Sall1 spalt-like transcription factor 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sall1provided by RGD
Official Full Name: spalt-like transcription factor 1provided by RGD
Primary source: RGD:1309916
See related: Ensembl:ENSRNOG00000013907 AllianceGenome:RGD:1309916
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and beta-catenin binding activity. Predicted to be involved in several processes, including animal organ development; negative regulation of ectoderm development; and regulation of transcription, DNA-templated. Predicted to act upstream of or within several processes, including limb morphogenesis; metanephric nephron morphogenesis; and nervous system development. Predicted to be located in chromocenter; cytoplasm; and heterochromatin. Predicted to be part of NuRD complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Townes-Brocks syndrome and middle lobe syndrome. Orthologous to human SALL1 (spalt like transcription factor 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 50.6), Liver (RPKM 39.5) and 2 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19p11

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (34179316..34196278)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (18005782..18022705)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (23387737..23405025)

Chromosome 19 - NC_086037.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Sall1 induces angiogenesis by stimulating VEGF-A promoter activity.
Title: Zinc-finger transcriptional factor Sall1 induces angiogenesis by activation of the gene for VEGF-A.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology 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 cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables beta-catenin binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of GABAergic neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in adrenal gland development	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of branching involved in ureteric bud morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in branching involved in ureteric bud morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic digestive tract development	ISO Inferred from Sequence Orthology more info
involved_in embryonic digit morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within forelimb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in gonad development	ISO Inferred from Sequence Orthology more info
involved_in heart development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within hindlimb morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inductive cell-cell signaling	ISO Inferred from Sequence Orthology more info
involved_in kidney development	ISO Inferred from Sequence Orthology more info
involved_in kidney epithelium development	ISO Inferred from Sequence Orthology more info
involved_in limb development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mesenchymal stem cell maintenance involved in metanephric nephron morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of mesenchymal to epithelial transition involved in metanephros morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in mesenchymal to epithelial transition involved in metanephros morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of ectoderm development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of mesoderm development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural tube closure	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural tube development	ISO Inferred from Sequence Orthology more info
acts_upstream_of neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within olfactory bulb development	ISO Inferred from Sequence Orthology more info
involved_in olfactory bulb interneuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in olfactory bulb mitral cell layer development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within olfactory nerve development	ISO Inferred from Sequence Orthology more info
involved_in pituitary gland development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of branching involved in ureteric bud morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of neuroblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ureteric bud development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ureteric bud invasion	ISO Inferred from Sequence Orthology more info
involved_in ureteric bud invasion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ventricular septum development	ISO Inferred from Sequence Orthology more info
involved_in ventricular septum development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of NuRD complex	ISO Inferred from Sequence Orthology more info
located_in chromocenter	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
part_of heterochromatin	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: sal-like protein 1

Names: sal-like 1

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_001107415.2 → NP_001100885.2 sal-like protein 1

See identical proteins and their annotated locations for NP_001100885.2

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000019

UniProtKB/TrEMBL

A0A8I5ZSH0, D3ZIF4

Related

ENSRNOP00000018628.4, ENSRNOT00000018629.8

Conserved Domains (6) summary

cd11674
Location:1055 → 1146

lambda-1; inner capsid protein lambda-1 or VP3

COG5048
Location:692 → 1160

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:699 → 719

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:994 → 1014

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:1125 → 1147

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:711 → 736

zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086037.1 Reference GRCr8

Range

34179316..34196278

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006255260.5 → XP_006255322.1 sal-like protein 1 isoform X1

See identical proteins and their annotated locations for XP_006255322.1

UniProtKB/TrEMBL

A0A8I5ZSH0, D3ZIF4

Conserved Domains (6) summary

cd11674
Location:1055 → 1146

lambda-1; inner capsid protein lambda-1 or VP3

COG5048
Location:692 → 1160

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:699 → 719

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:994 → 1014

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:1125 → 1147

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:711 → 736

zf-H2C2_2; Zinc-finger double domain
XM_063278015.1 → XP_063134085.1 sal-like protein 1 isoform X1

UniProtKB/TrEMBL

D3ZIF4
XM_039097721.2 → XP_038953649.1 sal-like protein 1 isoform X2

UniProtKB/TrEMBL

A6KD93

Related

ENSRNOP00000081273.1

Conserved Domains (6) summary

cd11674
Location:957 → 1048

lambda-1; inner capsid protein lambda-1 or VP3

sd00017
Location:601 → 621

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:613 → 638

zf-H2C2_2; Zinc-finger double domain

cd20908
Location:344 → 431

SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins