Chmp1a (charged multivesicular body protein 1A) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Chmp1a (charged multivesicular body protein 1A) Rattus norvegicus
Analyze
Symbol: Chmp1a
Name: charged multivesicular body protein 1A
RGD ID: 1311083
Description: Predicted to enable protein domain specific binding activity and protein homodimerization activity. Predicted to be involved in several processes, including midbody abscission; regulation of cell cycle process; and vacuolar transport. Predicted to act upstream of or within mitotic chromosome condensation and negative regulation of gene expression. Predicted to be located in several cellular components, including bounding membrane of organelle; microtubule cytoskeleton; and nuclear lumen. Predicted to be part of ESCRT III complex and nuclear pore. Predicted to be active in multivesicular body. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 8. Orthologous to human CHMP1A (charged multivesicular body protein 1A); PARTICIPATES IN endocytosis pathway; INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,4-dinitrotoluene; 2-methoxyethanol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: chromatin modifying protein 1A; LOC365024; Pcoln3; procollagen (type III) N-endopeptidase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81968,146,672 - 68,154,952 (-)NCBIGRCr8
mRatBN7.21951,238,153 - 51,246,433 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1951,238,160 - 51,246,436 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1958,033,361 - 58,041,363 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01958,713,074 - 58,721,354 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01960,931,961 - 60,939,963 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01956,001,724 - 56,010,004 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1956,001,724 - 56,010,004 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01966,707,177 - 66,715,457 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41953,521,981 - 53,530,261 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11953,529,029 - 53,531,632 (-)NCBI
Celera1950,473,734 - 50,481,997 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:9837962   PMID:11559747   PMID:11559748   PMID:14505570   PMID:14519844   PMID:16730941   PMID:17928862   PMID:18834074   PMID:19056867   PMID:19129479   PMID:20616062  
PMID:23376485  


Genomics

Comparative Map Data
Chmp1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81968,146,672 - 68,154,952 (-)NCBIGRCr8
mRatBN7.21951,238,153 - 51,246,433 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1951,238,160 - 51,246,436 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1958,033,361 - 58,041,363 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01958,713,074 - 58,721,354 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01960,931,961 - 60,939,963 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01956,001,724 - 56,010,004 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1956,001,724 - 56,010,004 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01966,707,177 - 66,715,457 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41953,521,981 - 53,530,261 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11953,529,029 - 53,531,632 (-)NCBI
Celera1950,473,734 - 50,481,997 (-)NCBICelera
Cytogenetic Map19q12NCBI
CHMP1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381689,644,435 - 89,657,708 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1689,640,816 - 89,657,738 (-)EnsemblGRCh38hg38GRCh38
GRCh371689,710,843 - 89,724,116 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361688,238,344 - 88,251,630 (-)NCBINCBI36Build 36hg18NCBI36
Build 341688,238,345 - 88,251,754NCBI
Celera1674,775,335 - 74,788,601 (-)NCBICelera
Cytogenetic Map16q24.3NCBI
HuRef1675,406,208 - 75,419,708 (-)NCBIHuRef
CHM1_11691,122,139 - 91,134,975 (-)NCBICHM1_1
T2T-CHM13v2.01695,728,224 - 95,742,519 (-)NCBIT2T-CHM13v2.0
Chmp1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398123,931,000 - 123,939,527 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8123,931,003 - 123,939,502 (-)EnsemblGRCm39 Ensembl
GRCm388123,204,261 - 123,212,788 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8123,204,264 - 123,212,763 (-)EnsemblGRCm38mm10GRCm38
MGSCv378125,728,161 - 125,736,688 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368126,090,354 - 126,098,828 (-)NCBIMGSCv36mm8
Celera8127,435,808 - 127,451,781 (-)NCBICelera
Cytogenetic Map8E1NCBI
cM Map872.08NCBI
Chmp1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555413,216,972 - 3,223,634 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555413,216,972 - 3,223,636 (-)NCBIChiLan1.0ChiLan1.0
CHMP1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21899,434,669 - 99,448,095 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan116105,348,049 - 105,361,467 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01670,398,021 - 70,411,383 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11690,003,892 - 90,017,653 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1690,003,892 - 90,017,653 (-)Ensemblpanpan1.1panPan2
CHMP1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1563,897,544 - 63,906,515 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl563,897,594 - 63,905,550 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha563,910,397 - 63,919,629 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0564,125,390 - 64,134,623 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl564,125,425 - 64,134,621 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1564,145,452 - 64,154,671 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0563,983,044 - 63,992,276 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0564,389,618 - 64,398,851 (+)NCBIUU_Cfam_GSD_1.0
Chmp1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934924,612,956 - 24,622,756 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936641366,569 - 376,337 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936641366,563 - 376,303 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHMP1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6351,866 - 358,653 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16351,878 - 358,655 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26478,538 - 485,468 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CHMP1A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1574,990,706 - 75,002,074 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl574,990,410 - 75,001,988 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666047498,027 - 509,396 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chmp1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624746302,404 - 309,644 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624746302,344 - 309,117 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Chmp1a
46 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:429
Count of miRNA genes:240
Interacting mature miRNAs:281
Transcripts:ENSRNOT00000021483
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194997648153225766Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat

Markers in Region
RH128055  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21951,238,262 - 51,238,458 (+)MAPPERmRatBN7.2
Rnor_6.01956,001,834 - 56,002,029NCBIRnor6.0
Rnor_5.01966,707,287 - 66,707,482UniSTSRnor5.0
RGSC_v3.41953,522,091 - 53,522,286UniSTSRGSC3.4
Celera1950,473,844 - 50,474,039UniSTS
RH 3.4 Map19710.21UniSTS
Cytogenetic Map19q12UniSTS
RH131695  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21951,237,653 - 51,237,870 (+)MAPPERmRatBN7.2
Rnor_6.01956,001,225 - 56,001,441NCBIRnor6.0
Rnor_5.01966,706,678 - 66,706,894UniSTSRnor5.0
RGSC_v3.41953,521,482 - 53,521,698UniSTSRGSC3.4
Celera1950,473,235 - 50,473,451UniSTS
RH 3.4 Map19708.21UniSTS
Cytogenetic Map19q12UniSTS
BE110224  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21951,244,824 - 51,244,990 (+)MAPPERmRatBN7.2
Rnor_6.01956,008,396 - 56,008,561NCBIRnor6.0
Rnor_5.01966,713,849 - 66,714,014UniSTSRnor5.0
RGSC_v3.41953,528,653 - 53,528,818UniSTSRGSC3.4
RH 3.4 Map19710.81UniSTS
Cytogenetic Map19q12UniSTS
AI102036  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21951,238,712 - 51,238,832 (+)MAPPERmRatBN7.2
Rnor_6.01956,002,284 - 56,002,403NCBIRnor6.0
Rnor_5.01966,707,737 - 66,707,856UniSTSRnor5.0
RGSC_v3.41953,522,541 - 53,522,660UniSTSRGSC3.4
Celera1950,474,294 - 50,474,413UniSTS
RH 3.4 Map19713.41UniSTS
Cytogenetic Map19q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000021483   ⟹   ENSRNOP00000021475
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1951,238,170 - 51,246,436 (-)Ensembl
Rnor_6.0 Ensembl1956,001,724 - 56,010,004 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000115232   ⟹   ENSRNOP00000094810
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1951,238,160 - 51,243,056 (-)Ensembl
RefSeq Acc Id: NM_001083313   ⟹   NP_001076782
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81968,146,672 - 68,154,952 (-)NCBI
mRatBN7.21951,238,153 - 51,246,433 (-)NCBI
Rnor_6.01956,001,724 - 56,010,004 (-)NCBI
Rnor_5.01966,707,177 - 66,715,457 (-)NCBI
RGSC_v3.41953,521,981 - 53,530,261 (-)RGD
Celera1950,473,734 - 50,481,997 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001076782 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92790 (Get FASTA)   NCBI Sequence Viewer  
  EDL92791 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000021475.4
  ENSRNOP00000094810.1
RefSeq Acc Id: NP_001076782   ⟸   NM_001083313
- UniProtKB: D4AE79 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000021475   ⟸   ENSRNOT00000021483
Ensembl Acc Id: ENSRNOP00000094810   ⟸   ENSRNOT00000115232

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AE79-F1-model_v2 AlphaFold D4AE79 1-196 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13701219
Promoter ID:EPDNEW_R11743
Type:initiation region
Name:Chmp1a_1
Description:charged multivesicular body protein 1A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01956,009,989 - 56,010,049EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311083 AgrOrtholog
BioCyc Gene G2FUF-5337 BioCyc
Ensembl Genes ENSRNOG00000016001 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021483.5 UniProtKB/TrEMBL
  ENSRNOT00000115232.1 UniProtKB/TrEMBL
Gene3D-CATH 6.10.140.1230 UniProtKB/TrEMBL
InterPro Snf7 UniProtKB/TrEMBL
NCBI Gene 365024 ENTREZGENE
PANTHER PTHR10476 UniProtKB/TrEMBL
  PTHR10476:SF17 UniProtKB/TrEMBL
Pfam Snf7 UniProtKB/TrEMBL
PhenoGen Chmp1a PhenoGen
RatGTEx ENSRNOG00000016001 RatGTEx
UniProt A0A8I6GLB8_RAT UniProtKB/TrEMBL
  D4AE79 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-12-06 Chmp1a  charged multivesicular body protein 1A  Chmp1a  chromatin modifying protein 1A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-03-22 Chmp1a  chromatin modifying protein 1A  Pcoln3_predicted  procollagen (type III) N-endopeptidase (predicted)  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2005-01-12 Pcoln3_predicted  procollagen (type III) N-endopeptidase (predicted)      Symbol and Name status set to approved 70820 APPROVED