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

Gene ID: 6493, updated on 19-Sep-2024

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; AllianceGenome:HGNC:10883
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
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Genomic context

See SIM2 in Genome Data Viewer
Location:
21q22.13
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (36699115..36749917)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (35081302..35132110)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (38071415..38122218)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene CLDN14 antisense RNA 1 Neighboring gene claudin 14 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18437 Neighboring gene proteasome 26S subunit, non-ATPase 4 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18439 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:37973046-37973546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:37973547-37974047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:37978989-37979489 Neighboring gene uncharacterized LOC105369308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38031921-38032420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38031419-38031920 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr21:38067894-38068806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38072642-38073235 Neighboring gene uncharacterized LOC107985492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38073236-38073828 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38077313-38078142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38078973-38079802 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38081463-38082292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38091813-38092599 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13289 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:38121986-38122511 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:38122512-38123036 Neighboring gene NANOG hESC enhancer GRCh37_chr21:38128709-38129210 Neighboring gene uncharacterized LOC105369305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38158985-38159520 Neighboring gene holocarboxylase synthetase Neighboring gene RNA, 5S ribosomal pseudogene 491

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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

EBI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC119447

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in embryonic pattern specification IEA
Inferred from Electronic Annotation
more info
 
involved_in lung development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
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 chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in nuclear body IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 

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)

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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.

Genomic

  1. NG_029519.2 RefSeqGene

    Range
    5002..55804
    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
    O60766, Q14190, Q15470, Q15471, Q15472, Q15473, Q16532, Q2TBD8
    Related
    ENSP00000290399.6, ENST00000290399.11
    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/TrEMBL
    H7BZX8
    Related
    ENST00000481185.1
    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: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    36699115..36749917
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047440953.1XP_047296909.1  single-minded homolog 2 isoform X3

  2. XM_017028442.3XP_016883931.1  single-minded homolog 2 isoform X2

    Conserved Domains (3) summary
    smart00091
    Location:79140
    PAS; PAS domain
    pfam08447
    Location:243326
    PAS_3; PAS fold
    cd19739
    Location:174
    bHLH-PAS_SIM2; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 2 (SIM2) and similar proteins
  3. XM_047440952.1XP_047296908.1  single-minded homolog 2 isoform X1

  4. XM_011529694.2XP_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)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    35081302..35132110
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324787.1XP_054180762.1  single-minded homolog 2 isoform X3

  2. XM_054324786.1XP_054180761.1  single-minded homolog 2 isoform X2

  3. XM_054324784.1XP_054180759.1  single-minded homolog 2 isoform X1

  4. XM_054324785.1XP_054180760.1  single-minded homolog 2 isoform X1