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STAG3L2 Gene

pseudogene   GIFtS: 33
GCID: GC07M074112

Stromal Antigen 3-Like 2 (Pseudogene)

(Previous name: stromal antigen 3-like 2)
  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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Aliases
Stromal Antigen 3-Like 2 (Pseudogene)1 2
Stromal Antigen 3-Like 21
STAG3L12
STAG3L2P2
STAG3L32
Stromal Antigen 3-Like Protein 23

External Ids:    HGNC: 338861   Entrez Gene: 4425822   Ensembl: ENSG000001608287   UniProtKB: P0CL843   

Export aliases for STAG3L2 gene to outside databases

Previous GC identifers: GC07M073914 GC07M073938 GC07M073632 GC07M074299


(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 STAG3L2 Gene:
STAG3L2 (stromal antigen 3-like 2 (pseudogene)) is a pseudogene. Diseases associated with STAG3L2 include williams-beuren syndrome.


(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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Regulatory elements:
   Regulatory transcription factor binding sites in the STAG3L2 gene promoter:
         C/EBPbeta   NF-kappaB   CBF-C   FAC1   CBF-B   CBF-A   CP1C   CP1A   NF-kappaB1   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): STAG3L2 promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat STAG3L2


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

Entrez Gene cytogenetic band: 7q11.23   Ensembl cytogenetic band:  7q11.23   HGNC cytogenetic band: 7q11.23

STAG3L2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
STAG3L2 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M074112:  view genomic region     (about GC identifiers)

Start:
74,112,305 bp from pter      End:
74,306,731 bp from pter
Size:
194,427 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 73,632,331-73,639,795     

(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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: ST3L2_HUMAN, P0CL84 (See protein sequence)
Recommended Name: Putative STAG3-like protein 2  
Size: 134 amino acids; 15630 Da
Caution: Could be the product of a pseudogene
Secondary accessions: A6NMT8 A8K0A1 Q32NE4 Q6NXR2 Q7L5M5 Q7Z5K6
Alternative splicing: 2 isoforms:  P0CL84-1   P0CL84-2   

Explore the universe of human proteins at neXtProt for STAG3L2: NX_P0CL84

Explore proteomics data for STAG3L2 at MOPED


See STAG3L2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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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:
 IPR020839 SCD
 IPR016024 ARM-type_fold

Graphical View of Domain Structure for InterPro Entry P0CL84

ProtoNet protein and cluster: P0CL84

UniProtKB/Swiss-Prot: ST3L2_HUMAN, P0CL84
Similarity: Belongs to the SCC3 family
Similarity: Contains 1 SCD (stromalin conservative) domain


STAG3L2 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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Animal Models:
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(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 UniProtKB/Swiss-Prot
ST3L2_HUMAN, P0CL84: Nucleus (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
mitochondrion3
nucleus2
cytosol1

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

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IEA--

STAG3L2 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 STAG3L2
Interactions:

    Search GeneGlobe Interaction Network for STAG3L2

(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 STAG3L2 (ST3L2)



(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,
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 STAG3L2 gene: 
NM_001025202.2  

6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000448772(uc022afy.1 uc022afz.1) ENST00000423186 ENST00000470380
ENST00000380775(uc011kfj.2) ENST00000359898 ENST00000429726
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GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for STAG3L2    About this scheme

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b
SP1:                                    
SP2:                    -               


ECgene alternative splicing isoforms for STAG3L2

(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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STAG3L2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GAAGGGGTGC
STAG3L2 Expression
About this image

STAG3L2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

STAG3L2 Protein Expression
    Custom PCR Arrays for STAG3L2
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for STAG3L2

(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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  --

ENSEMBL Gene Tree for STAG3L2 (if available)
TreeFam Gene Tree for STAG3L2 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for STAG3L2 gene
11 SIMAP similar genes for STAG3L2 using alignment to 1 protein entry:     ST3L2_HUMAN:
STAG3L1    STAG3L3    STAG3    DKFZp686C21148    DKFZp686I05169    DKFZp686P16143
DKFZp686P168    STAG2    STAG1    DKFZp781D1416    STAG1 variant protein

STAG3L2 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 STAG3L2 (see all 58)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 7 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs16357651,2
C--74297827(-) TGGCAC/TATGCC 1 -- int10--------
rs1450225161,2
C--74297840(+) ACGCCC/TGGCCT 1 -- int10--------
rs1929934161,2
--74297881(+) AGGACC/TCCAGG 1 -- int10--------
rs1176496351,2
C,F--74297908(+) TAACCC/GAGGAA 1 -- int11Minor allele frequency- G:0.07NA 120
rs1155617371,2
C,F--74297923(+) TAAATG/AAGGAC 1 -- int11Minor allele frequency- A:0.03WA 118
rs1159853811,2
F--74297932(+) ACAACG/AGAGGC 1 -- int11Minor allele frequency- A:0.03WA 118
rs1835760111,2
--74297992(+) TGGGCA/GGATCA 1 -- int10--------
rs1449434931,2
--74298327(+) GTGTGC/TGTGCG 1 -- nc-transcript-variant0--------
rs1881146821,2
--74298329(+) GTGTGC/TGCGTG 1 -- nc-transcript-variant0--------
rs1170561711,2
C,F--74298377(+) AGGGAT/CGGTTA 1 -- nc-transcript-variant1Minor allele frequency- C:0.07NA 120

HapMap Linkage Disequilibrium report for STAG3L2 (74112305 - 74306731 bp)

Structural Variations
     Database of Genomic Variants (DGV) 7 variations for STAG3L2:    About this table    
Variant IDTypeSubtypePubMed ID
nsv888380CNV Loss21882294
nsv888382CNV Gain21882294
esv24294CNV Gain19812545
nsv888381CNV Gain21882294
essv21300CNV CNV17122850
dgv2100e1CNV Complex17122850
nsv7402OTHER Inversion18451855

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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1 disease for STAG3L2:    
About MalaCards
williams-beuren syndrome


STAG3L2 for disorders           About GeneDecksing


Export disorders for STAG3L2 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 STAG3L2 gene integrated from 10 sources:
(articles sorted by number of sources associating them with STAG3L2)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  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. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (Nature 2003)
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  5. STAG3, a novel gene encoding a protein involved in meiotic chromosome pairing and location of STAG3-related genes flanking the Williams- Beuren syndrome deletion. (PubMed id 10698974)1 Pezzi N.... Barbero J.L. (FASEB J. 2000)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 442582 HGNC: 33886 Ensembl:ENSG00000160828 euGenes: HUgn442582 ECgene: STAG3L2
H-InvDB: STAG3L2

(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 STAG3L2 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 STAG3L2 gene:
Search GeneIP for patents involving STAG3L2

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



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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The GeneCards human gene database gene index: 1 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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