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SALL3 Gene

protein-coding   GIFtS: 47

GC18P074841
sal-like 3 (Drosophila)
(Previous name: sal (Drosophila)-like 3 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
ZNF796 1, 2
hSALL3 3
Descriptions
C2H2 zinc finger protein SALL3 2
Zinc finger protein SALL3 3
sal (Drosophila)-like 3 1
sal-like 3 2
sal-like 3 (Drosophila) 2
spalt-like zinc finger protein 2
External Ids
HGNC: 105271
Entrez Gene: 271642
UniProtKB: Q9BXA93
Ensembl: ENSG000001515147
Search outside databases for aliases for SALL3 gene

Previous GC identifers: GC18U990052 GC18P076766 GC18P076475 GC18P074839

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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UniProtKB/Swiss-Prot: SALL3_HUMAN, Q9BXA9
Function: Probable transcription factor

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
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Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the SALL3 gene  

Entrez Gene cytogenetic band: 18q23   Ensembl cytogenetic band:  18q23   HGNC cytogenetic band: 18q23

SALL3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 18         GeneLoc Exon Structure

GeneLoc location for GC18P074841:     (about GC identifiers)

Start:
74,841,263 bp from pter
End:
74,859,182 bp from pter
Size:
17,920 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000018.8  NT_010879.15  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: SALL3_HUMAN, Q9BXA9 (See protein sequence)
Recommended Name: Sal-like protein 3  
Size: 1300 amino acids; 135372 Da
Subcellular location: Nucleus (Probable)
Developmental stage: In fetal brain of the 24th gestational week
Secondary accessions: Q9UGH1
Alternative splicing: 4 isoforms:  Q9BXA9-1   Q9BXA9-2   Q9BXA9-3   Q9BXA9-4   

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_741996.2  

    ENSEMBL proteins: 
    ENSP00000299466 ENSP00000340501 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (SALL 3)
    Browse Abnova for Human Recombinant Proteins
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    2 Gene Ontology (GO) cellular component terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622 intracellular IEA--
    GO:0005634 nucleus IEA--
    About this table

    Antibodies for SALL3: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for SALL3
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (SALL 3), each with their AbpromiseSM
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Search Novus for antibodies for SALL3

    Assays for SALL3: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    3 InterPro domains/families:
     IPR015880 Znf_C2H2-like
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2


       GeneDecks  SALL3 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q9BXA9

    ProtoNet protein and cluster: Q9BXA9

    UniProtKB/Swiss-Prot: SALL3_HUMAN, Q9BXA9
    Similarity: Belongs to the sal C2H2-type zinc-finger protein family
    Similarity: Contains 9 C2H2-type zinc fingers

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (SALL3)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (SALL3)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_171999

                  Applied Biosystems Silencer® siRNAs for SALL3

                  Sigma-Aldrich siRNA for SALL3  
                         Sigma-Aldrich shRNA for SALL3  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Browse Clone Ranger at Invitrogen for clones
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_171999
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_171999
                                     untagged cDNA clone in CMV expression vector: NM_171999 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_171999

    UniProtKB/Swiss-Prot: SALL3_HUMAN, Q9BXA9
    Function: Probable transcription factor

    Genatlas biochemistry entry for SALL3:
    spalt (sal)-like,Drosophila SAL like gene 3,expressed in fetal brain and in several adult
    tissues,haploinsufficency in the 18q deletion syndrome and may be contributing to the phenotype

    8 MGI mutant phenotypes (inferred from 1 allele(MGI details for Sall3):

    behavior/neurologicalcraniofacialdigestive/alimentaryhomeostasis/metabolismlethality-prenatal/perinatal
    nervous systemrespiratory systemskeleton

    3 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677 DNA binding IEA--
    GO:0008270 zinc ion binding IEA--
    GO:0046872 metal ion binding IEA--
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section



    5 Interacting proteins for SALL3 (ENSP000002994663) via UniProtKB, MINT, and/or STRING
    InteractantInteraction Details
    GeneCardExternal ID(s)
    EPHA3ENSP000003374513STRING (score=.921)
    HOXA13ENSP000002227533STRING (score=.921)
    DNMT3AENSP000002647093STRING (score=.911)
    EPHA4ENSP000002818213STRING (score=.904)
    HOXD13ENSP000002495053STRING (score=.889)
    About this table

    2 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006350 transcription IEA--
    GO:0006355 regulation of transcription, DNA-dependent IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for SALL3

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (SALL3)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (SALL3)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_171999

                  Sigma-Aldrich siRNA for SALL3  
                         Sigma-Aldrich shRNA for SALL3  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_171999  

    REFSEQ mRNAs for SALL3 gene: 

    NM_171999.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_171999  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_171999
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_171999
                                     untagged cDNA clone in CMV expression vector: NM_171999 

    Additional cDNA sequence: BC148296.2 

    5 DOTS entries:

    DT.436404  DT.436647  DT.121091407  DT.70104457  DT.95290774 

    24/26 AceView cDNA sequences (see all 26 ):

    AI634411 AA649850 AI871434 AI656975 AI480087 AI637836 BF432623 NM_171999 
    BF739956 AW450071 AW137217 BE501147 BE220771 R42871 T07317 AI668981 
    AI475090 AW027492 AA429109 AI015631 AI949558 R37086 R21486 H92108 

    highest scoring ESTs for SALL3:

    AI055828 AI564778 AI566552 AI869498 AI871129 AW269333 BE222946 H23192 Z40278 AI480087 

    Unigene Cluster for SALL3:

    Sal-like 3 (Drosophila)
    Hs.700557  [show with all ESTs]
    Unigene Representative Sequence: NM_171999


    GeneLoc Exon Structure

    2 Ensembl transcripts including schematic representations:
    ENST00000299466  ENST00000339709  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    SALL3 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for SALL3

    1 / 2 / 3

    5 probe-sets matching SALL3 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    72559_at2, 3 U95-E 5 1.00 0.86 0.85 0.49 AI857524 0.40 1.00 0.76 1
    80288_at2, 3 U95-E 6 1.00 0.83 0.84 1.52 AI871434 0.60 1.00 0.82 1

    232847_at2, 3 U133-B 1 0.36 1.00 -- -- R21486 0.40 1.00 0.76 1

    1553411_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    232847_at2 U133Plus2 1 0.36 1.00 -- -- -- -- -- -- --
    GeneDecks  SALL3 for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: CTTTTCGTGT

    SOURCE GeneReport for Unigene cluster: Hs.700557

    UniProtKB/Swiss-Prot: SALL3_HUMAN, Q9BXA9
    Tissue specificity: Widely expressed in adult with highest levels in heart. Expressed in fetal
    brain (in neurons of hippocampus, cortex, mediodorsal and ventrolateral thalamic nuclei, putamen,
    cerebellum and brainstem)

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for SALL3 gene from 5/7 species (see all 7 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    SALL31   -- sal-like 3 (Drosophila) 77.96(n)
    77.19(a)
    607126  XM_843728.1  XP_848821.1 
    chimpanzee
    (Pan troglodytes)
    SALL31   -- sal-like 3 (Drosophila) 99.1(n)
    99.54(a)
    455483  XM_512182.2  XP_512182.2 
    rat
    (Rattus norvegicus)
    Sall31   -- sal-like 3 (Drosophila) 78.18(n)
    81.6(a)
    364910  XM_344708.3  XP_344709.3 
    mouse
    (Mus musculus)
    Sall31, 5 185
    sal-like 3 (Drosophila)1, 5 78.85(n)1
    81.92(a)1
    206891  NM_178280.31  NP_840064.21 
     AK0450515  AK0829995  (see all 15)
    chicken
    (Gallus gallus)
    SALL31   -- sal-like 3 (Drosophila) 68.62(n)
    73.16(a)
    395359  NM_204647.1  NP_989978.1 
    About this table        Species with no ortholog for SALL3

    ENSEMBL Gene Tree for SALL3
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for SALL3 gene
    SALL42  SALL12  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/109 NCBI SNPs in SALL3 are shown (see all 109 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 75)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 18 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs24474371,2
    A,C74854756(-) AGTGAC/GGGGCG 1 L/V mis1 ese30--------
    rs72408601,2
    A,C74854576(+) CGCCCA/GCTGTC 1 T/A mis1 ese30--------
    rs28489291,2
    H74839265(-) ATTAAG/AATTTT 1 -- ng514Minor allele frequency- A:0.00EU EA WA 420
    rs29272571,2
    C74840008(+) ATCCAA/GAAGTG 1 -- ng510--------
    rs24726441,2
    A,C,F74855454(+) TCCTAT/CGCGGG 1 Y/Y syn1 ese31Minor allele frequency- C:0.27NA 66
    rs29272581,2
    C,F74855355(-) CTCAGG/AGTCTC 1 T/T syn1 ese31Minor allele frequency- A:0.10NA 52
    rs72331941,2
    A,C74854479(+) TACGGC/TATGTC 1 G/G syn1 ese30--------
    rs4968091,2
    A,C,F,H,O74857661(-) AATGAG/ATGCGG 1 -- int114Minor allele frequency- A:0.07MN EA NA EU WA 2734
    rs102212851,2
    A,C,F,H74847215(+) AAACTG/ACAAAT 1 -- int14Minor allele frequency- A:0.01EU EA WA 418
    rs24726401,2
    A,C,F,H74852046(+) TTCCAT/CTATGG 1 -- int16Minor allele frequency- C:0.34EU EA WA NA 600
    About this table

    HapMap Linkage Disequilibrium images for SALL3 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 605079

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    7 PubMed articles for SALL3 gene:
    (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, and/or H-InvDB)
    About This Section

    Entrez Gene: 27164 HGNC: 10527 AceView: SALL3 Ensembl:ENSG00000151514 euGenes: HUgn27164
    ECgene: SALL3 H-InvDB: SALL3
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

      --
    (Available from WIS Yeda, Salk, Tufts)
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      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for SALL3:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Millipore Custom Antibody & Bulk Services
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     Millipore Immunoassay Services
     Millipore Target Screening & Profiling Services


     Predesigned and custom siRNAs for SALL3 Antibodies for SALL3
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for SALL3 Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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