Sim2 SIM bHLH transcription factor 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sim2provided by RGD
Official Full Name: SIM bHLH transcription factor 2provided by RGD
Primary source: RGD:1308016
See related: Ensembl:ENSRNOG00000054203 AllianceGenome:RGD:1308016
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and protein heterodimerization activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within embryonic pattern specification; lung development; and negative regulation of transcription by RNA polymerase II. Predicted to be located in nuclear body. Orthologous to human SIM2 (SIM bHLH transcription factor 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 46.5), Muscle (RPKM 27.3) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 11q11

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	11	NC_086029.1 (46883859..46923305)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	11	NC_051346.1 (33414218..33453663)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	11	NC_005110.4 (34315739..34355183)

Chromosome 11 - NC_086029.1 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: 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?

Ethanol at different concentrations induced Sim2 accumulation in primary cultures of rat neurons.
Title: Ethanol Activation of PKA Mediates Single-Minded 2 Expression in Neuronal Cells.
Sim2 may mediate neurotoxicity during hyperglycaemia and thereby play a critical role in the development of hyperglycaemia-induced cognitive deficits.
Title: Contribution of single-minded 2 to hyperglycaemia-induced neurotoxicity.

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General gene information

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Markers

Sim2 (e-PCR), detects polymorphism
- UniSTS:259656

RH138072 (e-PCR)
- UniSTS:220159

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 RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic pattern specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lung development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	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 nervous system development	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 nuclear body	IEA Inferred from Electronic Annotation more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: single-minded homolog 2

Names: single-minded 2; single-minded family bHLH transcription factor 2

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_001107108.3 → NP_001100578.1 single-minded homolog 2

See identical proteins and their annotated locations for NP_001100578.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000011

UniProtKB/TrEMBL

A6KPY2, D4AA36

Related

ENSRNOP00000069809.1, ENSRNOT00000081834.2

Conserved Domains (6) summary

smart00091
Location:79 → 140

PAS; PAS domain

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:230 → 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 → 649

SIM_C; Single-minded protein C-terminus

pfam08447
Location:243 → 329

PAS_3; PAS fold