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SALL1 Gene

protein-coding   GIFtS: 62
GCID: GC16M051217

Spalt-Like Transcription Factor 1

(Previous names: sal (Drosophila)-like 1, sal-like 1 (Drosophila))
(Previous symbol: TBS)
  See SALL1-related diseases
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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Spalt-Like Transcription Factor 11 2 3     Sal (Drosophila)-Like 11
TBS1 2 5     Sal-Like 1 (Drosophila)1
Zinc Finger Protein 7942 3     HEL-S-892
Zinc Finger Protein SALL12 3     Epididymis Secretory Protein Li 892
Zinc Finger Protein Spalt-12 3     Sal-Like Protein 12
Sal-12 3     HSal13
ZNF7942 3     SAL13
HSAL12 5     

External Ids:    HGNC: 105241   Entrez Gene: 62992   Ensembl: ENSG000001034497   OMIM: 6022185   UniProtKB: Q9NSC23   
ORGUL members:         

Export aliases for SALL1 gene to outside databases

Previous GC identifers: GC16M041583 GC16M050907 GC16M050948 GC16M049727 GC16M037057


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SALL1 Gene:
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, Jul 2008)

GeneCards Summary for SALL1 Gene:
SALL1 (spalt-like transcription factor 1) is a protein-coding gene. Diseases associated with SALL1 include townes-brocks syndrome, and mosaic trisomy 8. GO annotations related to this gene include beta-catenin binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is SALL3.

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

Gene Wiki entry for SALL1 Gene


(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 at NCBI GenBank:
NC_000016.9  NT_010498.16  NC_018927.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SALL1 gene promoter:
         ER-alpha   CUTL1   Nkx2-5   NF-kappaB   NF-kappaB1   Evi-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSALL1 promoter sequence
   Search Chromatin IP Primers for SALL1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SALL1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

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)
SALL1 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M051217:  view genomic region     (about GC identifiers)

Start:
51,169,886 bp from pter      End:
51,185,278 bp from pter
Size:
15,393 bases      Orientation:
minus strand

(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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: SALL1_HUMAN, Q9NSC2 (See protein sequence)
Recommended Name: Sal-like protein 1  
Size: 1324 amino acids; 140405 Da
Subunit: Interacts with HDAC1, HDAC2, RBBP4, RBPP7, MTA1 and MTA2 (By similarity). Interacts with FAM58A. Probably
associates with NuRD histone deacetylase complex (HDAC)
Developmental stage: In fetal brain exclusively in neurons of the subependymal region of hypothalamus lateral to
the third ventricle
Secondary accessions: Q99881 Q9NSC3 Q9P1R0
Alternative splicing: 2 isoforms:  Q9NSC2-1   Q9NSC2-2   

Explore the universe of human proteins at neXtProt for SALL1: NX_Q9NSC2

Explore proteomics data for SALL1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SALL1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

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

    ENSEMBL proteins: 
     ENSP00000251020   ENSP00000455582   ENSP00000456777   ENSP00000442827   ENSP00000407914  

    SALL1 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for SALL1

     
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    antibodies-online peptides for SALL1

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    antibodies-online antibodies for SALL1 (31 products) 

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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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    HGNC Gene Families:
    ZNF: Zinc fingers, C2H2-type

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

    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


    Find genes that share domains with SALL1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: 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

         Gene Ontology (GO): Selected molecular function terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding NAS9425907
    GO:0003682chromatin binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity NAS9425907
    GO:0004407contributes to histone deacetylase activity ISS--
    GO:0005515protein binding IPI18297069
         
    Find genes that share ontologies with SALL1           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for SALL1:
     Increased gamma-H2AX phosphory 

         13 MGI mutant phenotypes (inferred from 9 alleles(MGI details for Sall1):
     behavior/neurological  cardiovascular system  cellular  digestive/alimentary  embryogenesis 
     growth/size/body  hearing/vestibular/ear  limbs/digits/tail  mortality/aging  nervous system 
     normal  renal/urinary system  skeleton 

    Find genes that share phenotypes with SALL1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for SALL1: Sall1tm1Jkoh Sall1tm1Mrau Sall1tm1Ryn

       genOway: Develop your customized and physiologically relevant rodent model for SALL1

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    miRTarBase miRNAs that target SALL1:
    hsa-let-7e-5p (MIRT051534), hsa-mir-26b-5p (MIRT029033), hsa-mir-423-5p (MIRT038173), hsa-mir-103a-3p (MIRT027034), hsa-mir-16-5p (MIRT031523), hsa-mir-320a (MIRT044785), hsa-mir-744-5p (MIRT037498)

    Block miRNA regulation of human, mouse, rat SALL1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SALL1 (see all 83):
    hsa-miR-411* hsa-miR-300 hsa-miR-376b hsa-miR-106a hsa-miR-15a hsa-miR-519a hsa-miR-93 hsa-miR-3613-3p
    SwitchGear 3'UTR luciferase reporter plasmidSALL1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SALL1

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    Browse Sino Biological Human cDNA Clones
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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
    SALL1_HUMAN, Q9NSC2: Nucleus (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000792heterochromatin IDA15158448
    GO:0005634nucleus IDA12065233
    GO:0005737cytoplasm IDA12065233
    GO:0010369chromocenter IDA16443351
    GO:0016581colocalizes with NuRD complex ISS--

    Find genes that share ontologies with SALL1           About GenesLikeMe


    (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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    SuperPaths for SALL1 About    
    See pathways by source

    SuperPathContained pathways About
    1Wnt signaling pathway (KEGG)
    Wnt Signaling Pathway NetPath0.37
    2Transcriptional Regulatory Network in Embryonic Stem Cell
    Transcriptional Regulatory Network in Embryonic Stem Cell

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for SALL1
        Transcriptional Regulatory Network in Embryonic Stem Cell

    1 BioSystems Pathway for SALL1
        Wnt Signaling Pathway NetPath


        Pathway & Disease-focused RT2 Profiler PCR Array including SALL1: 
              Polycomb & Trithorax Target Genes in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for SALL1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SALL1 (Q9NSC23 ENSP000002510204) via UniProtKB, MINT, STRING, and/or I2D (see all 70)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000206454Q018603, ENSP000003730164I2D: score=1 STRING: ENSP00000373016
    ENSG00000229094Q018603, ENSP000003888424I2D: score=1 STRING: ENSP00000388842
    ENSG00000230336Q018603, ENSP000004000474I2D: score=1 STRING: ENSP00000400047
    ENSG00000233911Q018603, ENSP000003928774I2D: score=1 STRING: ENSP00000392877
    ENSG00000235068Q018603, ENSP000004050414I2D: score=1 STRING: ENSP00000405041
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 34):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IDA16443351
    GO:0001657ureteric bud development ISS--
    GO:0001658branching involved in ureteric bud morphogenesis ISS--
    GO:0001822kidney development IMP16971658
    GO:0001843neural tube closure IEA--

    Find genes that share ontologies with SALL1           About GenesLikeMe



    (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 SALL1

    2 Novoseek inferred chemical compound relationships for SALL1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    zinc 59.7 14 16088922 (2), 11102974 (1), 20439720 (1), 10965108 (1) (see all 13)
    arginine 0 2 12200128 (1)



    Find genes that share compounds with SALL1           About GenesLikeMe



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SALL1 gene (2 alternative transcripts): 
    NM_001127892.1  NM_002968.2  

    Unigene Cluster for SALL1:

    Sal-like 1 (Drosophila)
    Hs.135787  [show with all ESTs]
    Unigene Representative Sequence: NM_001127892
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000251020(uc021tie.1 uc021tif.1 uc010cbv.3) ENST00000566102
    ENST00000570206 ENST00000562674 ENST00000541611 ENST00000440970(uc021tid.1)

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SALL1 (see all 83):
    hsa-miR-411* hsa-miR-300 hsa-miR-376b hsa-miR-106a hsa-miR-15a hsa-miR-519a hsa-miR-93 hsa-miR-3613-3p
    SwitchGear 3'UTR luciferase reporter plasmidSALL1 3' UTR sequence
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat SALL1

    Additional mRNA sequence: 

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

    3 DOTS entries:

    DT.408356  DT.95196922  DT.75196640 

    Selected AceView cDNA sequences (see all 29):

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

    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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    SALL1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CACTTTCTTG
    SALL1 Expression
    About this image


    SALL1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 12) fully expand
     
     Kidney (Urinary System)    fully expand to see all 5 entries
             Metanephric Mesenchyme Cells Metanephric Mesenchyme
             Epithelial Tubule
             Human kidney epithelial cell spheroids
     
     Intermediate Mesoderm (Gastrulation Derivatives)    fully expand to see all 2 entries
             Intermediate mesoderm-like cells
     
     NULL (Uncategorized)    fully expand to see all 3 entries
             Mesoderm-like cells
     
     Neural Tube (Nervous System)    fully expand to see all 3 entries
             Metencephalon
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 2 entries
             Human embryonic stem cells (family)
    SALL1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SALL1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.135787

    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

        Pathway & Disease-focused RT2 Profiler PCR Array including SALL1: 
              Polycomb & Trithorax Target Genes in human mouse rat

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SALL1

    (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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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for SALL1 gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sall11 , 5 sal-like 1 (Drosophila)1, 5 87.8(n)1
    90.39(a)1
      8 (43.51 cM)5
    581981  NM_021390.31  NP_067365.21 
     890272485 
    chicken
    (Gallus gallus)
    Aves SALL11 sal-like 1 (Drosophila) 80.59(n)
    87.45(a)
      395446  NM_204707.1  NP_990038.1 
    lizard
    (Anolis carolinensis)
    Reptilia SALL16
    spalt-like transcription factor 1
    80(a)
    1 ↔ 1
    GL343227.1(855740-880271)
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC684182 hypothetical protein MGC68418 80.65(n)    AF310007.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.143052 Transcribed sequence with moderate similarity to protein more 75.68(n)    BG308878.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta salm3 oenocyte development specific RNA
    polymerase II more
    62(a)
    (best of 2)
        --
    worm
    (Caenorhabditis elegans)
    Secernentea sem-46
    Protein SEM-4 (sem-4) mRNA, complete cds
    30(a)
    1 → many
    I(7038900-7048834) WBGene00004773
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes FZF16
    Transcription factor involved in sulfite metabolis...
    26(a)
    1 → many
    VII(22304-23203) YGL254W


    ENSEMBL Gene Tree for SALL1 (if available)
    TreeFam Gene Tree for SALL1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SALL1 gene
    SALL32  ZNF2362  SALL22  SALL42  
    Selected SIMAP similar genes for SALL1 using alignment to 5 protein entries:     SALL1_HUMAN (see all proteins) (see all similar genes):
    SALL3    HZF16    PLAGL1    ZFS-4    ZFS-5    DKFZp547H249
    OVOL3    ZNF468    ZNF844    kr-znf3    ZNF    DKFZp434J0650
    ZNF692    ZNF791    ZNF516    ZNF672    ZNF697    ZNF702P

    Find genes that share paralogs with SALL1           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for SALL1
    PGOHUM00000257254


    (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 SALL1 (see all 455)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1048945351,2
    Cpathogenic152187671(-) CTCATA/C/GATCGT 6 * S stg10--------
    rs1048945381,2
    Cpathogenic152187819(-) TACCTC/TAGAGC 4 Q * stg10--------
    rs1048945371,2
    Cpathogenic152187960(-) CTTTAC/TGAACA 4 R * stg10--------
    rs1413213281,2
    Cuntested152187771(+) ATTGGA/G/TAGAAG 4 P S mis10--------
    rs58167471,2
    C--37067113(+) TACTT-/AAAAAA 2 -- int1 trp30--------
    rs58167481,2
    C--37067234(+) CACAT-/ACACACA 2 -- int10--------
    rs359293811,2
    C--51170435(+) TCGAC-/AAAAAA 2 -- ut312Minor allele frequency- A:0.25NA 4
    rs106517201,2
    C--51172277(+) CTAGGCTGT/-  
            
    CTTTC
    2 -- int11Minor allele frequency- -:0.00CSA 2
    rs342043871,2
    C--51177327(+) AAAAA-/A/AA  
            
    CTGTT
    2 -- int11CSA 2
    rs58167461,2
    C,F--51177339(+) AAAAA-/A/AA  
            
    CTGTT
    2 -- int12NA 4

    HapMap Linkage Disequilibrium report for SALL1 (51169886 - 51185278 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for SALL1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2658882CNV Deletion23128226
    nsv833224CNV Loss17160897
    dgv475n67CNV Gain20364138

    Human Gene Mutation Database (HGMD): SALL1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SALL1
    DNA2.0 Custom Variant and Variant Library Synthesis for SALL1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 602218   
    OMIM disorders: 107480  
    UniProtKB/Swiss-Prot: SALL1_HUMAN, Q9NSC2
  • Townes-Brocks syndrome (TBS) [MIM:107480]: Rare, autosomal dominant malformation syndrome with a
    combination of imperforate anus, triphalangeal and supernumerary thumbs, malformed ears and sensorineural hearing
    loss. Note=The disease is caused by mutations affecting the gene represented in this entry. Some individuals with
    SALL1 mutations manifest a phenotype overlapping with TBS and bronchio-oto-renal syndrome. Clinical features
    include dysplastic ears, hypoplastic kidneys with impaired renal function, gastroesophageal reflux,
    hypermetropia, hypospadias, and mild developmental delay. Affected individuals lack the characteristic anal or
    hand malformations of TBS

  • 11 diseases for SALL1:    
    About MalaCards
    townes-brocks syndrome    mosaic trisomy 8    lung sarcoma    townes-brocks branchiootorenal-like syndrome
    goldenhar syndrome    baller-gerold syndrome    imperforate anus    renal agenesis
    renal dysplasia    dysphagia    developmental disabilities

    7 diseases from the University of Copenhagen DISEASES database for SALL1:
    Imperforate anus     Goldenhar syndrome     Lung sarcoma     Renal agenesis
    Polydactyly     Sensorineural hearing loss     Baller-Gerold syndrome

    Find genes that share disorders with SALL1           About GenesLikeMe

    10 Novoseek inferred disease relationships for SALL1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    townes-brocks syndrome 99.2 47 20003547 (3), 16088922 (2), 16429401 (2), 17221874 (2) (see all 36)
    okihiro syndrome 92.6 4 19247946 (1), 18818376 (1), 16790473 (1)
    limb malformation 75.5 2 18000979 (2)
    renal agenesis 60.6 1 16670092 (1)
    microphthalmia 55.3 1 20003547 (1)
    renal dysplasia 54.9 1 10654325 (1)
    developmental disabilities 47.2 2 18818376 (1), 18024993 (1)
    heart defects congenital 38.5 2 15158448 (1), 17295837 (1)
    congenital malformation 23.6 1 16670092 (1)
    renal failure chronic 9.97 1 16971658 (1)

    GeneTests: SALL1
    GeneReviews: SALL1
    Genetic Association Database (GAD): SALL1
    Human Genome Epidemiology (HuGE) Navigator: SALL1 (3 documents)

    Export disorders for SALL1 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 SALL1 gene, integrated from 10 sources (see all 91):
    (articles sorted by number of sources associating them with SALL1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations in the SALL1 putative transcription factor gene cause Townes-Brocks syndrome. (PubMed id 9425907)1, 2, 3, 9 Kohlhase J.... Engel W. (Nat. Genet. 1998)
    2. Molecular analysis of SALL1 mutations in Townes-Brocks syndrome. (PubMed id 9973281)1, 2, 9 Kohlhase J.... Engel W. (Am. J. Hum. Genet. 1999)
    3. Townes-Brocks syndrome: detection of a SALL1 mutation hot spot and evidence for a position effect in one patient. (PubMed id 10533063)1, 2, 9 Marlin S.... Petit C. (Hum. Mutat. 1999)
    4. A SALL1 mutation causes a branchio-oto-renal syndrome-like phenotype. (PubMed id 10928856)1, 2, 9 Engels S.... McGaughran J. (J. Med. Genet. 2000)
    5. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PubMed id 20634891)1, 4 Jugessur A....Murray J.C. (PLoS ONE 2010)
    6. Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations. (PubMed id 18297069)1, 2 Unger S....Kohlhase J. (Nat. Genet. 2008)
    7. Isolation, characterization, and organ-specific expression of two novel human zinc finger genes related to the Drosophila gene spalt. (PubMed id 8975705)1, 2 Kohlhase J.... Stick R. (Genomics 1996)
    8. Detection of heterozygous SALL1 deletions by quantitative real time PCR proves the contribution of a SALL1 dosage effect in the pathogenesis of Townes-Brocks syndrome. (PubMed id 16429401)1, 9 Borozdin W....Kohlhase J. (Hum. Mutat. 2006)
    9. Transcriptional activation of the SALL1 by the human SIX1 homeodomain during kidney development. (PubMed id 16670092)1, 9 Chai L....Ma Y. (J. Biol. Chem. 2006)
    10. SALL1 mutation analysis in Townes-Brocks syndrome: twelve novel mutations and expansion of the phenotype. (PubMed id 16088922)1, 9 Botzenhart E.M....Kohlhase J. (Hum. Mutat. 2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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, Kegg, and/or H-InvDB)
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    Entrez Gene: 6299 HGNC: 10524 AceView: SALL1 Ensembl:ENSG00000103449 euGenes: HUgn6299
    ECgene: SALL1 H-InvDB: SALL1

    (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 SALL1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SALL1[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SALL1 gene:
    Search GeneIP for patents involving SALL1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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