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

Summary

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

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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?

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.
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.
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.
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.
SH3YL1 promotes Dock4-mediated cell migration and promotes Dock4-mediated Rac1 activation.
Title: Dock4 forms a complex with SH3YL1 and regulates cancer cell migration.
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.

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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 EBI GWAS CatalogPubMed

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

WI-21834 (e-PCR)
- UniSTS:6145

D10S275 (e-PCR)
- UniSTS:147992

D1S1425 (e-PCR)
- UniSTS:149621

G35510 (e-PCR)
- UniSTS:44150

RH103149 (e-PCR)
- UniSTS:97483

STS-AA024860 (e-PCR)
- UniSTS:41435

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)

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
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
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
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

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
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
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
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
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