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

Gene ID: 6297, updated on 3-Apr-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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Location:
14q11.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (21521080..21537121, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (15718455..15734493, complement)
105.20220307 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
  • 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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Related articles in PubMed

  1. SALL2 Is a Novel Prognostic Methylation Marker in Patients with Oral Squamous Carcinomas: Associations with SALL1 and SALL3 Methylation Status. Imai A, et al. DNA Cell Biol, 2019 Jul. PMID 31188017
  2. Sall2 knockdown exacerbates palmitic acid induced dysfunction and apoptosis of pancreatic NIT-1 beta cells. Wang Y, et al. Biomed Pharmacother, 2018 Aug. PMID 29783189
  3. Effect of siRNA-silencing of SALL2 gene on growth, migration and invasion of human ovarian carcinoma A2780 cells. Miao F, et al. BMC Cancer, 2017 Dec 11. PMID 29228922, Free PMC Article
  4. Developmental SALL2 transcription factor: a new player in cancer. Hermosilla VE, et al. Carcinogenesis, 2017 Jul 1. PMID 28430874
  5. The tumor suppressor protein p150(Sal2) in carcinogenesis. Sung CK, et al. Tumour Biol, 2015 Feb. PMID 25608837

See all (54) citations in PubMed

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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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_2023_10

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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