sall1a spalt-like transcription factor 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: sall1aprovided by ZNC
Official Full Name: spalt-like transcription factor 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-020228-2
See related: Ensembl:ENSDARG00000074319 AllianceGenome:ZFIN:ZDB-GENE-020228-2
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: sall1; sb:eu809; cb896spalt; id:ibd5077
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within embryonic pectoral fin morphogenesis and positive regulation of fibroblast growth factor receptor signaling pathway. Predicted to be active in nucleus. Is expressed in several structures, including fin; nervous system; neural keel; neural tube; and tail bud. Human ortholog(s) of this gene implicated in Townes-Brocks syndrome; middle lobe syndrome; and renal Wilms' tumor. Orthologous to human SALL1 (spalt like transcription factor 1). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 7

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	7	NC_007118.7 (37377335..37390778)
105	previous assembly	GRCz10 (GCF_000002035.5)	7	NC_007118.6 (37106077..37119520)

Chromosome 7 - NC_007118.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

fk32c12.y1 (e-PCR)
- UniSTS:200819

G45358 (e-PCR)
- UniSTS:106160

G47959 (e-PCR)
- UniSTS:108725

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
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 metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within embryonic pectoral fin morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of fibroblast growth factor receptor signaling pathway	IGI Inferred from Genetic Interaction 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
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: sal-like protein 1a

Names: cb896; sal-like 1a; spa1a; spalt1a

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.

mRNA and Protein(s)

NM_001146014.1 → NP_001139486.1 sal-like protein 1a

Status: PROVISIONAL

Source sequence(s)

CR388023

UniProtKB/TrEMBL

A0A8N7V0N8, F1QI36

Related

ENSDARP00000102655.3, ENSDART00000111842.5

Conserved Domains (5) summary

smart00355
Location:443 → 465

ZnF_C2H2; zinc finger

sd00017
Location:696 → 716

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:992 → 1012

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:1018 → 1040

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:708 → 733

zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007118.7 Reference GRCz11 Primary Assembly

Range

37377335..37390778

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021477534.2 → XP_021333209.1 sal-like protein 1a isoform X1

UniProtKB/TrEMBL

A0A1D5NSE4, A0A8M9Q7V5

Related

ENSDARP00000142758.1, ENSDART00000173652.2

Conserved Domains (5) summary

smart00355
Location:347 → 369

ZnF_C2H2; zinc finger

sd00017
Location:600 → 620

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:896 → 916

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:922 → 944

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:612 → 637

zf-H2C2_2; Zinc-finger double domain