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

Gene ID: 26751, updated on 27-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
  • 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. A novel mouse gene, Sh3yl1, is expressed in the anagen hair follicle. Aoki N, et al. J Invest Dermatol, 2000 May. PMID 10771491
  2. SH3YL1 protein as a novel biomarker for diabetic nephropathy in type 2 diabetes mellitus. Choi GS, et al. Nutr Metab Cardiovasc Dis, 2021 Feb 8. PMID 33223406
  3. Genes identified through genome-wide association studies of osteonecrosis in childhood acute lymphoblastic leukemia patients. Gagné V, et al. Pharmacogenomics, 2019 Nov. PMID 31686588, Free PMC Article
  4. Identification of a Novel Coregulator, SH3YL1, That Interacts With the Androgen Receptor N-Terminus. Blessing AM, et al. Mol Endocrinol, 2015 Oct. PMID 26305679, Free PMC Article
  5. Dock4 forms a complex with SH3YL1 and regulates cancer cell migration. Kobayashi M, et al. Cell Signal, 2014 May. PMID 24508479

See all (27) citations in PubMed

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

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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