Human Gene CHMP1A (uc002fnv.4) Description and Page Index
  Description: Homo sapiens charged multivesicular body protein 1A (CHMP1A), transcript variant 1, mRNA.
RefSeq Summary (NM_001083314): 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: 6 Strand: -
Coding Region
   Position: hg19 chr16:89,712,322-89,723,996 Size: 11,675 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other 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 (240 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIOMIM
PubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: A6NG32_HUMAN
DESCRIPTION: SubName: Full=Charged multivesicular body protein 1a;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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
  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 -85.60197-0.435 Picture PostScript Text
3' UTR -651.561483-0.439 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
  ModBase Predicted Comparative 3D Structure on A6NG32
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  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: A6NG32, A6NG32_HUMAN, NM_001083314, NP_001076783, uc002fnv.3
UCSC ID: uc002fnv.4
RefSeq Accession: NM_001083314
Protein: A6NG32

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001083314.3
exon count: 6CDS single in 3' UTR: no RNA size: 2408
ORF size: 723CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1367.00frame 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.