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    Sall1 spalt-like transcription factor 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 307740, updated on 9-Dec-2024

    Summary

    Official Symbol
    Sall1provided by RGD
    Official Full Name
    spalt-like transcription factor 1provided by RGD
    Primary source
    RGD:1309916
    See related
    EnsemblRapid:ENSRNOG00000013907 AllianceGenome:RGD:1309916
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and beta-catenin binding activity. Predicted to be involved in several processes, including forebrain development; negative regulation of ectoderm development; and regulation of DNA-templated transcription. Predicted to act upstream of or within several processes, including limb morphogenesis; metanephric nephron morphogenesis; and regulation of transcription by RNA polymerase II. Predicted to be located in chromocenter; cytoplasm; and heterochromatin. Predicted to be part of NuRD complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Townes-Brocks syndrome; middle lobe syndrome; and renal Wilms' tumor. Orthologous to human SALL1 (spalt like transcription factor 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 50.6), Liver (RPKM 39.5) and 2 other tissues See more
    Orthologs
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    Genomic context

    See Sall1 in Genome Data Viewer
    Location:
    19p11
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (34179316..34196278)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (18005782..18022705)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (23387737..23405025)

    Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134483297 Neighboring gene transfer RNA proline (anticodon AGG) 28 Neighboring gene uncharacterized LOC102553576 Neighboring gene uncharacterized LOC134483619 Neighboring gene uncharacterized LOC134483620

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Pathways from PubChem

    General gene information

    Gene Ontology Provided by RGD

    Items 1 - 25 of 49
    Process Evidence Code Pubs
    acts_upstream_of GABAergic neuron differentiation  
    involved_in adrenal gland development  
    involved_in biological_process  
    acts_upstream_of branching involved in ureteric bud morphogenesis  
    involved_in branching involved in ureteric bud morphogenesis  
    involved_in embryonic digestive tract development  
    involved_in embryonic digit morphogenesis  
    acts_upstream_of_or_within forelimb morphogenesis  
    involved_in gonad development  
    involved_in heart development  
    acts_upstream_of_or_within hindlimb morphogenesis  
    acts_upstream_of_or_within inductive cell-cell signaling  
    involved_in kidney development  
    involved_in kidney epithelium development  
    involved_in limb development  
    acts_upstream_of_or_within mesenchymal stem cell maintenance involved in metanephric nephron morphogenesis  
    acts_upstream_of mesenchymal to epithelial transition involved in metanephros morphogenesis  
    involved_in mesenchymal to epithelial transition involved in metanephros morphogenesis  
    involved_in negative regulation of DNA-templated transcription  
    involved_in negative regulation of ectoderm development  
    acts_upstream_of_or_within negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis  
    involved_in negative regulation of mesoderm development  
    acts_upstream_of_or_within negative regulation of smoothened signaling pathway  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II  
    involved_in negative regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within neural tube closure  
    acts_upstream_of_or_within neural tube development  
    acts_upstream_of neuron differentiation  
    acts_upstream_of_or_within olfactory bulb development  
    involved_in olfactory bulb interneuron differentiation  
    involved_in olfactory bulb mitral cell layer development  
    acts_upstream_of_or_within olfactory nerve development  
    involved_in olfactory nerve development  
    involved_in pituitary gland development  
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of Wnt signaling pathway  
    acts_upstream_of_or_within positive regulation of branching involved in ureteric bud morphogenesis  
    acts_upstream_of_or_within positive regulation of neuron differentiation  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within regulation of neuroblast proliferation  
    involved_in regulation of transcription by RNA polymerase II  
    acts_upstream_of smoothened signaling pathway  
    acts_upstream_of transcription by RNA polymerase II  
    acts_upstream_of_or_within ureteric bud development  
    acts_upstream_of_or_within ureteric bud invasion  
    involved_in ureteric bud invasion  
    acts_upstream_of_or_within ventricular septum development  
    involved_in ventricular septum development  
    Items 1 - 25 of 49
    Component Evidence Code Pubs
    part_of NuRD complex  
    located_in chromocenter  
    located_in cytoplasm  
    located_in heterochromatin  
    is_active_in nucleus  
    located_in nucleus  

    General protein information

    Preferred Names
    sal-like protein 1
    Names
    sal-like 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001107415.2 → NP_001100885.2  sal-like protein 1

      See identical proteins and their annotated locations for NP_001100885.2

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      A0A8I5ZSH0, D3ZIF4
      Related
      ENSRNOP00000018628.4, ENSRNOT00000018629.9
      Conserved Domains (6) summary
      cd11674
      Location:1055 → 1146
      lambda-1; inner capsid protein lambda-1 or VP3
      COG5048
      Location:692 → 1160
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:699 → 719
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:994 → 1014
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:1125 → 1147
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:711 → 736
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086037.1 Reference GRCr8

      Range
      34179316..34196278
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006255260.5 → XP_006255322.1  sal-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006255322.1

      UniProtKB/TrEMBL
      A0A8I5ZSH0, D3ZIF4
      Conserved Domains (6) summary
      cd11674
      Location:1055 → 1146
      lambda-1; inner capsid protein lambda-1 or VP3
      COG5048
      Location:692 → 1160
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:699 → 719
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:994 → 1014
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:1125 → 1147
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:711 → 736
      zf-H2C2_2; Zinc-finger double domain
    2. XM_063278015.1 → XP_063134085.1  sal-like protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZSH0, D3ZIF4
    3. XM_039097721.2 → XP_038953649.1  sal-like protein 1 isoform X2

      UniProtKB/TrEMBL
      A6KD93
      Conserved Domains (6) summary
      cd11674
      Location:957 → 1048
      lambda-1; inner capsid protein lambda-1 or VP3
      sd00017
      Location:601 → 621
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:896 → 916
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:922 → 944
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:613 → 638
      zf-H2C2_2; Zinc-finger double domain
      cd20908
      Location:344 → 431
      SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
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