Human Gene SALL1 (uc021tif.1) Description and Page Index
Description: Homo sapiens sal-like 1 (Drosophila) (SALL1), transcript variant 1, mRNA. RefSeq Summary (NM_001127892): 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]. Transcript (Including UTRs) Position: hg19 chr16:51,171,023-51,185,183 Size: 14,161 Total Exon Count: 3 Strand: - Coding Region Position: hg19 chr16:51,171,023-51,175,841 Size: 4,819 Coding Exon Count: 2
ID:SALL1_HUMAN DESCRIPTION: RecName: Full=Sal-like protein 1; AltName: Full=Spalt-like transcription factor 1; AltName: Full=Zinc finger protein 794; AltName: Full=Zinc finger protein SALL1; AltName: Full=Zinc finger protein Spalt-1; Short=HSal1; Short=Sal-1; FUNCTION: Transcriptional repressor involved in organogenesis (By similarity). 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). TISSUE SPECIFICITY: Highest levels in kidney. Lower levels in adult brain (enriched in corpus callosum, lower expression in substantia nigra) and liver. DEVELOPMENTAL STAGE: In fetal brain exclusively in neurons of the subependymal region of hypothalamus lateral to the third ventricle. DISEASE: Defects in SALL1 are the cause of Townes-Brocks syndrome (TBS) [MIM:107480]. TBS is a rare, autosomal dominant malformation syndrome with a combination of imperforate anus, triphalangeal and supernumerary thumbs, malformed ears and sensorineural hearing loss. Note=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. SIMILARITY: Belongs to the sal C2H2-type zinc-finger protein family. SIMILARITY: Contains 9 C2H2-type zinc fingers. WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SALL1";
Genetic Association Studies of Complex Diseases and Disorders
Genetic Association Database (archive): SALL1 CDC HuGE Published Literature: SALL1 Positive Disease Associations: Luteinizing Hormone Related Studies:
Luteinizing Hormone Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics.
Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on Q9NSC2
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.
Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
Gene Ontology (GO) Annotations with Structured Vocabulary
Molecular Function: GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding GO:0003676 nucleic acid binding GO:0003677 DNA binding GO:0003700 transcription factor activity, sequence-specific DNA binding GO:0005515 protein binding GO:0008013 beta-catenin binding GO:0043565 sequence-specific DNA binding GO:0044212 transcription regulatory region DNA binding GO:0046872 metal ion binding GO:0004407 histone deacetylase activity