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SALL1 Gene

protein-coding   GIFtS: 60

GC16M049727
sal-like 1 (Drosophila)
(Previous name: sal (Drosophila)-like 1 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: TBS)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
HSAL1 2, 5
HSal1 3
Hsal1 1
SAL1 3
TBS 2, 5
ZNF794 1, 2
Descriptions
Spalt-like transcription factor 1 2, 3
Zinc finger protein SALL1 3
sal (Drosophila)-like 1 1
sal-like 1 2
sal-like 1 (Drosophila) 2
External Ids
HGNC: 105241
Entrez Gene: 62992
UniProtKB: Q9NSC23
Ensembl: ENSG000001034497
Search outside databases for aliases for SALL1 gene

Previous GC identifers: GC16M041583 GC16M051217 GC16M050907 GC16M050948

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for SALL1:
The protein encoded by this gene is a zinc finger transcriptional repressor and may be part of the
NuRD histone deacetylase complex (HDAC). Defects in this gene are a cause of Townes-Brocks
syndrome (TBS) as well as bronchio-oto-renal syndrome (BOR). Two transcript variants encoding
different isoforms have been found for this gene. [provided by RefSeq]

UniProtKB/Swiss-Prot: SALL1_HUMAN, Q9NSC2
Function: Transcriptional repressor involved in organogenesis (By similarity)

Gene Wiki entry for SALL1

(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)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the SALL1 gene  

Entrez Gene cytogenetic band: 16q12.1   Ensembl cytogenetic band:  16q12.1   HGNC cytogenetic band: 16q12.1

SALL1 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 16         GeneLoc Exon Structure

GeneLoc location for GC16M049727:     (about GC identifiers)

Start:
49,727,387 bp from pter
End:
49,742,684 bp from pter
Size:
15,298 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000016.8  NT_010498.15  
(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)
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UniProtKB/Swiss-Prot: SALL1_HUMAN, Q9NSC2 (See protein sequence)
Recommended Name: Sal-like protein 1  
Size: 1324 amino acids; 140391 Da
Subunit: Interacts with HDAC1, HDAC2, RBBP4, RBPP7, MTA1 and MTA2 (By similarity). Interacts with
FAM58A. Probably associates with NuRD histone deacetylase complex (HDAC)
Subcellular location: Nucleus (By similarity)
Developmental stage: In fetal brain exclusively in neurons of the subependymal region of
hypothalamus lateral to the third ventricle
Secondary accessions: Q99881 Q9NSC3 Q9P1R0

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins (2 alternative transcripts): 
    NP_001121364.1  NP_002959.2  


    ENSEMBL proteins: 
    ENSP00000251020 


    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 (SALL1)
    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 SALL1: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse Antibodies at Sigma-Aldrich
    R&D Systems Antibodies for SALL1
    Antibodies from Abcam (SALL1), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (SALL1)
    Search Novus for antibodies for SALL1

    Assays for SALL1: 
    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  SALL1 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q9NSC2

    ProtoNet protein and cluster: Q9NSC2

    UniProtKB/Swiss-Prot: SALL1_HUMAN, Q9NSC2
    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 (SALL1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (SALL1)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_002968

                  Applied Biosystems Silencer® siRNAs for SALL1

                  Sigma-Aldrich siRNA for SALL1  
                         Sigma-Aldrich shRNA for SALL1  
                         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 clones in CMV expression vector (see all 2): NM_001127892
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001127892
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_001127892 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_002968

    UniProtKB/Swiss-Prot: SALL1_HUMAN, Q9NSC2
    Function: Transcriptional repressor involved in organogenesis (By similarity)

    Genatlas biochemistry entry for SALL1:
    brain specific transcription factor,Drosophila homeotic gene Sal-like 1,expressed in corpus
    callosum and substantia nigra

    12 MGI mutant phenotypes (inferred from 5 alleles(MGI details for Sall1):

    behavior/neurologicaldigestive/alimentaryembryogenesisgrowth/size
    hearing/vestibular/earlethality-prenatal/perinatallife span-post-weaning/aginglimbs/digits/tailnervous system
    renal/urinary systemskeleton

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003700 transcription factor activity TAS9425907
    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


     Gene Network CentralTM Interacting Genes and Proteins Network for  SALL1 


    5/16 Interacting proteins for SALL1 (ENSP000002510203) via UniProtKB, MINT, and/or STRING (see all 16 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SIX1ENSP000002471823STRING (score=.94)
    SHHENSP000002972613STRING (score=.875)
    EPHA3ENSP000003374513STRING (score=.865)
    HOXA13ENSP000002227533STRING (score=.865)
    EPHA4ENSP000002818213STRING (score=.845)
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001657 ureteric bud development IEA--
    GO:0006350 transcription IEA--
    GO:0006355 regulation of transcription, DNA-dependent IEA--
    GO:0009653 anatomical structure morphogenesis TAS9425907
    GO:0031129 inductive cell-cell signaling 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 SALL1
    1 Novoseek chemical compound relationship for SALL1 gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    zinc 60.68 13 16088922 (2), 11102974 (1), 10965108 (1), 12925729 (1) (see all 12)
    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 (SALL1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (SALL1)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_002968

                  Sigma-Aldrich siRNA for SALL1  
                         Sigma-Aldrich shRNA for SALL1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_001127892  NM_002968  

    REFSEQ mRNAs for SALL1 gene (2 alternative transcripts): 

    NM_001127892.1   NM_002968.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_001127892  NM_002968  

                   OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001127892
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001127892
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_001127892 

    Additional cDNA sequence: 

    AK295103.1 AK307835.1 BC113881.1 BC113906.1 BC131548.1 Y18265.1 

    3 DOTS entries:

    DT.408356  DT.95196922  DT.75196640 

    24/29 AceView cDNA sequences (see all 29 ):

    AA932313 AU132405 AW166367 AA709028 BP350402 AU131453 AU123635 BP360753 
    NM_002968 AI376951 AI291817 AU130989 AA071082 AI002870 AI762905 BX505300 
    BM465643 Y18265 AI221270 AA856601 BF923314 AW768829 AU152837 AI291969 

    highest scoring ESTs for SALL1:

    AA856601 BM465643 Y18265 AA071082 AA709028 AA932313 AI002870 AI174371 AI221270 AI245549 

    Unigene Cluster for SALL1:

    Sal-like 1 (Drosophila)
    Hs.135787  [show with all ESTs]
    Unigene Representative Sequence: NM_001127892


    GeneLoc Exon Structure

    1 Ensembl transcript including schematic representation:
    ENST00000251020  
    (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

    SALL1 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for SALL1

    1 / 2 / 3

    6 probe-sets matching SALL1 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    32985_at2, 3 U95-A 1 1.00 1.00 0.97 0.87 AF017655 0.20 1.00 0.72 1
    76244_at2, 3 U95-E 1 1.00 1.00 0.98 1.16 AA856601 0.80 1.00 0.91 1

    206893_at2, 3 U133-A 1 1.00 1.00 -- -- NM_002968 0.60 1.00 0.82 1

    229273_at2, 3 U133-B 1 1.00 1.00 -- -- AU152837 0.60 1.00 0.82 1

    206893_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    229273_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    GeneDecks  SALL1 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: CACTTTCTTG

    SOURCE GeneReport for Unigene cluster: Hs.135787

    Expression variation in blood from EXPOLDB for SALL1

    UniProtKB/Swiss-Prot: SALL1_HUMAN, Q9NSC2
    Tissue specificity: Highest levels in kidney. Lower levels in adult brain (enriched in corpus
    callosum, lower expression in substantia nigra) and liver

    (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 SALL1 gene from 5/11 species (see all 11 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    SALL11   -- sal-like 1 (Drosophila) 91.17(n)
    94.1(a)
    487284  XM_544410.2  XP_544410.2 
    chimpanzee
    (Pan troglodytes)
    SALL11   -- sal-like 1 (Drosophila) 99.49(n)
    99.15(a)
    473281  XM_528651.2  XP_528651.2 
    cow
    (Bos taurus)
    SALL11   -- sal-like 1 (Drosophila) 90.24(n)
    93.38(a)
    514467  XM_592327.3  XP_592327.2 
    rat
    (Rattus norvegicus)
    Sall11   -- sal-like 1 (Drosophila) 88.04(n)
    91.17(a)
    307740  XM_226329.4  XP_226329.2 
    mouse
    (Mus musculus)
    Sall11, 5 85
    sal-like 1 (Drosophila)1, 5 87.69(n)1
    90.83(a)1
    581981  NM_021390.21  NP_067365.11 
     AA3864395  AB0514095  (see all 12)
    About this table        Species with no ortholog for SALL1

    ENSEMBL Gene Tree for SALL1
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for SALL1 gene
    SALL32  SALL42  

    Pseudogenes
    1 related pseudogene


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


    10/87 NCBI SNPs in SALL1 are shown (see all 87 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 45)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 16 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs99382851,2
    A,C,F,H49744541(+) CGCCCC/TAATTC 1 -- ng314Minor allele frequency- T:0.43EU EA WA 414
    --
    rs46147231,2
    C,F,H49728676(+) ACTAAT/CAGGTG 2 I/V mis1 ese35Minor allele frequency- C:0.40WA EU EA 536
    --
    rs47855051,2
    A,C49743978(+) CTGAGA/CGCAGC 1 -- ng310--------
    --
    rs10544781,2
    C49727522(-) CATGCA/CCTTTC 2 -- ut311Minor allele frequency- C:0.00MN 184
    --
    rs133361291,2
    C49733159(+) GCCGCC/TGCTGC 2 S/G mis1 ese30--------
    rs37437671,2
    F49728332(+) GTTATA/GTCGCT 2 -- ut311Minor allele frequency- G:0.04EA 1492
    rs19650241,2
    A,C,F,H,O49731060(-) CCCCTC/TGAGAT 2 L/L syn1 ese37Minor allele frequency- T:0.33NA PA EU EA WA 670
    rs116452881,2
    A,C,F,H49730178(+) CTCTCA/GTGAAT 2 H/H syn1 ese33Minor allele frequency- G:0.11EU EA 300
    --
    rs37437681,2
    F49728788(+) GCTGCA/GTACTG 2 Y/Y syn1 ese31Minor allele frequency- G:0.01EA 1496
    rs14653381,2
    A,C,F,H49729171(-) AGAGAA/GTGAAC 1 -- int14Minor allele frequency- G:0.47EU EA WA 412
    About this table

    HapMap Linkage Disequilibrium images for SALL1 (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: 602218   disorders: 107480  107480  

    UniProtKB/Swiss-Prot: SALL1_HUMAN, Q9NSC2

  • Defects in SALL1 are the cause of Townes-Brocks syndrome (TBS) [MIM:107840]. TBS is a
    rare, autosomal dominant malformation syndrome with a combination of imperforate anus,
    triphalangeal and supernumerary thumbs, malformed ears and sensorineural hearing loss
  • Defects in SALL1 may cause a phenotype overlapping with TBS, similar to bronchio-oto-renal
    syndrome (BOR) [MIM:113650]. BOR is an autosomal dominant disorder, manifested by various
    combinations of preauricular pits, branchial fistulae or cysts, lacrimal duct stenosis, hearing
    loss, structural defects of the outer, middle, or inner ear, and renal dysplasia. Associated
    defects include asthenic habitus, long narrow facies, constricted palate, deep overbite, and
    myopia. Hearing loss may be due to Mondini type cochlear defect and stapes fixation
  • 9 Novoseek disease relationships for SALL1 gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    townes-brocks syndrome 99.26 43 16088922 (2), 16429401 (2), 17295837 (2), 19005989 (2) (see all 34)
    okihiro syndrome 91.56 2 18818376 (1), 16790473 (1)
    limb malformation 72.20 2 18000979 (2)
    renal agenesis 62.87 1 16670092 (1)
    renal dysplasia 56.91 1 10654325 (1)
    developmental disabilities 49.89 2 18818376 (1), 18024993 (1)
    heart defects congenital 41.35 2 15158448 (1), 17295837 (1)
    congenital malformation 26.51 1 16670092 (1)
    renal failure chronic 13.06 1 16971658 (1)
    About this table

    GeneTests: SALL1
    Townes-Brocks Syndrome

    Human Gene Mutation Database: SALL1

    (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

    10/63 PubMed articles for SALL1 gene (see all 63 ):
    (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: 6299 HGNC: 10524 AceView: SALL1 Ensembl:ENSG00000103449 euGenes: HUgn6299
    ECgene: SALL1 H-InvDB: SALL1
    (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=SALL1
    (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 SALL1:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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