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

    Gene ID: 6297, updated on 7-Jul-2024

    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; 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
    NEW
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    Try the new Transcript table

    Genomic context

    See SALL2 in Genome Data Viewer
    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

    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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ10414, FLJ55746, KIAA0360

    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)

    NEW Try the new Transcript table

    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_001291446.2NP_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: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_001291447.2NP_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: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
      Consensus CDS
      CCDS91849.1
      UniProtKB/TrEMBL
      B4DK65, F5H433
      Related
      ENSP00000438493.2, ENST00000537235.2
      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_005407.3NP_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: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_111966.2 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_011537064.2XP_011535366.1  sal-like protein 2 isoform X1

      UniProtKB/TrEMBL
      H0YFS7
      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_011537065.3XP_011535367.1  sal-like protein 2 isoform X2

      UniProtKB/TrEMBL
      B4DK65
      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

    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_054376554.1XP_054232529.1  sal-like protein 2 isoform X1

      UniProtKB/TrEMBL
      H0YFS7
    2. XM_054376555.1XP_054232530.1  sal-like protein 2 isoform X2

      UniProtKB/TrEMBL
      B4DK65