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    SH3YL1 SH3 and SYLF domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 26751, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SH3YL1provided by HGNC
    Official Full Name
    SH3 and SYLF domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:29546
    See related
    Ensembl:ENSG00000035115 MIM:617314; AllianceGenome:HGNC:29546
    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
    RAY
    Summary
    Enables phosphatase binding activity and phosphatidylinositol binding activity. Predicted to be involved in regulation of ruffle assembly. Predicted to act upstream of or within phosphatidylinositol biosynthetic process. Located in ruffle membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 16.8), thyroid (RPKM 9.9) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SH3YL1 in Genome Data Viewer
    Location:
    2p25.3
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (218136..264824, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (218391..265079, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (218136..264824, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 110 member C Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:67739-68240 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:150593-151572 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:151573-152550 Neighboring gene uncharacterized LOC105373324 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:162049-163248 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:197602-198801 Neighboring gene MPRA-validated peak3578 silencer Neighboring gene MPRA-validated peak3579 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15215 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:284666-285865 Neighboring gene uncharacterized LOC101927262 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11100 Neighboring gene acid phosphatase 1 Neighboring gene ALK and LTK ligand 2

    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 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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SH3YL1 protein as a novel biomarker for diabetic nephropathy in type 2 diabetes mellitus.
      Title: SH3YL1 protein as a novel biomarker for diabetic nephropathy in type 2 diabetes mellitus.
    2. The analyses of variants in theACP1-SH3YL1locus derived from whole exome sequencing data showed an association of several correlatedSNPs (rs11553746, rs2290911, rs7595075, rs2306060 and rs79716074). The rs79716074 defines *B haplotypeof theAPC1gene, which is well known for its functional role
      Title: Genes identified through genome-wide association studies of osteonecrosis in childhood acute lymphoblastic leukemia patients.
    3. This study shows that SH3YL1 cooperates with ESCRT-I in the sorting and degradation of the EGF receptor.
      Title: SH3YL1 cooperates with ESCRT-I in the sorting and degradation of the EGF receptor.
    4. a novel AR-interacting protein, Src homology 3 (SH3)-domain containing, Ysc84-like 1 (SH3YL1), whose interaction with the receptor is dependent upon this polyproline domain, was identified.
      Title: Identification of a Novel Coregulator, SH3YL1, That Interacts With the Androgen Receptor N-Terminus.
    5. SH3YL1 promotes Dock4-mediated cell migration and promotes Dock4-mediated Rac1 activation.
      Title: Dock4 forms a complex with SH3YL1 and regulates cancer cell migration.
    6. results provide new insight into the SH3YL1 molecular mechanism of dorsal ruffle formation and its regulation by phosphoinositide metabolism
      Title: SH3YL1 regulates dorsal ruffle formation by a novel phosphoinositide-binding domain.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide association study in the genetic analysis of idiopathic thrombophilia project suggests sex-specific regulation of mitochondrial DNA levels.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: TMEM18

    Homology

    Clone Names

    • FLJ39121, DKFZp586F1318

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatase binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in phosphatidylinositol biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of ruffle assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in ruffle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ruffle membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SH3 domain-containing YSC84-like protein 1
    Names
    SH3 domain containing, Ysc84-like 1

    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_001159597.3 → NP_001153069.1  SH3 domain-containing YSC84-like protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001153069.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      AK026507, BC008375, CK821806
      Consensus CDS
      CCDS54332.1
      Related
      ENSP00000384276.1, ENST00000403712.6
      Conserved Domains (2) summary
      cd11525
      Location:11 → 209
      SYLF_SH3YL1_like; The SYLF domain (also called DUF500), a novel lipid-binding module, of SH3 domain containing Ysc84-like 1 (SH3YL1) and similar proteins
      cd11841
      Location:268 → 321
      SH3_SH3YL1_like; Src homology 3 domain of SH3 domain containing Ysc84-like 1 (SH3YL1) protein

    2. NM_001282682.2 → NP_001269611.1  SH3 domain-containing YSC84-like protein 1 isoform 3

      See identical proteins and their annotated locations for NP_001269611.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in its 5' UTR, lacks a portion of the 5' coding region, uses an alternate start codon, and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK292312, CK821806, DA271598, DB076978
      Consensus CDS
      CCDS62841.1
      UniProtKB/Swiss-Prot
      Q96HL8
      Related
      ENSP00000383928.1, ENST00000403658.5
      Conserved Domains (2) summary
      cd11841
      Location:172 → 225
      SH3_SH3YL1_like; Src homology 3 domain of SH3 domain containing Ysc84-like 1 (SH3YL1) protein
      cl01109
      Location:2 → 113
      SYLF; The SYLF domain (also called DUF500), a novel lipid-binding module

    3. NM_001282687.2 → NP_001269616.1  SH3 domain-containing YSC84-like protein 1 isoform 4

      See identical proteins and their annotated locations for NP_001269616.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in its 5' UTR, lacks a portion of the 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (4) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC079779, AL050373, CK821806
      Consensus CDS
      CCDS62842.1
      UniProtKB/Swiss-Prot
      Q96HL8
      Related
      ENSP00000485824.1, ENST00000626873.2
      Conserved Domains (2) summary
      cd11841
      Location:191 → 244
      SH3_SH3YL1_like; Src homology 3 domain of SH3 domain containing Ysc84-like 1 (SH3YL1) protein
      cl01109
      Location:2 → 113
      SYLF; The SYLF domain (also called DUF500), a novel lipid-binding module

    4. NM_015677.4 → NP_056492.2  SH3 domain-containing YSC84-like protein 1 isoform 1

      See identical proteins and their annotated locations for NP_056492.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      BC008374, CK821806, DB244375, HY040340
      Consensus CDS
      CCDS42646.2
      UniProtKB/Swiss-Prot
      A8K8E7, B7WNJ4, B7WPL6, Q8NEL2, Q96HL8, Q9H5X4, Q9Y3V5
      Related
      ENSP00000348471.5, ENST00000356150.10
      Conserved Domains (2) summary
      cd11525
      Location:11 → 209
      SYLF_SH3YL1_like; The SYLF domain (also called DUF500), a novel lipid-binding module, of SH3 domain containing Ysc84-like 1 (SH3YL1) and similar proteins
      cd11841
      Location:287 → 340
      SH3_SH3YL1_like; Src homology 3 domain of SH3 domain containing Ysc84-like 1 (SH3YL1) protein

    RNA

    1. NR_104223.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains alternate 5' exon structure, compared to variant 1. This variant is represented as non-coding because it lacks the start codon found in variant 1 and does not contain an in-frame ORF for which translation is supported.
      Source sequence(s)
      AC079779, AK292312, BC043234, CK821806
      Related
      ENST00000468321.5

    2. NR_104224.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) contains alternate 5' exon structure, and lacks several 3' exons but contains an alternate 3' terminal exon, compared to variant 1. This variant is represented as non-coding because it lacks the start codon found in variant 1 and does not contain an in-frame ORF for which translation is supported.
      Source sequence(s)
      AC079779, BC030778, DB076978
      Related
      ENST00000402632.5

    3. NR_104225.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) contains an alternate 5' terminal exon and uses an alternate splice site in the 3' region, compared to variant 1. This variant is represented as non-coding because it lacks the start codon found in variant 1 and does not contain an in-frame ORF for which translation is supported.
      Source sequence(s)
      AK026507, AK026586, CK821806, CX758922
      Related
      ENST00000463865.5

    4. NR_104226.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) contains alternate 5' exon structure, includes an additional exon in the central region and lacks an alternate exon in the 3' region, compared to variant 1. This variant is represented as non-coding because it lacks the start codon found in variant 1 and does not contain an in-frame ORF for which translation is supported.
      Source sequence(s)
      AC079779, BC043403, CK821806
      Related
      ENST00000473104.5

    5. NR_104227.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) contains alternate 5' exon structure, includes two additional exons in the central region, and uses an alternate splice site and lacks an exon in the 3' region, compared to variant 1. This variant is represented as non-coding because translation of the in-frame ORF would render the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC079779, AK096440, BC008374, BC043234, CK821806

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      218136..264824 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      218391..265079 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96HL8.1 GenPept UniProtKB/Swiss-Prot:Q96HL8

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