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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

STAG3L2 Gene

pseudogene   GIFtS: 35
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)
About This Section

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000007.13  NC_018918.2  NT_007933.15  NT_079593.2  
Regulatory elements:
   SABiosciences 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
   Search SABiosciences Chromatin IP Primers for STAG3L2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: ST3L2_HUMAN, P0CL84 (See protein sequence)
Recommended Name: Putative STAG3-like protein 2  
Size: 134 amino acids; 15630 Da
Subcellular location: Nucleus (By similarity)
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

STAG3L2 Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --

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Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

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

STAG3L2 for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Animal Models:
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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for STAG3L2

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for STAG3L2 (ST3L2)

Search CenterWatch for drugs/clinical trials and news about STAG3L2

(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,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for STAG3L2 gene: 
NM_001025202.2  

Unigene Cluster for STAG3L2:

Stromal antigen 3-like 2
Hs.666638  [show with all ESTs]
Unigene Representative Sequence: NR_040584
6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000448772(uc022afy.1 uc022afz.1) ENST00000423186 ENST00000470380
ENST00000380775(uc011kfj.2) ENST00000359898 ENST00000429726
miRNA
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Additional mRNA sequence: 

BC119761.1 NR_040584.1 

24/28 DOTS entries (see all 28):

DT.95144561  DT.92440157  DT.97858533  DT.101966161  DT.100042088  DT.100660821  DT.102844297  DT.121042089 
DT.100021083  DT.95359170  DT.100651468  DT.102840637  DT.87015684  DT.92469733  DT.97858534  DT.100660814 
DT.102844296  DT.121057671  DT.121057960  DT.121058095  DT.40114452  DT.75102820  DT.91743304  DT.92469775 

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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

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


Genevestigator expression for STAG3L2

SOURCE GeneReport for Unigene cluster: Hs.666638
    SABiosciences Custom PCR Arrays for STAG3L2
Primer
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QIAGEN QuantiFast Probe-based Assays in human, mouse, rat STAG3L2
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)
About This Section
  --

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)
About This Section
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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/58 SNPs in STAG3L2 are shown (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, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
2 diseases 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)
About This Section

PubMed articles for STAG3L2 gene integrated from 9 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. (2004)
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
  3. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (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. (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. (2000)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 442582 HGNC: 33886 Ensembl:ENSG00000160828 euGenes: HUgn442582 ECgene: STAG3L2
H-InvDB: STAG3L2

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
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.)
About This Section
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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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About This Section

 
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 Proteins for STAG3L2
 Antibodies for STAG3L2
 ELISAs for STAG3L2
 CLIAs for STAG3L2
 Search LifeMap BioReagents cell lines for STAG3L2
 Gene Synthesis
 Protein Engineering
 Variant Library Synthesis
 Codon Optimization
 Protein Production and Purification
 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for STAG3L2
 SwitchGear 3'UTR luciferase reporter plasmids for STAG3L2
 SwitchGear Promoter luciferase reporter plasmids for STAG3L2
 Search ThermoFisher Antibodies for STAG3L2
 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat STAG3L2
 inGenious Targeting Laboratory - Custom generated mouse model solutions for STAG3L2
 inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for STAG3L2
Customized:
 lentivirus for stable overexpression of STAG3L2
 lentivirus expression plasmids for stable overexpression of STAG3L2
 adenovirus for overexpression of STAG3L2
 Search LSBio for Antibodies for STAG3L2
Customized transgenic rodents for:
 Humanization
 Biomarker expression
 Off-target effect monitoring
 Translational medicine
 Tissue-specific gene expresssion
 Time-controlled gene expresssion
       
GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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transforming growth factor, beta 1
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