting nexin-25 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AA626308, AC073344, AF113223, AY601647
    Consensus CDS
    CCDS34116.1
    UniProtKB/Swiss-Prot
    Q3ZT30, Q8N6K3, Q9H3E2
    UniProtKB/TrEMBL
    B3KTI8
    Related
    ENSP00000426255.1, ENST00000504273.5
    Conserved Domains (4) summary
    cd06878
    Location:502 → 624
    PX_SNX25; The phosphoinositide binding Phox Homology domain of Sorting Nexin 25
    cd08720
    Location:291 → 399
    RGS_SNX25; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 25 (SNX25) protein
    pfam02194
    Location:2 → 160
    PXA; PXA domain
    pfam08628
    Location:701 → 807
    Nexin_C; Sorting nexin C terminal

  2. NM_001378032.2 → NP_001364961.1  sorting nexin-25 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC073344
    Conserved Domains (5) summary
    TIGR01612
    Location:331 → 691
    235kDa-fam; reticulocyte binding/rhoptry protein
    cd06878
    Location:699 → 821
    PX_SNX25; The phosphoinositide binding Phox Homology domain of Sorting Nexin 25
    cd08720
    Location:488 → 596
    RGS_SNX25; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 25 (SNX25) protein
    pfam02194
    Location:166 → 321
    PXA; PXA domain
    pfam08628
    Location:898 → 1004
    Nexin_C; Sorting nexin C terminal

  3. NM_001378034.2 → NP_001364963.1  sorting nexin-25 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC073344
    Consensus CDS
    CCDS93675.1
    UniProtKB/TrEMBL
    A0A494C0S0
    Related
    ENSP00000498676.1, ENST00000652585.2
    Conserved Domains (4) summary
    cd06878
    Location:666 → 788
    PX_SNX25; The phosphoinositide binding Phox Homology domain of Sorting Nexin 25
    cd08720
    Location:455 → 563
    RGS_SNX25; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 25 (SNX25) protein
    pfam02194
    Location:166 → 321
    PXA; PXA domain
    pfam08628
    Location:865 → 971
    Nexin_C; Sorting nexin C terminal

  4. NM_001378035.2 → NP_001364964.1  sorting nexin-25 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC073344
    Conserved Domains (4) summary
    cd08720
    Location:455 → 563
    RGS_SNX25; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 25 (SNX25) protein
    pfam02194
    Location:166 → 321
    PXA; PXA domain
    pfam08628
    Location:810 → 916
    Nexin_C; Sorting nexin C terminal
    cl02563
    Location:666 → 768
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  5. NM_001378036.2 → NP_001364965.1  sorting nexin-25 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC073344
    Conserved Domains (4) summary
    cd06878
    Location:666 → 788
    PX_SNX25; The phosphoinositide binding Phox Homology domain of Sorting Nexin 25
    cd08720
    Location:455 → 563
    RGS_SNX25; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 25 (SNX25) protein
    pfam02194
    Location:166 → 321
    PXA; PXA domain
    pfam08628
    Location:865 → 944
    Nexin_C; Sorting nexin C terminal

  6. NM_001378037.2 → NP_001364966.1  sorting nexin-25 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC073344
    Conserved Domains (4) summary
    cd08720
    Location:455 → 563
    RGS_SNX25; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 25 (SNX25) protein
    pfam02194
    Location:166 → 321
    PXA; PXA domain
    pfam08628
    Location:810 → 889
    Nexin_C; Sorting nexin C terminal
    cl02563
    Location:666 → 768
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  7. NM_001378038.2 → NP_001364967.1  sorting nexin-25 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC073344
    Conserved Domains (1) summary
    pfam02194
    Location:166 → 321
    PXA; PXA domain

  8. NM_001378039.2 → NP_001364968.1  sorting nexin-25 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC073344
    Conserved Domains (1) summary
    pfam02194
    Location:166 → 321
    PXA; PXA domain

  9. NM_001378040.2 → NP_001364969.1  sorting nexin-25 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC073344
    Conserved Domains (1) summary
    pfam02194
    Location:166 → 321
    PXA; PXA domain

  10. NM_001423234.1 → NP_001410163.1  sorting nexin-25 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC073344

RNA

  1. NR_186775.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC073344

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    185204237..185378642
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    188547948..188721939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_031953.2: Suppressed sequence

    Description
    NM_031953.2: This RefSeq was removed because currently there is insufficient support for the transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H3E2.2 GenPept UniProtKB/Swiss-Prot:Q9H3E2

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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