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    SNX25 sorting nexin 25 [ Homo sapiens (human) ]

    Gene ID: 83891, updated on 17-Jun-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
    mouse all
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    Genomic context

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    See SNX25 in Genome Data Viewer
    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.

    Chemical Information
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