Human Gene CHMP1A (uc002fnu.4) Description and Page Index
  Description: Homo sapiens charged multivesicular body protein 1A (CHMP1A), transcript variant 2, mRNA.
RefSeq Summary (NM_002768): This gene encodes a member of the CHMP/Chmp family of proteins which are involved in multivesicular body sorting of proteins to the interiors of lysosomes. The initial prediction of the protein sequence encoded by this gene suggested that the encoded protein was a metallopeptidase. The nomenclature has been updated recently to reflect the correct biological function of this encoded protein. Several transcripts encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012].
Transcript (Including UTRs)
   Position: hg19 chr16:89,710,839-89,724,193 Size: 13,355 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr16:89,712,474-89,723,996 Size: 11,523 Coding Exon Count: 7 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr16:89,710,839-89,724,193)mRNA (may differ from genome)Protein (196 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
PubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Charged multivesicular body protein 1a; AltName: Full=Chromatin-modifying protein 1a; Short=CHMP1a; AltName: Full=Vacuolar protein sorting-associated protein 46-1; Short=Vps46-1; Short=hVps46-1;
FUNCTION: Probable peripherally associated 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 cytokinesis. Involved in recruiting VPS4A and/or VPS4B to the midbody of dividing cells. May also be involved in chromosome condensation. Targets the Polycomb group (PcG) protein BMI1/PCGF4 to regions of condensed chromatin. May play a role in stable cell cycle progression and in PcG gene silencing.
SUBUNIT: Probable peripherally associated 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 CHMP1B. Interacts with VPS4A. Interacts with VPS4B. Interacts with PHF1. Interacts with IST1.
INTERACTION: O95630:STAMBP; NbExp=3; IntAct=EBI-1057156, EBI-396676; P40818:USP8; NbExp=2; IntAct=EBI-1057156, EBI-1050865;
SUBCELLULAR LOCATION: Cytoplasm. Endosome membrane; Peripheral membrane protein. Nucleus matrix. Note=The cytoplasmic form is partially membrane-associated and localizes to early endosomes. The nuclear form remains associated with the chromosome scaffold during mitosis. On overexpression, it localizes to nuclear bodies characterized by nuclease-resistant condensed chromatin.
TISSUE SPECIFICITY: Expressed in placenta, cultured skin fibroblasts and in osteoblast cell line MG-63.
INDUCTION: By muristerone.
SIMILARITY: Belongs to the SNF7 family.
CAUTION: Was originally (PubMed:8863740) thought to be a metalloprotease (PRSM1). This was based on a wrong translation of the ORF which gave rise to a putative protein of 318 AA containing a pattern reminiscent of zinc metalloproteases.
SEQUENCE CAUTION: Sequence=AAC50775.1; Type=Erroneous translation; Note=Wrong choice of frame; Sequence=BAA07557.1; Type=Erroneous translation; Note=Wrong choice of frame;

-  MalaCards Disease Associations
  MalaCards Gene Search: CHMP1A
Diseases sorted by gene-association score: pontocerebellar hypoplasia, type 8* (1350), distichiasis (12), borna disease (7)
* = Manually curated disease association

-  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: 65.30 RPKM in Testis
Total median expression: 1814.26 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 -85.60197-0.435 Picture PostScript Text
3' UTR -718.961635-0.440 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


ModBase Predicted Comparative 3D Structure on Q9HD42
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 orthologGenome BrowserNo orthologNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
  Ensembl  SGD
  Protein Sequence  Protein Sequence
  Alignment  Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
GO:0019904 protein domain specific binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0000920 cell separation after cytokinesis
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006508 proteolysis
GO:0006997 nucleus organization
GO:0007034 vacuolar transport
GO:0007049 cell cycle
GO:0007076 mitotic chromosome condensation
GO:0007080 mitotic metaphase plate congression
GO:0010824 regulation of centrosome duplication
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0016458 gene silencing
GO:0036258 multivesicular body assembly
GO:0039702 viral budding via host ESCRT complex
GO:0045786 negative regulation of cell cycle
GO:0045892 negative regulation of transcription, DNA-templated
GO:0051301 cell division
GO:1901673 regulation of mitotic spindle assembly
GO:1904903 ESCRT III complex disassembly

Cellular Component:
GO:0000794 condensed nuclear chromosome
GO:0000815 ESCRT III complex
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005815 microtubule organizing center
GO:0010008 endosome membrane
GO:0012505 endomembrane system
GO:0016020 membrane
GO:0016363 nuclear matrix
GO:0070062 extracellular exosome

-  Descriptions from all associated GenBank mRNAs
  BC010000 - Homo sapiens chromatin modifying protein 1A, mRNA (cDNA clone IMAGE:4135487), complete cds.
BC007527 - Homo sapiens procollagen (type III) N-endopeptidase, mRNA (cDNA clone IMAGE:3507056), partial cds.
U58048 - Human metallopeptidase PRSM1 mRNA, complete cds.
D38554 - Homo sapiens KIAA0047 mRNA, partial cds.
JD536644 - Sequence 517668 from Patent EP1572962.
JD338305 - Sequence 319329 from Patent EP1572962.
JD473102 - Sequence 454126 from Patent EP1572962.
JD493509 - Sequence 474533 from Patent EP1572962.
JD233635 - Sequence 214659 from Patent EP1572962.
JD144780 - Sequence 125804 from Patent EP1572962.
JD521026 - Sequence 502050 from Patent EP1572962.
JD545555 - Sequence 526579 from Patent EP1572962.
JD287602 - Sequence 268626 from Patent EP1572962.
JD498556 - Sequence 479580 from Patent EP1572962.
AK302055 - Homo sapiens cDNA FLJ57657 complete cds, highly similar to Charged multivesicular body protein 1a.
JD535685 - Sequence 516709 from Patent EP1572962.
DQ583848 - Homo sapiens piRNA piR-50960, complete sequence.
JD445154 - Sequence 426178 from Patent EP1572962.
JD272366 - Sequence 253390 from Patent EP1572962.
JD354662 - Sequence 335686 from Patent EP1572962.
JD122749 - Sequence 103773 from Patent EP1572962.
JD130023 - Sequence 111047 from Patent EP1572962.
JD370563 - Sequence 351587 from Patent EP1572962.
JD494399 - Sequence 475423 from Patent EP1572962.
JD448972 - Sequence 429996 from Patent EP1572962.
JD409204 - Sequence 390228 from Patent EP1572962.
JD493654 - Sequence 474678 from Patent EP1572962.
JD055724 - Sequence 36748 from Patent EP1572962.
JD512111 - Sequence 493135 from Patent EP1572962.
JD251835 - Sequence 232859 from Patent EP1572962.
JD391028 - Sequence 372052 from Patent EP1572962.
JD191385 - Sequence 172409 from Patent EP1572962.
JD149698 - Sequence 130722 from Patent EP1572962.
JD048547 - Sequence 29571 from Patent EP1572962.
JD285234 - Sequence 266258 from Patent EP1572962.
JD482405 - Sequence 463429 from Patent EP1572962.
JD228125 - Sequence 209149 from Patent EP1572962.
JD112836 - Sequence 93860 from Patent EP1572962.
JD049433 - Sequence 30457 from Patent EP1572962.
BC132711 - Homo sapiens chromatin modifying protein 1A, mRNA (cDNA clone MGC:164342 IMAGE:40146733), complete cds.
BC132713 - Homo sapiens chromatin modifying protein 1A, mRNA (cDNA clone MGC:164344 IMAGE:40146735), complete cds.
JD296914 - Sequence 277938 from Patent EP1572962.
JD475910 - Sequence 456934 from Patent EP1572962.
JD557013 - Sequence 538037 from Patent EP1572962.
JD134931 - Sequence 115955 from Patent EP1572962.
AF281063 - Homo sapiens charged multivesicular body protein 1/chromatin modifying protein 1 mRNA, complete cds.
HQ258103 - Synthetic construct Homo sapiens clone IMAGE:100072412 chromatin modifying protein 1A (CHMP1A), transcript variant 2 (CHMP1A) gene, encodes complete protein.
KJ891759 - Synthetic construct Homo sapiens clone ccsbBroadEn_01153 CHMP1A gene, encodes complete protein.
BT006841 - Homo sapiens procollagen (type III) N-endopeptidase mRNA, complete cds.
AB528569 - Synthetic construct DNA, clone: pF1KE1007, Homo sapiens CHMP1A gene for chromatin modifying protein 1A, without stop codon, in Flexi system.
DQ576188 - Homo sapiens piRNA piR-44300, complete sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: A2RU09, CHM1A_HUMAN, CHMP1, KIAA0047, NM_002768, NP_002759, PCOLN3, PRSM1, Q14468, Q15779, Q96G31, Q9HD42, uc002fnu.3
UCSC ID: uc002fnu.4
RefSeq Accession: NM_002768
Protein: Q9HD42 (aka CHM1A_HUMAN)
CCDS: CCDS45552.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_002768.4
exon count: 7CDS single in 3' UTR: no RNA size: 2428
ORF size: 591CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1382.00frame shift in genome: no % Coverage: 99.79
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.