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SH3YL1 Gene

protein-coding   GIFtS: 47
GCID: GC02M000208

SH3 And SYLF Domain Containing 1

(Previous names: SH3 domain containing, Ysc84-like 1 (S. cerevisiae))
  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
SH3 And SYLF Domain Containing 11 2
SH3 Domain Containing, Ysc84-Like 1 (S. Cerevisiae)1
RAY2
SH3 Domain Containing, Ysc84-Like 12
SH3 Domain-Containing YSC84-Like Protein 12

External Ids:    HGNC: 295461   Entrez Gene: 267512   Ensembl: ENSG000000351157   UniProtKB: Q96HL83   
ORGUL members:         

Export aliases for SH3YL1 gene to outside databases

Previous GC identifer: GC02M000212


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SH3YL1 Gene:
SH3YL1 (SH3 and SYLF domain containing 1) is a protein-coding gene. Diseases associated with SH3YL1 include wiskott-aldrich syndrome. GO annotations related to this gene include phosphatase binding and phosphatidylinositol binding.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000002.12  NC_018913.2  NT_005334.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the SH3YL1 gene promoter:
         STAT5B   p53   Pax-2   STAT3   Pax-2a   Meis-1   GATA-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSH3YL1 promoter sequence
   Search Chromatin IP Primers for SH3YL1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SH3YL1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2p25.3   Ensembl cytogenetic band:  2p25.3   HGNC cytogenetic band: 2p25.3

SH3YL1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SH3YL1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M000208:  view genomic region     (about GC identifiers)

Start:
217,730 bp from pter      End:
266,398 bp from pter
Size:
48,669 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SH3Y1_HUMAN, Q96HL8 (See protein sequence)
Recommended Name: SH3 domain-containing YSC84-like protein 1  
Size: 342 amino acids; 37148 Da
Subunit: Interacts with SH3D19 (By similarity)
1 PDB 3D structure from and Proteopedia for SH3YL1:
2D8H (3D)    
Secondary accessions: A8K8E7 B7WNJ4 B7WPL6 Q8NEL2 Q9H5X4 Q9Y3V5
Alternative splicing: 5 isoforms:  Q96HL8-1   Q96HL8-2   Q96HL8-3   Q96HL8-4   Q96HL8-5   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SH3YL1: NX_Q96HL8

Explore proteomics data for SH3YL1 at MOPED


See SH3YL1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (4 alternative transcripts): 
NP_001153069.1  NP_001269611.1  NP_001269616.1  NP_056492.2  

ENSEMBL proteins: 
 ENSP00000384276   ENSP00000385668   ENSP00000384269   ENSP00000348471   ENSP00000383928  
 ENSP00000441266   ENSP00000416312   ENSP00000399519   ENSP00000474411   ENSP00000415723  
 ENSP00000384910   ENSP00000410235   ENSP00000404143  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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2 InterPro protein domains:
 IPR001452 SH3_domain
 IPR007461 Ysc84_actin-binding

Graphical View of Domain Structure for InterPro Entry Q96HL8

ProtoNet protein and cluster: Q96HL8

1 Blocks protein domain: IPB001452 SH3 domain signature

UniProtKB/Swiss-Prot: SH3Y1_HUMAN, Q96HL8
Similarity: Belongs to the SH3YL1 family
Similarity: Contains 1 SH3 domain


SH3YL1 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding ----
GO:0019902phosphatase binding IDA--
GO:0035091phosphatidylinositol binding IDA--
     
SH3YL1 for ontologies           About GeneDecksing


Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SH3YL1
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miRNA
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Inhib. RNA
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In Situ Assay
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SH3YL1


(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
plasma membrane5
cytoskeleton3
cytosol3
nucleus2

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0032587ruffle membrane IDA--

SH3YL1 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SH3YL1
Interactions:

    Search GeneGlobe Interaction Network for SH3YL1

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for SH3YL1 (Q96HL82, 3 ENSP000004041434) via UniProtKB, MINT, STRING, and/or I2D (see all 107)
InteractantInteraction Details
GeneCardExternal ID(s)
GFAPP141362, 3, ENSP000002534084MINT-67449 I2D: score=5 STRING: ENSP00000253408
VIMP086702, 3, ENSP000002242374MINT-65852 I2D: score=5 STRING: ENSP00000224237
SH3D19Q5HYK73, ENSP000003029134I2D: score=3 STRING: ENSP00000302913
ACTBP607093, ENSP000003499604I2D: score=1 STRING: ENSP00000349960
HELZP426943, ENSP000003515244I2D: score=1 STRING: ENSP00000351524
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Gene Ontology (GO): 2 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006661phosphatidylinositol biosynthetic process IEA--
GO:1900027regulation of ruffle assembly IEA--

SH3YL1 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for SH3YL1 (SH3Y1)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for SH3YL1 gene (4 alternative transcripts): 
NM_001159597.2  NM_001282682.1  NM_001282687.1  NM_015677.3  

Unigene Cluster for SH3YL1:

SH3 domain containing, Ysc84-like 1 (S. cerevisiae)
Hs.515951  [show with all ESTs]
Unigene Representative Sequence: AK123829
Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 29):
ENST00000460974 ENST00000403712 ENST00000463865(uc002qvz.3) ENST00000403657(uc002qvv.3 uc002qvw.3 uc010ewe.3)
ENST00000473104(uc002qwc.1) ENST00000405430 ENST00000356150(uc002qvx.3 uc002qvy.3)
ENST00000403658 ENST00000468321(uc002qwa.3) ENST00000479739 ENST00000451005
ENST00000472012 ENST00000431160 ENST00000471948 ENST00000481932 ENST00000488044
ENST00000497051 ENST00000488979
miRNA
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OriGene ORF clones in mouse, rat for SH3YL1
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GenScript: all cDNA clones in your preferred vector (see all 2): SH3YL1 (NM_015677)
DNA2.0 Custom Codon Optimized Gene Synthesis Service for SH3YL1
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SH3YL1
Primer
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  QuantiTect SYBR Green Assays in human, mouse, rat SH3YL1
  QuantiFast Probe-based Assays in human, mouse, rat SH3YL1

Additional mRNA sequence: 

AK026507.1 AK026586.1 AK055801.1 AK096440.1 AK123829.1 AK292312.1 AL050373.1 BC008374.1 
BC008375.1 BC013286.1 BC030778.1 BC034974.1 BC043234.1 BC043403.1 CR457361.1 

Selected DOTS entries (see all 29):

DT.99984839  DT.100812716  DT.115626  DT.100030203  DT.100024587  DT.95254819  DT.91969003  DT.100802905 
DT.40129436  DT.95297589  DT.121013659  DT.97844160  DT.100812715  DT.100812717  DT.95297599  DT.121013793 
DT.91965837  DT.95297603  DT.75188006  DT.75141062  DT.97844156  DT.100720652  DT.121013734  DT.121013801 

Selected AceView cDNA sequences (see all 253):

AI378782 AA587779 BX504179 BE222018 BQ420455 BX095549 AA977886 AW243303 
CK821806 AI701285 BU686677 CK429778 BQ271076 CD369140 BU076045 BQ631794 
BQ642068 BI335880 AI803411 CR623594 CR622262 AW300455 BQ065806 BM312071 

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for SH3YL1 (see all 11)    About this scheme

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14 ^ 15a · 15b · 15c · 15d · 15e ^ 16 ^
SP1:              -     -     -                             -                             -     -                                         -     -     -         
SP2:                                      -     -           -                                   -                                         -     -     -         
SP3:                                                        -                                                                                   -     -         
SP4:                    -     -     -     -     -     -     -                             -     -                                         -     -     -         
SP5:                          -     -     -     -     -     -                             -     -                                         -     -     -         

ExUns: 17 ^ 18 ^ 19a · 19b · 19c
SP1:        -                     
SP2:  -     -                     
SP3:  -     -                     
SP4:        -                     
SP5:  -     -                     


ECgene alternative splicing isoforms for SH3YL1

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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SH3YL1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GTAGACTTGT
SH3YL1 Expression
About this image

SH3YL1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SH3YL1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.515951
    Custom PCR Arrays for SH3YL1
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SH3YL1

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals and fungi.

Orthologs for SH3YL1 gene from Selected species (see all 16)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Sh3yl11 , 5 Sh3 domain YSC-like 11, 5 86.37(n)1
92.94(a)1
  12 (13.01 cM)5
240571  NM_013709.41  NP_038737.11 
 309116685 
chicken
(Gallus gallus)
Aves SH3YL11 SH3 domain containing, Ysc84-like 1 (S. cerevisiae) 74.92(n)
77.64(a)
  421908  XM_004940490.1  XP_004940547.1 
lizard
(Anolis carolinensis)
Reptilia SH3YL16
SH3 and SYLF domain containing 1
75(a)
1 ↔ 1
1(160036329-160075821)
tropical clawed frog
(Xenopus tropicalis)
Amphibia sh3yl11 SH3 and SYLF domain containing 1 75.29(n)
87.07(a)
  100135211  NM_001113912.1  NP_001107384.1 
zebrafish
(Danio rerio)
Actinopterygii sh3yl11 SH3 domain containing, Ysc84-like 1 (S. cerevisiae) 62.66(n)
67.27(a)
  566522  XM_689794.6  XP_694886.2 
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LSB31 LSB3 54.28(n)
53.16(a)
  850580   NP_219497.4 


ENSEMBL Gene Tree for SH3YL1 (if available)
TreeFam Gene Tree for SH3YL1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for SH3YL1 gene
4 SIMAP similar genes for SH3YL1 using alignment to 7 protein entries:     SH3Y1_HUMAN (see all proteins):
SH3GL2    SH3GL1    ARHGEF7    ITSN1

SH3YL1 for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for SH3YL1 (see all 904)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1437692431,2
--217754(+) ATGGGG/TGAGCG 2 -- int10--------
rs1808705471,2
--217758(+) GGGAGA/CGCAAA 2 -- int10--------
rs1500827091,2
--217809(+) GTGGAC/TTTAAT 2 -- int10--------
rs67102331,2
C,F,A,H--217826(+) CATGAG/CATAGA 2 -- int112Minor allele frequency- C:0.39NS EA NA WA CSA 786
rs1857141621,2
--217834(+) AGAAGA/GACGAA 2 -- int10--------
rs1383675751,2
--217921(+) GGAGGA/GGCAGG 2 -- int10--------
rs1492498761,2
--218093(+) AGACAC/TAGGAC 2 -- int10--------
rs1905715431,2
--218152(+) ACTTAC/GTAAAC 2 -- ut310--------
rs1444742601,2
C--218165(+) TTAAAA/TATTTT 2 -- ut310--------
rs755222351,2
C--218198(+) TCACCA/GTAAGT 2 -- ut310--------

HapMap Linkage Disequilibrium report for SH3YL1 (217730 - 266398 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for SH3YL1 (see all 16):    About this table    
Variant IDTypeSubtypePubMed ID
esv1550511CNV Deletion17803354
esv1237216CNV Deletion17803354
esv994728CNV Deletion20482838
nsv508735CNV Insertion20534489
nsv2561CNV Insertion18451855
esv2751887CNV Loss17911159
nsv833159CNV Loss17160897
nsv833148CNV Loss17160897
nsv519763CNV Loss19592680
nsv873529CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing SH3YL1
DNA2.0 Custom Variant and Variant Library Synthesis for SH3YL1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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1 disease for SH3YL1:    
About MalaCards
wiskott-aldrich syndrome


SH3YL1 for disorders           About GeneDecksing

Genetic Association Database (GAD): SH3YL1

Export disorders for SH3YL1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for SH3YL1 gene, integrated from 10 sources (see all 14):
(articles sorted by number of sources associating them with SH3YL1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. SH3YL1 regulates dorsal ruffle formation by a novel phosphoinositide-binding domain. (PubMed id 21624956)1, 3 Hasegawa J....Itoh T. (J. Cell Biol. 2011)
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  3. Bcl2-associated athanogene 3 interactome analysis reveals a new role in modulating proteasome activity. (PubMed id 23824909)1 Chen Y....Ge F. (amp 2013)
  4. Comprehensive analysis of interactions between the Src-associated protein in mitosis of 68 kDa and the human Src-homology 3 proteome. (PubMed id 22745667)1 Asbach B....Wagner R. (PLoS ONE 2012)
  5. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
  6. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
  7. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  8. A human protein-protein interaction network: a resource for annotating the proteome. (PubMed id 16169070)1 Stelzl U.... Wanker E.E. (Cell 2005)
  9. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (Nature 2005)
  10. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W.... Wilson R.K. (Nature 2005)

(in PubMed, OMIM, and NCBI Bookshelf)
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 26751 HGNC: 29546 AceView: SH3YL1 Ensembl:ENSG00000035115 euGenes: HUgn26751
ECgene: SH3YL1 H-InvDB: SH3YL1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for SH3YL1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SH3YL1 gene:
Search GeneIP for patents involving SH3YL1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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