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

Gene ID: 6297, updated on 14-Oct-2018

Summary

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; Vega:OTTHUMG00000168826
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

Genomic context

See SALL2 in Genome Data Viewer
Location:
14q11.2
Exon count:
5
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (21521080..21537216, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (21989231..22005337, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene RAB2B, member RAS oncogene family Neighboring gene TOX high mobility group box family member 4 Neighboring gene methyltransferase like 3 Neighboring gene RBBP4 pseudogene 5 Neighboring gene olfactory receptor family 10 subfamily G member 3

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10414, FLJ55746, KIAA0360

Gene Ontology Provided by GOA

Process Evidence Code Pubs
eye development IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neural tube development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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
    5001..21137
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001291446.1NP_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/Swiss-Prot
    Q9Y467
    UniProtKB/TrEMBL
    B4DK65
    Related
    ENSP00000440054.1, OTTHUMP00000239560, ENST00000546363.5, OTTHUMT00000401245
    Conserved Domains (4) summary
    sd00017
    Location:240260
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:778798
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:557578
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:252277
    zf-H2C2_2; Zinc-finger double domain
  2. NM_001291447.1NP_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/Swiss-Prot
    Q9Y467
    UniProtKB/TrEMBL
    B4DK65, E7EW59
    Related
    ENSP00000396773.2, OTTHUMP00000239561, ENST00000450879.2, OTTHUMT00000401246
    Conserved Domains (4) summary
    sd00017
    Location:238258
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:776796
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:555576
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:250275
    zf-H2C2_2; Zinc-finger double domain
  3. NM_001364564.1NP_001351493.1  sal-like protein 2 isoform d

    Status: REVIEWED

    Source sequence(s)
    AL161747
    Conserved Domains (4) summary
    smart00355
    Location:371393
    ZnF_C2H2; zinc finger
    sd00017
    Location:373393
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:690711
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:385410
    zf-H2C2_2; Zinc-finger double domain
  4. NM_005407.2NP_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
    Q9Y467
    Related
    ENSP00000483562.1, OTTHUMP00000276071, ENST00000614342.1, OTTHUMT00000401242
    Conserved Domains (3) summary
    sd00017
    Location:375395
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:692713
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:387412
    zf-H2C2_2; Zinc-finger double domain

RNA

  1. NR_111966.1 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, OTTHUMT00000401243
  2. NR_111967.1 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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    21521080..21537216 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (4) summary
    sd00017
    Location:375395
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:913933
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:692713
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:387412
    zf-H2C2_2; Zinc-finger double domain
  2. XM_011537065.2XP_011535367.1  sal-like protein 2 isoform X2

    Conserved Domains (4) summary
    sd00017
    Location:373393
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:911931
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:690711
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:385410
    zf-H2C2_2; Zinc-finger double domain
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