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    SALL2 spalt like transcription factor 2 [ Homo sapiens (human) ]

    Gene ID: 6297, updated on 3-Nov-2024

    Summary

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    Official Symbol
    SALL2provided by HGNC
    Official Full Name
    spalt like transcription factor 2provided by HGNC
    Primary source
    HGNC:HGNC:10526
    See related
    Ensembl:ENSG00000165821 MIM:602219; AllianceGenome:HGNC:10526
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    COLB; HSAL2; Sal-2; ZNF795; p150(Sal2)
    Summary
    This gene encodes a protein containing multiple zinc finger domains. The encoded protein functions in optical fissure closure during development of the eye in the embryo. Mutations in this gene are associated with ocular coloboma. [provided by RefSeq, Jul 2016]
    Expression
    Broad expression in brain (RPKM 13.4), ovary (RPKM 8.7) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SALL2 in Genome Data Viewer
    Location:
    14q11.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (21521080..21537121, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (15718455..15734493, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (21989231..22005255, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903283 Neighboring gene RAB2B, member RAS oncogene family Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8108 Neighboring gene TOX high mobility group box family member 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8110 Neighboring gene methyltransferase 3, N6-adenosine-methyltransferase complex catalytic subunit Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8111 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:21987519-21988018 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:21991711-21991897 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:21992413-21993240 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:21994071-21994898 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:21994899-21995726 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:22002164-22003029 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:22010043-22010544 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:22010545-22011044 Neighboring gene MPRA-validated peak2117 silencer Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:22025683-22026226 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:22026227-22026770 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:22026789-22026975 Neighboring gene RBBP4 pseudogene 5 Neighboring gene olfactory receptor family 10 subfamily G member 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SALL2 methylation statistically correlated with a decrease in disease free survival in patients with oral squamous carcinoma.
      Title: SALL2 Is a Novel Prognostic Methylation Marker in Patients with Oral Squamous Carcinomas: Associations with SALL1 and SALL3 Methylation Status.
    2. Sall2 may play a significant role in NIT-1 cell function.
      Title: Sall2 knockdown exacerbates palmitic acid induced dysfunction and apoptosis of pancreatic NIT-1 beta cells.
    3. Using RNA interference, the role of Spalt-like gene-2 (SALL2) was investigated in human ovarian carcinoma (OC) A2780 cells. Found downregulation of SALL2 promoted growth of the OC cell line.
      Title: Effect of siRNA-silencing of SALL2 gene on growth, migration and invasion of human ovarian carcinoma A2780 cells.
    4. Understanding SALL2 function and the molecular mechanisms governing its expression and activity is critical to comprehend why and how SALL2 could contribute to disease. This knowledge will open new perspectives for the development of molecular targeted approaches in disease
      Title: Developmental SALL2 transcription factor: a new player in cancer.
    5. Sall2 enhanced the p16 minigene blocking of cell cycle progression and p16 knockdown with siRNA abolished most of the Sall2 inhibition of cell cycle progression
      Title: Sal-like protein 2 upregulates p16 expression through a proximal promoter element.
    6. Mechanisms of silencing SALL2 in OVCA cell lines and primary tumors and possible therapeutic approaches for ovarian carcinoma are discussed in this review.
      Title: The tumor suppressor protein p150(Sal2) in carcinogenesis.
    7. A role for SALL2 in eye morphogenesis and loss of function of the gene causes ocular coloboma in humans and mice.
      Title: Mutation of SALL2 causes recessive ocular coloboma in humans and mice.
    8. The SALL2 P2 promoter is hypermethylated in a majority of serous ovarian carcinomas.
      Title: Promoter methylation of the SALL2 tumor suppressor gene in ovarian cancers.
    9. c-MYC may come under negative regulation by p150, consistent with the action of p150 as a putative tumor suppressor.
      Title: The polyoma virus large T binding protein p150 is a transcriptional repressor of c-MYC.
    10. Here, the authors report that human papillomavirus type 16 E6 targets the cellular factor p150(Sal2), which positively regulates p21(WAF1) transcription.
      Title: Human papillomavirus type 16 E6 inhibits p21(WAF1) transcription independently of p53 by inactivating p150(Sal2).
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Coloboma, ocular, autosomal recessive
    MedGen: C4011974 OMIM: 216820 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10414, FLJ55746, KIAA0360

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in eye development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    sal-like protein 2
    Names
    zinc finger protein 795
    zinc finger protein SALL2
    zinc finger protein Spalt-2

    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.

    Genomic

    1. NG_051069.1 RefSeqGene

      Range
      15871..21137
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001291446.2 → NP_001278375.1  sal-like protein 2 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two segments in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AK296414, BC090958, DC306696, DT216192
      UniProtKB/TrEMBL
      H0YFS7
      Related
      ENSP00000440054.1, ENST00000546363.5
      Conserved Domains (4) summary
      sd00017
      Location:240 → 260
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:778 → 798
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:557 → 578
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:252 → 277
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001291447.2 → NP_001278376.1  sal-like protein 2 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, initiates translation at an alternate start codon, and lacks two segments in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (c) has distinct N- and C-termini and is shorter than isoform a.
      Source sequence(s)
      AK296414, BC090958, DC307767, DC309911
      Consensus CDS
      CCDS76656.1
      UniProtKB/TrEMBL
      B4DK65, E7EW59
      Related
      ENSP00000396773.2, ENST00000450879.2
      Conserved Domains (4) summary
      sd00017
      Location:238 → 258
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:776 → 796
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:555 → 576
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:250 → 275
      zf-H2C2_2; Zinc-finger double domain

    3. NM_001364564.1 → NP_001351493.1  sal-like protein 2 isoform d

      Status: REVIEWED

      Source sequence(s)
      AL161747
      Consensus CDS
      CCDS91849.1
      UniProtKB/TrEMBL
      B4DK65, F5H433
      Related
      ENSP00000438493.2, ENST00000537235.2
      Conserved Domains (4) summary
      smart00355
      Location:371 → 393
      ZnF_C2H2; zinc finger
      sd00017
      Location:373 → 393
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:690 → 711
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:385 → 410
      zf-H2C2_2; Zinc-finger double domain

    4. NM_005407.3 → NP_005398.2  sal-like protein 2 isoform a

      See identical proteins and their annotated locations for NP_005398.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      BC090958, BC136528, DC306696
      Consensus CDS
      CCDS32045.1
      UniProtKB/Swiss-Prot
      B2RMX6, B9EGK8, Q8N656, Q9Y467, Q9Y4G1
      UniProtKB/TrEMBL
      H0YFS7
      Related
      ENSP00000483562.1, ENST00000614342.1
      Conserved Domains (3) summary
      sd00017
      Location:375 → 395
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:692 → 713
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:387 → 412
      zf-H2C2_2; Zinc-finger double domain

    RNA

    1. NR_111966.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks a large segment in the 3' region, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.
      Source sequence(s)
      AK001276, BC090958, DC306696
      Related
      ENST00000613414.4

    2. NR_111967.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' terminal exon and lacks a large segment in the 3' region, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.
      Source sequence(s)
      AK289358, BC090958, DC307767, DC309911

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      21521080..21537121 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011537064.2 → XP_011535366.1  sal-like protein 2 isoform X1

      UniProtKB/TrEMBL
      H0YFS7
      Conserved Domains (4) summary
      sd00017
      Location:375 → 395
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:913 → 933
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:692 → 713
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:387 → 412
      zf-H2C2_2; Zinc-finger double domain

    2. XM_011537065.3 → XP_011535367.1  sal-like protein 2 isoform X2

      UniProtKB/TrEMBL
      B4DK65
      Conserved Domains (4) summary
      sd00017
      Location:373 → 393
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:911 → 931
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:690 → 711
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:385 → 410
      zf-H2C2_2; Zinc-finger double domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      15718455..15734493 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376554.1 → XP_054232529.1  sal-like protein 2 isoform X1

    2. XM_054376555.1 → XP_054232530.1  sal-like protein 2 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y467.5 GenPept UniProtKB/Swiss-Prot:Q9Y467

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