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STAG3L1 Gene

pseudogene   GIFtS: 36
GCID: GC07P074988

Stromal Antigen 3-Like 1 (Pseudogene)

(Previous name: stromal antigen 3-like 1)
  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 1 (Pseudogene)1 2
Stromal Antigen 3-Like 11
STAG3L1P2
STAG3L22
STAG3L32
Stromal Antigen 3-Like Protein 13

External Ids:    HGNC: 338521   Entrez Gene: 544412   Ensembl: ENSG000002055837   UniProtKB: P0CL833   

Export aliases for STAG3L1 gene to outside databases

Previous GC identifers: GC07P074827 GC07P074321


(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 STAG3L1 Gene:
STAG3L1 (stromal antigen 3-like 1 (pseudogene)) is a pseudogene. Diseases associated with STAG3L1 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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RefSeq DNA sequence:
NC_000007.14  NC_018918.2  NT_007933.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the STAG3L1 gene promoter:
         C/EBPbeta   CBF-C   Evi-1   FAC1   CBF-A   CBF-B   CP1A   CP1C   NF-Y   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSTAG3L1 promoter sequence
   Search Chromatin IP Primers for STAG3L1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat STAG3L1


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

STAG3L1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
STAG3L1 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07P074988:  view genomic region     (about GC identifiers)

Start:
74,988,447 bp from pter      End:
75,024,657 bp from pter
Size:
36,211 bases      Orientation:
plus strand

1 alternative location:
Chr7+,CRA_TCAG 74,321,511-74,330,054     

(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: ST3L1_HUMAN, P0CL83 (See protein sequence)
Recommended Name: Putative STAG3-like protein 1  
Size: 205 amino acids; 23775 Da
Caution: Could be the product of a pseudogene
Secondary accessions: A6NMT8 A8K0A1 Q32NE4 Q6NXR2 Q7L5M5 Q7Z5K6

Explore the universe of human proteins at neXtProt for STAG3L1: NX_P0CL83

Explore proteomics data for STAG3L1 at MOPED


See STAG3L1 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 P0CL83

ProtoNet protein and cluster: P0CL83

UniProtKB/Swiss-Prot: ST3L1_HUMAN, P0CL83
Similarity: Belongs to the SCC3 family
Similarity: Contains 1 SCD (stromalin conservative) domain


STAG3L1 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
ST3L1_HUMAN, P0CL83: Nucleus (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
mitochondrion2
nucleus2
cytosol1
endoplasmic reticulum1
peroxisome1
plasma membrane1

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

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

STAG3L1 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 STAG3L1
Interactions:

    Search GeneGlobe Interaction Network for STAG3L1

(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 STAG3L1 (ST3L1)



(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 STAG3L1 gene (2 alternative transcripts): 
NM_001002840.1  NM_018991.2  

Unigene Clusters for STAG3L1:

Stromal antigen 3-like 1
Hs.632310  [show with all ESTs], Hs.661254  [show with all ESTs]
Unigene Representative Sequences: NR_040583, BM806192
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000402225(uc011kfw.2) ENST00000456374(uc003ucx.3) ENST00000404291(uc003uda.3)
ENST00000487154 ENST00000339898(uc011kfx.2 uc022agf.1) ENST00000338421
ENST00000436837(uc022agg.1)
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Additional mRNA sequence: BC119762.1 

Selected DOTS entries (see all 63):

DT.87015684  DT.75102820  DT.40114452  DT.95199166  DT.92440157  DT.121058095  DT.102840637  DT.40239389 
DT.95234416  DT.95152391  DT.100874947  DT.97860953  DT.100021083  DT.100042088  DT.121058151  DT.95364040 
DT.100660821  DT.102840653  DT.95212898  DT.121057728  DT.121116944  DT.40224144  DT.100878800  DT.102844297 

7 AceView cDNA sequences:

AU279428 AA923656 CD557430 NM_001002840 NM_018991 BE386003 BC066937 

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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STAG3L1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GGGTGGGGGA
STAG3L1 Expression
About this image

STAG3L1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

STAG3L1 Protein Expression

SOURCE GeneReport for Unigene clusters: Hs.632310 Hs.661254
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for STAG3L1

(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 STAG3L1 (if available)
TreeFam Gene Tree for STAG3L1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for STAG3L1 gene
11 SIMAP similar genes for STAG3L1 using alignment to 2 protein entries:     ST3L1_HUMAN (see all proteins):
STAG3L2    STAG3L3    STAG3    DKFZp781D1416    STAG1 variant protein    STAG1
DKFZp686C21148    DKFZp686I05169    DKFZp686P16143    DKFZp686P168    STAG2

STAG3L1 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 STAG3L1 (see all 19)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 7 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1997480331,2
F--74991307(+) GAGCCA/CCCAGC 1 -- nc-transcript-variant1Minor allele frequency- C:0.01EU 525
rs2005269781,2
F--74991320(+) ATGATC/ATTTTC 1 -- nc-transcript-variant1Minor allele frequency- A:0.02EU 641
rs2004571371,2
C--74991834(+) GGTGTA/GAGCCA 1 -- int10--------
rs773013421,2
C--74992847(-) AATGTC/TTTTTT 1 -- int10--------
rs2001569021,2
C--74994593(+) CCGCAC/TGCCTG 1 -- nc-transcript-variant0--------
rs2016432011,2
--74994660(+) TTGTCA/GTGGTT 1 -- int10--------
rs2007830231,2
--74996012(+) TCCTTC/TCCCAG 1 -- int10--------
rs2003886701,2
C--74996835(+) ACACG-/CACACAC 1 -- nc-transcript-variant0--------
rs2015533881,2
C--74996873(+) CATTCA/TCTGTC 1 -- nc-transcript-variant0--------
rs2011213691,2
C--74997384(+) CCGAGA/GTGGGA 1 -- int10--------

HapMap Linkage Disequilibrium report for STAG3L1 (74988447 - 75024657 bp)

Structural Variations
     Database of Genomic Variants (DGV) 7 variations for STAG3L1:    About this table    
Variant IDTypeSubtypePubMed ID
nsv821387CNV Deletion20802225
nsv831035CNV Loss17160897
esv25179CNV Gain19812545
nsv528969CNV Gain19592680
nsv888381CNV Gain21882294
essv14753CNV CNV17122850
dgv2102e1CNV Complex17122850

Site Specific Mutation Identification with PCR Assays
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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 STAG3L1:    
About MalaCards
williams-beuren syndrome


STAG3L1 for disorders           About GeneDecksing


Export disorders for STAG3L1 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 STAG3L1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with STAG3L1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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)
  2. The DNA sequence of human chromosome 7. (PubMed id 12853948)2 Hillier L.W.... Wilson R.K. (Nature 2003)
  3. 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)
  4. 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)
  5. Toward a complete human genome sequence. (PubMed id 9847074)1 Sulston J.E. and Waterston R. (Genome Res. 1998)

(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: 54441 HGNC: 33852 AceView: LOC441260 Ensembl:ENSG00000205583 euGenes: HUgn54441
ECgene: STAG3L1 H-InvDB: STAG3L1

(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 STAG3L1 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 STAG3L1 gene:
Search GeneIP for patents involving STAG3L1

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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 SwitchGear Promoter luciferase reporter plasmids for STAG3L1
 Search ThermoFisher Antibodies for STAG3L1
 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat STAG3L1
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for STAG3L1
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for STAG3L1
 Search LSBio for Antibodies for STAG3L1
Customized transgenic rodents for:
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