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SALL4 Gene

protein-coding   GIFtS: 59

GC20M049833
sal-like 4 (Drosophila)
(Previous name: sal (Drosophila)-like 4 )
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
DRRS 2
HSAL4 2, 5
MGC133050 2
OTTHUMP00000031296 2
ZNF797 1, 2
dJ1112F19.1 1, 2
Descriptions
Zinc finger protein SALL4 3
sal (Drosophila)-like 4 1
sal-like 4 2
sal-like 4 (Drosophila) 2
External Ids
HGNC: 159241
Entrez Gene: 571672
UniProtKB: Q9UJQ43
Ensembl: ENSG000001011157
Search outside databases for aliases for SALL4 gene

Previous GC identifers: GC20M050129 GC20M051039 GC20M051086

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for SALL4:
The protein encoded by this gene may be a zinc finger transcription factor. Defects in this gene
are a cause of Duane-radial ray syndrome (DRRS). [provided by RefSeq]

UniProtKB/Swiss-Prot: SALL4_HUMAN, Q9UJQ4
Function: Probable transcription factor

Gene Wiki entry for SALL4

(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 SALL4 gene  

Entrez Gene cytogenetic band: 20q13.13-q13.2   Ensembl cytogenetic band:  20q13.2   HGNC cytogenetic band: 20q13.2

SALL4 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 20         GeneLoc Exon Structure

GeneLoc location for GC20M049833:     (about GC identifiers)

Start:
49,833,988 bp from pter
End:
49,852,421 bp from pter
Size:
18,434 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000020.9  NT_011362.9  
(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)
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UniProtKB/Swiss-Prot: SALL4_HUMAN, Q9UJQ4 (See protein sequence)
Recommended Name: Sal-like protein 4  
Size: 1053 amino acids; 112231 Da
Subunit: Interacts with NANOG (By similarity)
Subcellular location: Nucleus (Probable)
Secondary accessions: Q540H3

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_065169.1  

    ENSEMBL proteins: 
    ENSP00000379319 ENSP00000217086 ENSP00000360594 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Sigma-Aldrich AQUA Peptides for SALL4  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (Sall4)
    Human Recombinant Proteins from Abnova (SALL4)
                    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 SALL4: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for SALL4
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (Sall4), each with their AbpromiseSM
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Novus Biologicals Antibodies for SALL4

    Assays for SALL4: 
    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  SALL4 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q9UJQ4

    ProtoNet protein and cluster: Q9UJQ4

    UniProtKB/Swiss-Prot: SALL4_HUMAN, Q9UJQ4
    Similarity: Belongs to the sal C2H2-type zinc-finger protein family
    Similarity: Contains 7 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 (SALL4)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (SALL4)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_020436

                  Applied Biosystems Silencer® siRNAs for SALL4

                  Sigma-Aldrich siRNA for SALL4  
                         Sigma-Aldrich shRNA for SALL4  
                         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_020436
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_020436
                                     untagged cDNA clone in CMV expression vector: NM_020436 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_020436

    UniProtKB/Swiss-Prot: SALL4_HUMAN, Q9UJQ4
    Function: Probable transcription factor

    15/18 MGI mutant phenotypes (inferred from 10 alleles(MGI details for Sall4) (see all 18 ):

    behavior/neurologicalcraniofacialdigestive/alimentaryembryogenesis
    growth/sizehearing/vestibular/earimmune systemlethality-postnatallethality-prenatal/perinatal
    life span-post-weaning/aginglimbs/digits/tailmusclenervous systemrenal/urinary system

    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


    2 Sigma-Aldrich "Your Favorite Gene" Pathways for  SALL4  (Your Favorite Gene powered by Ingenuity) 
     Role of NANOG in Mammalian Embryonic Stem Cell Pluripotency
     Role of Oct4 in Mammalian Embryonic Stem Cell Pluripotency

       GeneDecks  SALL4 for the pathways selected above  
    About GeneDecksing


    5/13 Interacting proteins for SALL4 (ENSP000002170863) via UniProtKB, MINT, and/or STRING (see all 13 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TBX5ENSP000003099133STRING (score=.986)
    FAM58AENSP000002763453STRING (score=.953)
    NANOGP8ENSP000002293073STRING (score=.949)
    BMI1ENSP000003659093STRING (score=.922)
    GATA4ENSP000003344583STRING (score=.904)
    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 SALL4
    1 Novoseek chemical compound relationship for SALL4 gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    zinc 37.42 2 16086360 (1), 16411190 (1)
    About this table


    (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 (SALL4)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (SALL4)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_020436

                  Sigma-Aldrich siRNA for SALL4  
                         Sigma-Aldrich shRNA for SALL4  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_020436  

    REFSEQ mRNAs for SALL4 gene: 

    NM_020436.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_020436  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_020436
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_020436
                                     untagged cDNA clone in CMV expression vector: NM_020436 

    Additional cDNA sequence: 

    AK001666.1 AY170621.1 AY170622.1 AY172738.1 BC111714.1 

    5 DOTS entries:

    DT.108738  DT.40255005  DT.100725623  DT.120827482  DT.95148058 

    24/35 AceView cDNA sequences (see all 35 ):

    NM_020436 AW582834 BX089818 AY170622 AY172738 BX479229 AW270757 AA399371 
    AA419623 AK001666 CD656859 AI334028 AI968562 AY170621 AI632569 BQ278036 
    BM557759 CD644001 CD642385 CD655292 BF056751 AA738181 AA601246 CD642332 

    highest scoring ESTs for SALL4:

    AI638036 AK001666 AU132898 AY170621 AY170622 AY172738 CD642332 CD642385 CD655292 AA399371 

    Unigene Cluster for SALL4:

    Sal-like 4 (Drosophila)
    Hs.517113  [show with all ESTs]
    Unigene Representative Sequence: NM_020436


    GeneLoc Exon Structure

    5/6 Alternative Splicing Database (ASD) splice patterns (SP) for SALL4 (see all 6 )

    ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c · 5d · 5e ^ 6 ^ 7a · 7b
    SP1:              -     -     -     -     -     -                                                   
    SP2:                                -     -                                                         
    SP3:              -     -     -     -     -     -                             -                     
    SP4:              -     -     -     -     -     -     -     -     -     -     -                     
    SP5:                          -     -                                                               

    About this scheme

    ECgene alternative splicing isoforms for SALL4

    3 Ensembl transcripts including schematic representations:
    ENST00000395997  ENST00000217086  ENST00000371539  
    (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

    SALL4 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for SALL4

    1 / 2 / 3

    3 probe-sets matching SALL4 gene


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

    48384_at2, 3 U95-B 1 1.00 1.00 1.00 1.00 AI638036 0.80 1.00 0.91 1

    229661_at2, 3 U133-B 2 1.00 0.95 -- -- NM_020436 0.60 1.00 0.82 1

    229661_at2 U133Plus2 2 1.00 0.95 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: CTCAATGGCG

    SOURCE GeneReport for Unigene cluster: Hs.517113

    UniProtKB/Swiss-Prot: SALL4_HUMAN, Q9UJQ4
    Tissue specificity: Expressed in testis

    (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 SALL4 gene from 5/8 species (see all 8 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    SALL41   -- sal-like 4 (Drosophila) 86.24(n)
    87.25(a)
    485931  XM_543055.2  XP_543055.2 
    chimpanzee
    (Pan troglodytes)
    SALL41   -- sal-like 4 (Drosophila) 99.65(n)
    99.53(a)
    458342  XM_514728.2  XP_514728.2 
    cow
    (Bos taurus)
    SALL41   -- sal-like 4 (Drosophila) 79.97(n)
    79.7(a)
    541170  XM_614880.3  XP_614880.2 
    mouse
    (Mus musculus)
    Sall41, 5 2 (99.00 cM)5
    sal-like 4 (Drosophila)1, 5 78.61(n)1
    75.74(a)1
    993771  NM_175303.31  NP_780512.21 
     AA4077175  AF2855885  (see all 27)
    chicken
    (Gallus gallus)
    RCJMB04_22p101   -- sal-like 4 (Drosophila) 66.07(n)
    64.96(a)
    769286  XM_001232528.1  XP_001232529.1 
    About this table        Species with no ortholog for SALL4

    ENSEMBL Gene Tree for SALL4
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for SALL4 gene
    SALL32  SALL12  

    Pseudogenes
    2 related pseudogenes


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


    10/176 NCBI SNPs in SALL4 are shown (see all 176 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 67)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 20 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs60214511,2
    A,C,F,H49852802(+) CGGCTT/GTATTT 1 -- ng3116Minor allele frequency- G:0.16EU EA WA NA 1474
    rs130377021,2
    C,F,H49853173(+) TACAAT/CGCAAA 1 -- ng31 tfbs34Minor allele frequency- C:0.05EU EA WA 368
    rs60913751,2
    C,F,H49840037(+) CTTGAT/GGCTTT 1 L/I mis1 ese311Minor allele frequency- G:0.07EU EA WA NA 966
    rs130417031,2
    C,F,H49854068(+) AATACA/CTAGAA 1 -- ng3111Minor allele frequency- C:0.06NA EU EA WA 976
    rs169962491,2
    C,F,H49853439(+) TTATTA/GCAGAA 1 -- ng31 tfbs311Minor allele frequency- G:0.04NA EU EA WA 978
    --
    rs60214521,2
    A49854256(+) aatttA/Cattta 1 -- ng310--------
    rs60214371,2
    A,C,F,H49840569(+) ATGGAT/CGTGTT 1 T/T syn1 ese37Minor allele frequency- C:0.34EU EA WA NA 562
    --
    rs130388931,2
    C,F,H49841373(+) TCTAGC/TGCCAC 1 A/A syn17Minor allele frequency- T:0.22NA EU EA WA 540
    rs130432481,2
    C,F,H49840392(+) GCGCCG/AGTGCT 1 T/T syn1 ese38Minor allele frequency- A:0.04EU EA WA 826
    --
    rs178027351,2
    C,F,H49838909(+) GCAGAC/GGAGAA 1 S/S syn1 ese37Minor allele frequency- G:0.06NA EU EA WA 554
    About this table

    HapMap Linkage Disequilibrium images for SALL4 (up to first 250kb)

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

    OMIM: 607343   disorders: 607323  147750  

    UniProtKB/Swiss-Prot: SALL4_HUMAN, Q9UJQ4

  • Defects in SALL4 are the cause of Duane-radial ray syndrome (DRRS) [MIM:607323]; also
    known as Okihiro syndrome. DRRS is a disorder characterized by the association of forearm
    malformations with Duane retraction syndrome
  • Defects in SALL4 are the cause of IVIC syndrome [MIM:147750]. IVIC syndrome is an
    autosomal dominant condition characterized by upper limbs anomalies (radial ray defects, carpal
    bones fusion), extraocular motor disturbances, congenital bilateral non-progressive mixed hearing
    loss. Other less consistent malformations include heart involvement, mild thrombocytopenia and
    leukocytosis (before age 50), shoulder girdle hypoplasia, imperforate anus, kidney malrotation or
    rectovaginal fistula. The IVIC syndrome is an allelic disorder of Duane-radial ray syndrome (DRRS)
    with a similar phenotype
  • 1 Novoseek disease relationship for SALL4 gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    okihiro syndrome 98.91 12 16402211 (2), 16411190 (2), 15286162 (1), 16790473 (1) (see all 8)
    About this table

    GeneTests: SALL4
    SALL4-Related Disorders

    Human Gene Mutation Database: SALL4
    Human Genome Epidemiology Navigator: SALL4 (1 document)

    (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

    10/30 PubMed articles for SALL4 gene (see all 30 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Disorders
    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: 57167 HGNC: 15924 AceView: SALL4 Ensembl:ENSG00000101115 euGenes: HUgn57167
    ECgene: SALL4 H-InvDB: SALL4
    (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

    NameDescription
    GeneReviewshttp://www.genetests.org/query?gene=SALL4
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (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 SALL4:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for SALL4 Antibodies for SALL4
     Explore super-pooled esiRNAs Proteins for SALL4
     Lentivirus-delivered shRNAs for SALL4 Browse small molecules at Sigma-Aldrich
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