Human Gene SIM1 (ENST00000369208.8) from GENCODE V44
  Description: Homo sapiens SIM bHLH transcription factor 1 (SIM1), transcript variant 1, mRNA. (from RefSeq NM_005068)
RefSeq Summary (NM_005068): SIM1 and SIM2 genes are Drosophila single-minded (sim) gene homologs. SIM1 transcript was detected only in fetal kidney out of various adult and fetal tissues tested. Since the sim gene plays an important role in Drosophila development and has peak levels of expression during the period of neurogenesis,it was proposed that the human SIM gene is a candidate for involvement in certain dysmorphic features (particularly the facial and skull characteristics), abnormalities of brain development, and/or cognitive disability of Down syndrome. [provided by RefSeq, Jul 2008]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Gencode Transcript: ENST00000369208.8
Gencode Gene: ENSG00000112246.10
Transcript (Including UTRs)
   Position: hg38 chr6:100,385,009-100,464,921 Size: 79,913 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg38 chr6:100,390,361-100,463,468 Size: 73,108 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:100,385,009-100,464,921)mRNA (may differ from genome)Protein (766 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SIM1_HUMAN
DESCRIPTION: RecName: Full=Single-minded homolog 1; AltName: Full=Class E basic helix-loop-helix protein 14; Short=bHLHe14;
FUNCTION: Transcriptional factor that may have pleiotropic effects during embryogenesis and in the adult.
SUBUNIT: Efficient DNA binding requires dimerization with another bHLH protein. Heterodimer of SIM1 and ARNT.
SUBCELLULAR LOCATION: Nucleus (Potential).
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.
SIMILARITY: Contains 1 PAC (PAS-associated C-terminal) domain.
SIMILARITY: Contains 2 PAS (PER-ARNT-SIM) domains.
SIMILARITY: Contains 1 Single-minded C-terminal domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SIM1";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SIM1
Diseases sorted by gene-association score: obesity due to sim1 deficiency* (350), prader-willi-like syndrome due to point mutation* (350), obesity* (132), obesity, sim1-related* (100), prader-willi-like syndrome associated with chromosome 6* (100), 6q16 deletion syndrome* (25), down syndrome (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 2.49 RPKM in Kidney - Cortex
Total median expression: 8.15 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -236.60775-0.305 Picture PostScript Text
3' UTR -1214.705352-0.227 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011598 - HLH_dom
IPR001610 - PAC
IPR000014 - PAS
IPR013767 - PAS_fold
IPR013655 - PAS_fold_3
IPR010578 - SIM_C

Pfam Domains:
PF00010 - Helix-loop-helix DNA-binding domain
PF00989 - PAS fold
PF08447 - PAS fold
PF06621 - Single-minded protein C-terminus

ModBase Predicted Comparative 3D Structure on P81133
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0046982 protein heterodimerization activity
GO:0046983 protein dimerization activity

Biological Process:
GO:0001657 ureteric bud development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007399 nervous system development
GO:0030154 cell differentiation

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  U70212 - Human SIM1 mRNA, complete cds.
AB590099 - Synthetic construct DNA, clone: pFN21AB9761, Homo sapiens SIM1 gene for single-minded homolog 1, without stop codon, in Flexi system.
BC111931 - Synthetic construct Homo sapiens clone IMAGE:40080751, MGC:133464 SIM1 protein (SIM1) mRNA, encodes complete protein.
BC118500 - Synthetic construct Homo sapiens clone IMAGE:40080760, MGC:155333 SIM1 protein (SIM1) mRNA, encodes complete protein.
AK308090 - Homo sapiens cDNA, FLJ98038.
AL049965 - Homo sapiens mRNA; cDNA DKFZp564A232 (from clone DKFZp564A232).
JD374479 - Sequence 355503 from Patent EP1572962.
JD235623 - Sequence 216647 from Patent EP1572962.
JD243775 - Sequence 224799 from Patent EP1572962.
JD049827 - Sequence 30851 from Patent EP1572962.
JD350269 - Sequence 331293 from Patent EP1572962.
JD530758 - Sequence 511782 from Patent EP1572962.
JD307358 - Sequence 288382 from Patent EP1572962.
JD089724 - Sequence 70748 from Patent EP1572962.
AK309566 - Homo sapiens cDNA, FLJ99607.
JD167907 - Sequence 148931 from Patent EP1572962.
JD462274 - Sequence 443298 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BHLHE14, ENST00000369208.1, ENST00000369208.2, ENST00000369208.3, ENST00000369208.4, ENST00000369208.5, ENST00000369208.6, ENST00000369208.7, NM_005068, P81133, Q5TDP7, SIM1_HUMAN, uc063qgu.1, uc063qgu.2
UCSC ID: ENST00000369208.8
RefSeq Accession: NM_005068
Protein: P81133 (aka SIM1_HUMAN)
CCDS: CCDS5045.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.