sim1a SIM bHLH transcription factor 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: sim1aprovided by ZNC
Official Full Name: SIM bHLH transcription factor 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-020829-1
See related: Ensembl:ENSDARG00000023316 AllianceGenome:ZFIN:ZDB-GENE-020829-1
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: sim1
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within nervous system development and proximal tubule development. Predicted to be located in nucleus. Is expressed in several structures, including basal plate midbrain region; central nervous system; corpuscles of Stannius; intermediate mesoderm; and pronephros. Human ortholog(s) of this gene implicated in obesity. Orthologous to human SIM1 (SIM bHLH transcription factor 1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 16

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	16	NC_007127.7 (1470418..1503023, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	16	NC_007127.6 (1446530..1479135, complement)

Chromosome 16 - NC_007127.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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?

Data indicate that nephron proximal tubule patterning is reliant on sim1a transcription factor activity.
Title: Nephron proximal tubule patterning and corpuscles of Stannius formation are regulated by the sim1a transcription factor and retinoic acid in zebrafish.
Sim1a contributes to control of lateral positioning of longitudinal hypothalamic-spinal axons by negative regulation of robo3a.1 expression, which in turn attenuates the repulsive activity of Robo2.
Title: Sim1a and Arnt2 contribute to hypothalamo-spinal axon guidance by regulating Robo2 activity via a Robo3-dependent mechanism.
commitment of basal diencephalic DA neurons is regulated by the combined action of the neural protein Olig2 and its downstream neuronal specific effector Sim1
Title: Neural protein Olig2 acts upstream of the transcriptional regulator Sim1 to specify diencephalic dopaminergic neurons.
Results describe the ontogeny of vasotocin-expressing cells in zebrafish, and the selective requirement for the transcriptional regulators orthopedia and single-minded 1 in the preoptic area.
Title: Ontogeny of vasotocin-expressing cells in zebrafish: selective requirement for the transcriptional regulators orthopedia and single-minded 1 in the preoptic area.
role of sim1 in zebrafish neuroendocrine cell development is evolutionarily conserved with that of mammals
Title: The zebrafish bHLH PAS transcriptional regulator, single-minded 1 (sim1), is required for isotocin cell development.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein dimerization activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within axon guidance	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within diencephalon development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within dopaminergic neuron differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within dopaminergic neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hypothalamus cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within pronephric proximal tubule development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pronephros development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within proximal straight tubule development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within proximal straight tubule development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: single-minded homolog 1-A

Names: single-minded family bHLH transcription factor 1a

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_178222.3 → NP_835740.2 single-minded homolog 1-A

Status: VALIDATED

Source sequence(s)

BX005277, CU905511

UniProtKB/Swiss-Prot

Q98SJ5

UniProtKB/TrEMBL

A0A8N7UZU3, F1QMF7

Related

ENSDARP00000033085.5, ENSDART00000036348.6

Conserved Domains (5) summary

cd00083
Location:2 → 52

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

cd00130
Location:229 → 328

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam00989
Location:79 → 141

PAS; PAS fold

pfam06621
Location:359 → 647

SIM_C; Single-minded protein C-terminus

pfam08447
Location:243 → 329

PAS_3; PAS fold