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STAG3L3 Gene

pseudogene   GIFtS: 31
GCID: GC07M072440

Stromal Antigen 3-Like 3

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(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 31 2
STAG3L12
STAG3L22
Stromal Antigen 3-Like Protein 33

External Ids:    HGNC: 338451   Entrez Gene: 4425782   Ensembl: ENSG000001743537   UniProtKB: P0CL853   

Export aliases for STAG3L3 gene to outside databases

Previous GC identifers: GC07M072109 GC07M071801


(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 STAG3L3 Gene:
STAG3L3 (stromal antigen 3-like 3) is a pseudogene.


(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 STAG3L3 gene promoter:
         C/EBPbeta   NF-YA   CBF-C   Evi-1   FAC1   CBF-A   CBF-B   CP1A   CP1C   NF-Y   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSTAG3L3 promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat STAG3L3


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

STAG3L3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
STAG3L3 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M072440:  view genomic region     (about GC identifiers)

Start:
72,440,227 bp from pter      End:
72,476,455 bp from pter
Size:
36,229 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 71,801,835-71,809,277     

(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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: ST3L3_HUMAN, P0CL85 (See protein sequence)
Recommended Name: STAG3-like protein 3  
Size: 134 amino acids; 15609 Da
Secondary accessions: A6NMT8 A8K0A1 Q32NE4 Q6NXR2 Q7L5M5 Q7Z5K6
Alternative splicing: 2 isoforms:  P0CL85-1   P0CL85-2   

Explore the universe of human proteins at neXtProt for STAG3L3: NX_P0CL85

Explore proteomics data for STAG3L3 at MOPED


See STAG3L3 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 P0CL85

ProtoNet protein and cluster: P0CL85

UniProtKB/Swiss-Prot: ST3L3_HUMAN, P0CL85
Similarity: Belongs to the SCC3 family
Similarity: Contains 1 SCD (stromalin conservative) domain


Find genes that share domains with STAG3L3           About GenesLikeMe


(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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, 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
ST3L3_HUMAN, P0CL85: 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--

Find genes that share ontologies with STAG3L3           About GenesLikeMe


(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 STAG3L3
Interactions:

    Search GeneGlobe Interaction Network for STAG3L3

(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 STAG3L3 (ST3L3)



(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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for STAG3L3 gene: 
NM_001013739.2  

8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000436857(uc003twv.3 uc011kem.2) ENST00000428423(uc003txa.3 uc022afo.1)
ENST00000608210 ENST00000448173 ENST00000423834(uc022afq.1 uc010laq.1)
ENST00000569650 ENST00000308103(uc022afn.1 uc022afp.1) ENST00000426587

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GeneLoc Exon Structure


(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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STAG3L3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
STAG3L3 Expression
About this image

STAG3L3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

STAG3L3 Protein Expression
    Custom PCR Arrays for STAG3L3
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In Situ
Assay Products:
 

 
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(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 STAG3L3 (if available)
TreeFam Gene Tree for STAG3L3 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for STAG3L3 gene
5 SIMAP similar genes for STAG3L3 using alignment to 1 protein entry:     ST3L3_HUMAN:
STAG3L1    STAG3L2    STAG3    STAG2    STAG1

Find genes that share paralogs with STAG3L3           About GenesLikeMe



(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 STAG3L3 (see all 22)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 7 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1475595091,2
--72468030(+) GACAGA/TGAATG 1 -- nc-transcript-variant0--------
rs2002564731,2
C--72469999(+) TTAAGG/TATAAG 1 -- nc-transcript-variant0--------
rs1379919351,2
C,F--72470031(+) CACTGC/ACACAC 1 -- nc-transcript-variant2Minor allele frequency- A:0.00NA EU 5863
rs1420075831,2
C,F--72470046(+) CTCTCT/CGTCCA 1 -- nc-transcript-variant1Minor allele frequency- C:0.01NA 4534
rs1872011621,2
C,F--72470276(+) CCACCT/CGTCTC 1 -- int11Minor allele frequency- C:0.03EU 157
rs794701701,2
C,F--72470313(+) CAGGCG/ATGCGG 1 -- nc-transcript-variant2Minor allele frequency- A:0.03NA EU 181
rs2010497531,2
C--72472016(+) ATTGTA/GCCAAC 1 -- int10--------
rs749076451,2
C--72472036(+) GGCCAA/TAAGGC 1 -- int11Minor allele frequency- T:0.00NA 2
rs1921239751,2
--72472852(+) ACAGGA/GAAAAA 1 -- int10--------
rs1997891631,2
F--72473595(+) GCTGGT/GGGCTC 1 -- nc-transcript-variant1Minor allele frequency- G:0.01EU 765

HapMap Linkage Disequilibrium report for STAG3L3 (72440227 - 72476455 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for STAG3L3 (see all 12):    About this table    
Variant IDTypeSubtypePubMed ID
esv2734660CNV Deletion23290073
nsv821246CNV Deletion20802225
nsv469664CNV Loss16826518
nsv831025CNV Loss17160897
esv34349CNV Gain17911159
nsv428171CNV Gain18775914
esv26856CNV Gain19812545
nsv888362CNV Gain21882294
nsv520573CNV Gain+Loss19592680
dgv2095e1CNV Complex17122850

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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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  --

(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 STAG3L3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with STAG3L3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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)
  2. 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)
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  4. The DNA sequence of human chromosome 7. (PubMed id 12853948)2 Hillier L.W.... Wilson R.K. (Nature 2003)
  5. 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)
  6. 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)
  7. (PubMed id )2 

(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: 442578 HGNC: 33845 Ensembl:ENSG00000174353 euGenes: HUgn442578 ECgene: STAG3L3
H-InvDB: STAG3L3

(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 STAG3L3 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 STAG3L3 gene:
Search GeneIP for patents involving STAG3L3

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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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