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

STAG3L1 Gene

pseudogene   GIFtS: 37
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)
About This Section

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

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 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_079595.2  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for STAG3L1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 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: ST3L1_HUMAN, P0CL83 (See protein sequence)
Recommended Name: Putative STAG3-like protein 1  
Size: 205 amino acids; 23775 Da
Subcellular location: Nucleus (By similarity)
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 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P0CL83

  • STAG3L1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    STAG3L1 Protein Expression

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    Cloud-Clone Corp. Proteins for STAG3L1 

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

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

    STAG3L1 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 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,
    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 STAG3L1

    (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 STAG3L1 (ST3L1)

    Search CenterWatch for drugs/clinical trials and news about STAG3L1

    (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,
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    About This Section

    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)
    miRNA
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    Inhib. RNA
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    Additional mRNA sequence: BC119762.1 

    24/63 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 NM_001002840 NM_018991 AA923656 CD557430 BC066937 BE386003 

    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™, 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

    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


    See STAG3L1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for STAG3L1

    SOURCE GeneReport for Unigene clusters: Hs.632310 Hs.661254
        SABiosciences Custom PCR Arrays for STAG3L1
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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)
    About This Section
      --

    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)
    About This Section
    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) 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

    10/19 SNPs in STAG3L1 are shown (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

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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 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)
    About This Section

    PubMed articles for STAG3L1 gene integrated from 9 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. (2006)
    2. The DNA sequence of human chromosome 7. (PubMed id 12853948)2 Hillier L.W.... Wilson R.K. (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. (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. (2000)
    5. Toward a complete human genome sequence. (PubMed id 9847074)1 Wilson R. (1998)

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

    (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 STAG3L1 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 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, 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
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 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 


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