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

Gene ID: 26751, updated on 7-Jun-2020

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
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
Expression
Ubiquitous expression in kidney (RPKM 16.8), thyroid (RPKM 9.9) and 24 other tissues See more
Orthologs

Genomic context

See SH3YL1 in Genome Data Viewer
Location:
2p25.3
Exon count:
19
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (218136..264866, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (218136..264820, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 110 member C Neighboring gene uncharacterized LOC105373324 Neighboring gene uncharacterized LOC101927262 Neighboring gene acid phosphatase 1 Neighboring gene ALK and LTK ligand 2

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: TMEM18

Homology

Clone Names

  • FLJ39121, DKFZp586F1318

Gene Ontology Provided by GOA

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

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001159597.2NP_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, HY040340
    Consensus CDS
    CCDS54332.1
    UniProtKB/Swiss-Prot
    Q96HL8
    Related
    ENSP00000384276.1, ENST00000403712.6
    Conserved Domains (2) summary
    cd11525
    Location:11209
    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:268321
    SH3_SH3YL1_like; Src homology 3 domain of SH3 domain containing Ysc84-like 1 (SH3YL1) protein
  2. NM_001282682.1NP_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:172225
    SH3_SH3YL1_like; Src homology 3 domain of SH3 domain containing Ysc84-like 1 (SH3YL1) protein
    cl01109
    Location:2113
    SYLF; The SYLF domain (also called DUF500), a novel lipid-binding module
  3. NM_001282687.1NP_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:191244
    SH3_SH3YL1_like; Src homology 3 domain of SH3 domain containing Ysc84-like 1 (SH3YL1) protein
    cl01109
    Location:2113
    SYLF; The SYLF domain (also called DUF500), a novel lipid-binding module
  4. NM_015677.4NP_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
    Q96HL8
    Related
    ENSP00000348471.5, ENST00000356150.10
    Conserved Domains (2) summary
    cd11525
    Location:11209
    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:287340
    SH3_SH3YL1_like; Src homology 3 domain of SH3 domain containing Ysc84-like 1 (SH3YL1) protein

RNA

  1. NR_104223.1 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_104224.2 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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    218136..264866 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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