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SIM2 SIM bHLH transcription factor 2 [ Homo sapiens (human) ]

Gene ID: 6493, updated on 11-Sep-2019

Summary

Official Symbol
SIM2provided by HGNC
Official Full Name
SIM bHLH transcription factor 2provided by HGNC
Primary source
HGNC:HGNC:10883
See related
Ensembl:ENSG00000159263 MIM:600892
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
SIM; bHLHe15; HMC13F06; HMC29C01
Summary
This gene represents a homolog of the Drosophila single-minded (sim) gene, which encodes a transcription factor that is a master regulator of neurogenesis. The encoded protein is ubiquitinated by RING-IBR-RING-type E3 ubiquitin ligases, including the parkin RBR E3 ubiquitin protein ligase. This gene maps within the so-called Down syndrome chromosomal region, and is thus thought to contribute to some specific Down syndrome phenotypes. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2014]
Expression
Biased expression in kidney (RPKM 5.4), esophagus (RPKM 4.7) and 4 other tissues See more
Orthologs

Genomic context

See SIM2 in Genome Data Viewer
Location:
21q22.13
Exon count:
12
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 21 NC_000021.9 (36699115..36750219)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (38071991..38122510)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369301 Neighboring gene claudin 14 Neighboring gene proteasome 26S subunit, non-ATPase 4 pseudogene 1 Neighboring gene uncharacterized LOC105369308 Neighboring gene uncharacterized LOC107985492 Neighboring gene holocarboxylase synthetase Neighboring gene uncharacterized LOC105369305 Neighboring gene RNA, 5S ribosomal pseudogene 491

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?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association analysis identifies 11 risk variants associated with the asthma with hay fever phenotype.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC119447

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
embryonic pattern specification IEA
Inferred from Electronic Annotation
more info
 
lung development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
nervous system development IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nuclear body IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
single-minded homolog 2
Names
class E basic helix-loop-helix protein 15
single-minded family bHLH transcription factor 2
transcription factor SIM2

NCBI Reference Sequences (RefSeq)

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_029519.1 RefSeqGene

    Range
    4425..55228
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005069.6NP_005060.1  single-minded homolog 2 long isoform

    See identical proteins and their annotated locations for NP_005060.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (SIM2) represents the longer transcript and encodes the longer isoform (long).
    Source sequence(s)
    AP000697, BC052313, BC110444, BM848475, U80456
    Consensus CDS
    CCDS13646.1
    UniProtKB/Swiss-Prot
    Q14190
    Related
    ENSP00000290399.6, ENST00000290399.10
    Conserved Domains (6) summary
    cd00083
    Location:252
    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:229328
    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:79159
    PAS; PAS fold
    pfam06621
    Location:359660
    SIM_C; Single-minded protein C-terminus
    pfam08447
    Location:243329
    PAS_3; PAS fold
    pfam15830
    Location:578653
    DUF4712; Domain of unknown function (DUF4712)
  2. NM_009586.5NP_033664.2  single-minded homolog 2 short isoform

    See identical proteins and their annotated locations for NP_033664.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (SIM2s) contains alternate 3' exon structure, and it thus differs in the 3' coding region and 3' UTR, compared to variant SIM2. The encoded isoform (short) has a distinct C-terminus and is shorter than isoform long.
    Source sequence(s)
    AP000697, BC052313, BC110444, BM848475, U80457
    UniProtKB/Swiss-Prot
    Q14190
    Conserved Domains (4) summary
    cd00083
    Location:252
    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:88158
    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 ...
    pfam06621
    Location:359523
    SIM_C; Single-minded protein C-terminus
    pfam08447
    Location:243329
    PAS_3; PAS fold

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p13 Primary Assembly

    Range
    36699115..36750219
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028442.2XP_016883931.1  single-minded homolog 2 isoform X2

  2. XM_011529694.1XP_011527996.1  single-minded homolog 2 isoform X1

    Conserved Domains (4) summary
    cd00130
    Location:128227
    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 ...
    pfam06621
    Location:258559
    SIM_C; Single-minded protein C-terminus
    pfam08447
    Location:142228
    PAS_3; PAS fold
    pfam15830
    Location:477552
    DUF4712; Domain of unknown function (DUF4712)

RNA

  1. XR_001754891.2 RNA Sequence

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