Human Gene CHCHD3 (ENST00000262570.10_12) from GENCODE V47lift37
  Description: coiled-coil-helix-coiled-coil-helix domain containing 3, transcript variant 2 (from RefSeq NM_017812.4)
Gencode Transcript: ENST00000262570.10_12
Gencode Gene: ENSG00000106554.13_14
Transcript (Including UTRs)
   Position: hg19 chr7:132,469,631-132,766,850 Size: 297,220 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr7:132,470,398-132,766,697 Size: 296,300 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:132,469,631-132,766,850)mRNA (may differ from genome)Protein (227 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CHCH3_HUMAN
DESCRIPTION: RecName: Full=Coiled-coil-helix-coiled-coil-helix domain-containing protein 3, mitochondrial;
FUNCTION: Required for maintenance of mitochondrial crista integrity and mitochondrial function. May act as a scaffolding protein that stabilizes protein complexes involved in crista architecture and protein import. Has also been shown to function as a transcription factor which binds to the BAG1 promoter and represses BAG1 transcription.
SUBUNIT: Interacts with HSPA1A/HSPA1B and OPA1, preferentially with the soluble OPA1 form (By similarity). Component of the MINOS/MitOS complex, that includes IMMT, HSPA9 and CHCHD3 and associates with mitochondrial outer membrane proteins SAMM50, MTX1 and MTX2. Interacts with CHCHD6.
INTERACTION: Q15834:CCDC85B; NbExp=2; IntAct=EBI-743375, EBI-739674; P62136:PPP1CA; NbExp=2; IntAct=EBI-743375, EBI-357253;
SUBCELLULAR LOCATION: Mitochondrion inner membrane; Lipid-anchor; Intermembrane side (By similarity). Cytoplasm. Nucleus.
TISSUE SPECIFICITY: Detected at low levels in brain, placenta, lung, liver, kidney and pancreas with increased levels in heart and skeletal muscle. Higher expression in primary lung cancers than in normal lung tissue.
SIMILARITY: Contains 1 CHCH domain.

-  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


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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 43.48 RPKM in Muscle - Skeletal
Total median expression: 747.23 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -68.60153-0.448 Picture PostScript Text
3' UTR -207.30767-0.270 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
IPR007964 - DUF737

Pfam Domains:
PF05300 - MICOS complex subunit MIC19/MIC25

SCOP Domains:
47072 - Cysteine alpha-hairpin motif

ModBase Predicted Comparative 3D Structure on Q9NX63
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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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0005515 protein binding
GO:0019902 phosphatase binding
GO:0032947 protein complex scaffold

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007007 inner mitochondrial membrane organization
GO:0008053 mitochondrial fusion
GO:0042407 cristae formation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0016020 membrane
GO:0061617 MICOS complex
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK000427 - Homo sapiens cDNA FLJ20420 fis, clone KAT02462.
BC014839 - Homo sapiens coiled-coil-helix-coiled-coil-helix domain containing 3, mRNA (cDNA clone MGC:5334 IMAGE:2901125), complete cds.
AK129533 - Homo sapiens cDNA FLJ26022 fis, clone PCD03106.
BC011596 - Homo sapiens coiled-coil-helix-coiled-coil-helix domain containing 3, mRNA (cDNA clone MGC:1047 IMAGE:3346346), complete cds.
AK310236 - Homo sapiens cDNA, FLJ17278.
HQ447383 - Synthetic construct Homo sapiens clone IMAGE:100070704; CCSB002407_02 coiled-coil-helix-coiled-coil-helix domain containing 3 (CHCHD3) gene, encodes complete protein.
KJ894090 - Synthetic construct Homo sapiens clone ccsbBroadEn_03484 CHCHD3 gene, encodes complete protein.
AB528286 - Synthetic construct DNA, clone: pF1KB8182, Homo sapiens CHCHD3 gene for coiled-coil-helix-coiled-coil-helix domain containing 3, without stop codon, in Flexi system.
JD171245 - Sequence 152269 from Patent EP1572962.
JD083522 - Sequence 64546 from Patent EP1572962.
JD208407 - Sequence 189431 from Patent EP1572962.
JD332572 - Sequence 313596 from Patent EP1572962.
JD375859 - Sequence 356883 from Patent EP1572962.
JD068917 - Sequence 49941 from Patent EP1572962.
JD086217 - Sequence 67241 from Patent EP1572962.
JD092641 - Sequence 73665 from Patent EP1572962.
JD027276 - Sequence 8300 from Patent EP1572962.
JD031691 - Sequence 12715 from Patent EP1572962.
JD483232 - Sequence 464256 from Patent EP1572962.
JD093708 - Sequence 74732 from Patent EP1572962.
JD456132 - Sequence 437156 from Patent EP1572962.
JD249082 - Sequence 230106 from Patent EP1572962.
JD486754 - Sequence 467778 from Patent EP1572962.
JD212078 - Sequence 193102 from Patent EP1572962.
AK294071 - Homo sapiens cDNA FLJ53726 complete cds, highly similar to Coiled-coil-helix-coiled-coil-helixdomain-containing protein 3.
JD417339 - Sequence 398363 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9NX63 (Reactome details) participates in the following event(s):

R-HSA-1307802 MIA40:ERV1 (CHCHD4:GFER) oxidizes cysteine residues to cystine disulfide bonds
R-HSA-8949613 Cristae formation
R-HSA-1268020 Mitochondrial protein import
R-HSA-1592230 Mitochondrial biogenesis
R-HSA-392499 Metabolism of proteins
R-HSA-1852241 Organelle biogenesis and maintenance

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000262570.1, ENST00000262570.2, ENST00000262570.3, ENST00000262570.4, ENST00000262570.5, ENST00000262570.6, ENST00000262570.7, ENST00000262570.8, ENST00000262570.9, MIC19, MIC19_HUMAN, MINOS3, NM_017812, Q9NX63, uc317hbp.1, uc317hbp.2
UCSC ID: ENST00000262570.10_12
RefSeq Accession: NM_017812.4
Protein: Q9NX63 (aka CHCH3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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