Human Gene CHMP4C (uc003ycl.3) Description and Page Index
  Description: Homo sapiens charged multivesicular body protein 4C (CHMP4C), mRNA.
RefSeq Summary (NM_152284): CHMP4C belongs to the chromatin-modifying protein/charged multivesicular body protein (CHMP) family. These proteins are components of ESCRT-III (endosomal sorting complex required for transport III), a complex involved in degradation of surface receptor proteins and formation of endocytic multivesicular bodies (MVBs). Some CHMPs have both nuclear and cytoplasmic/vesicular distributions, and one such CHMP, CHMP1A (MIM 164010), is required for both MVB formation and regulation of cell cycle progression (Tsang et al., 2006 [PubMed 16730941]).[supplied by OMIM, Mar 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AK000049.1, SRR5189655.54306.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968189, SAMEA1968540 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000297265.5/ ENSP00000297265.4 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr8:82,644,688-82,671,748 Size: 27,061 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr8:82,644,862-82,670,779 Size: 25,918 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:82,644,688-82,671,748)mRNA (may differ from genome)Protein (233 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CHM4C_HUMAN
DESCRIPTION: RecName: Full=Charged multivesicular body protein 4c; AltName: Full=Chromatin-modifying protein 4c; Short=CHMP4c; AltName: Full=SNF7 homolog associated with Alix 3; AltName: Full=SNF7-3; Short=hSnf7-3; AltName: Full=Vacuolar protein sorting-associated protein 32-3; Short=Vps32-3; Short=hVps32-3;
FUNCTION: Probable core component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. Involved in HIV- 1 p6- and p9-dependent virus release.
SUBUNIT: Probable core component of the endosomal sorting required for transport complex III (ESCRT-III). ESCRT-III components are thought to multimerize to form a flat lattice on the perimeter membrane of the endosome. Several assembly forms of ESCRT-III may exist that interact and act sequentally. Self-associates. Interacts with CHMP2A. Interacts with CHMP4A. Interacts with CHMP4B. Interacts with CHMP6. Interacts with VPS4A. Interacts with PDCD6IP; the interaction is direct.
SUBCELLULAR LOCATION: Cytoplasm, cytosol. Late endosome membrane; Peripheral membrane protein (Probable).
TISSUE SPECIFICITY: Expressed in heart, spleen and kidney.
DOMAIN: The acidic C-terminus and the basic N-termminus are thought to render the protein in a closed, soluble and inactive conformation through an autoinhibitory intramolecular interaction. The open and active conformation, which enables membrane binding and oligomerization, is achieved by interaction with other cellular binding partners, probably including other ESCRT components (By similarity).
MISCELLANEOUS: Its overexpression strongly inhibits HIV-1 release.
SIMILARITY: Belongs to the SNF7 family.

-  MalaCards Disease Associations
  MalaCards Gene Search: CHMP4C
Diseases sorted by gene-association score: hiv-1 (2)

-  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: 23.16 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 217.75 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 -77.74174-0.447 Picture PostScript Text
3' UTR -282.06969-0.291 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
IPR005024 - Snf7

Pfam Domains:
PF03357 - Snf7

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3C3R
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q96CF2
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
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0000920 cell separation after cytokinesis
GO:0006997 nucleus organization
GO:0007034 vacuolar transport
GO:0007080 mitotic metaphase plate congression
GO:0009838 abscission
GO:0010824 regulation of centrosome duplication
GO:0015031 protein transport
GO:0016197 endosomal transport
GO:0016236 macroautophagy
GO:0019058 viral life cycle
GO:0032466 negative regulation of cytokinesis
GO:0036258 multivesicular body assembly
GO:0039702 viral budding via host ESCRT complex
GO:0044878 mitotic cytokinesis checkpoint
GO:0050792 regulation of viral process
GO:0090611 ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway
GO:1901673 regulation of mitotic spindle assembly
GO:1902188 positive regulation of viral release from host cell

Cellular Component:
GO:0000815 ESCRT III complex
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005829 cytosol
GO:0016020 membrane
GO:0030496 midbody
GO:0031902 late endosome membrane
GO:0090543 Flemming body


-  Descriptions from all associated GenBank mRNAs
  BC014321 - Homo sapiens chromatin modifying protein 4C, mRNA (cDNA clone MGC:22825 IMAGE:3828410), complete cds.
AK314873 - Homo sapiens cDNA, FLJ95774, Homo sapiens Snf7 homologue associated with Alix 3 (Shax3), mRNA.
AK000049 - Homo sapiens cDNA FLJ20042 fis, clone COL00424.
JD520719 - Sequence 501743 from Patent EP1572962.
JD127712 - Sequence 108736 from Patent EP1572962.
JD195523 - Sequence 176547 from Patent EP1572962.
JD444245 - Sequence 425269 from Patent EP1572962.
AY329086 - Homo sapiens SNF7-3 mRNA, complete cds.
AB120734 - Homo sapiens Shax3 mRNA for Snf7 homologue associated with Alix 3, complete cds.
KJ895187 - Synthetic construct Homo sapiens clone ccsbBroadEn_04581 CHMP4C gene, encodes complete protein.
JD171467 - Sequence 152491 from Patent EP1572962.
JD102068 - Sequence 83092 from Patent EP1572962.
JD501208 - Sequence 482232 from Patent EP1572962.
JD340913 - Sequence 321937 from Patent EP1572962.
JD079364 - Sequence 60388 from Patent EP1572962.
JD105274 - Sequence 86298 from Patent EP1572962.
JD420084 - Sequence 401108 from Patent EP1572962.
JD278849 - Sequence 259873 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04144 - Endocytosis

Reactome (by CSHL, EBI, and GO)

Protein Q96CF2 (Reactome details) participates in the following event(s):

R-HSA-917693 ESCRT Disassembly
R-HSA-917700 MVB Vesicle Formation
R-HSA-3159232 Recruitment Of HIV Virion Budding Machinery
R-HSA-917729 Endosomal Sorting Complex Required For Transport (ESCRT)
R-HSA-162588 Budding and maturation of HIV virion
R-HSA-199991 Membrane Trafficking
R-HSA-162599 Late Phase of HIV Life Cycle
R-HSA-5653656 Vesicle-mediated transport
R-HSA-162587 HIV Life Cycle
R-HSA-162906 HIV Infection
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: B2RBZ1, CHM4C_HUMAN, NM_152284, NP_689497, Q96CF2, SHAX3
UCSC ID: uc003ycl.3
RefSeq Accession: NM_152284
Protein: Q96CF2 (aka CHM4C_HUMAN)
CCDS: CCDS6233.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_152284.3
exon count: 5CDS single in 3' UTR: no RNA size: 1847
ORF size: 702CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1562.00frame shift in genome: no % Coverage: 99.89
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.