Chmp2b (charged multivesicular body protein 2B) - Rat Genome Database

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Gene: Chmp2b (charged multivesicular body protein 2B) Rattus norvegicus
Analyze
Symbol: Chmp2b
Name: charged multivesicular body protein 2B
RGD ID: 1306781
Description: Predicted to enable protein domain specific binding activity. Involved in modulation of chemical synaptic transmission; regulation of modification of postsynaptic structure; and regulation of postsynapse organization. Is active in glutamatergic synapse and postsynaptic density. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis; chromosome 3-linked frontotemporal dementia; and frontotemporal dementia. Orthologous to human CHMP2B (charged multivesicular body protein 2B); PARTICIPATES IN autophagy pathway; endocytosis pathway; INTERACTS WITH 17beta-estradiol; bisphenol A; Brodifacoum.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: chromatin modifying protein 2B; LOC363720; RGD1306781; similar to CGI-84 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2113,337,478 - 3,364,015 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl113,337,494 - 3,385,181 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1111,933,444 - 11,959,985 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0114,726,555 - 4,753,090 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0113,831,588 - 3,858,120 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0112,666,405 - 2,692,213 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl112,665,285 - 2,692,198 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0112,649,767 - 2,676,685 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4112,984,295 - 3,090,399 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1112,983,240 - 3,025,923 (-)NCBI
Celera113,315,643 - 3,340,019 (-)NCBICelera
Cytogenetic Map11p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Regulation of postsynaptic function by the dementia-related ESCRT-III subunit CHMP2B. Chassefeyre R, etal., J Neurosci. 2015 Feb 18;35(7):3155-73. doi: 10.1523/JNEUROSCI.0586-14.2015.
2. 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.
3. Progressive neuronal inclusion formation and axonal degeneration in CHMP2B mutant transgenic mice. Ghazi-Noori S, etal., Brain. 2012 Mar;135(Pt 3):819-32.
4. Mutations in CHMP2B are not a cause of frontotemporal lobar degeneration in Finnish patients. Kaivorinne AL, etal., Eur J Neurol. 2010 Nov;17(11):1393-5.
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. ALS phenotypes with mutations in CHMP2B (charged multivesicular body protein 2B). Parkinson N, etal., Neurology. 2006 Sep 26;67(6):1074-7. Epub 2006 Jun 28.
7. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Comprehensive gene review and curation RGD comprehensive gene curation
12. Presymptomatic generalized brain atrophy in frontotemporal dementia caused by CHMP2B mutation. Rohrer JD, etal., Dement Geriatr Cogn Disord. 2009;27(2):182-6. Epub 2009 Feb 7.
13. How do ESCRT proteins control autophagy? Rusten TE and Stenmark H, J Cell Sci. 2009 Jul 1;122(Pt 13):2179-83.
14. No association of chromatin-modifying protein 2B with sporadic frontotemporal dementia. Schumacher A, etal., Neurobiol Aging. 2007 Nov;28(11):1789-90. Epub 2006 Sep 18.
15. Mutations in the endosomal ESCRTIII-complex subunit CHMP2B in frontotemporal dementia. Skibinski G, etal., Nat Genet. 2005 Aug;37(8):806-8. Epub 2005 Jul 24.
Additional References at PubMed
PMID:17928862   PMID:19056867   PMID:20616062   PMID:23051622   PMID:23533145   PMID:24107264   PMID:24878737   PMID:25468996   PMID:36907288  


Genomics

Comparative Map Data
Chmp2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2113,337,478 - 3,364,015 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl113,337,494 - 3,385,181 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1111,933,444 - 11,959,985 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0114,726,555 - 4,753,090 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0113,831,588 - 3,858,120 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0112,666,405 - 2,692,213 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl112,665,285 - 2,692,198 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0112,649,767 - 2,676,685 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4112,984,295 - 3,090,399 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1112,983,240 - 3,025,923 (-)NCBI
Celera113,315,643 - 3,340,019 (-)NCBICelera
Cytogenetic Map11p12NCBI
CHMP2B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38387,227,309 - 87,255,556 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl387,227,271 - 87,255,556 (+)EnsemblGRCh38hg38GRCh38
GRCh37387,276,459 - 87,304,706 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36387,359,287 - 87,387,339 (+)NCBINCBI36Build 36hg18NCBI36
Celera388,029,539 - 88,057,175 (+)NCBICelera
Cytogenetic Map3p11.2NCBI
HuRef387,289,650 - 87,317,924 (+)NCBIHuRef
CHM1_1387,228,955 - 87,257,241 (+)NCBICHM1_1
T2T-CHM13v2.0387,301,665 - 87,329,903 (+)NCBIT2T-CHM13v2.0
Chmp2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391665,336,014 - 65,359,648 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1665,336,014 - 65,359,612 (-)EnsemblGRCm39 Ensembl
GRCm381665,539,128 - 65,562,762 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1665,539,128 - 65,562,726 (-)EnsemblGRCm38mm10GRCm38
MGSCv371665,539,378 - 65,562,942 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361665,457,393 - 65,480,957 (-)NCBIMGSCv36mm8
Celera1665,808,257 - 65,831,806 (-)NCBICelera
Cytogenetic Map16C1.3NCBI
cM Map1637.26NCBI
Chmp2b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554076,014,478 - 6,047,916 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554076,014,478 - 6,047,916 (-)NCBIChiLan1.0ChiLan1.0
CHMP2B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1387,376,335 - 87,405,108 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0387,358,297 - 87,386,556 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1389,471,993 - 89,500,127 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl389,471,993 - 89,501,241 (+)Ensemblpanpan1.1panPan2
CHMP2B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.131789,586 - 817,925 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl31791,139 - 817,895 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha31832,132 - 860,469 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.031773,787 - 802,124 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl31773,790 - 802,084 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.131752,283 - 780,608 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.031801,151 - 829,486 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0311,104,318 - 1,132,658 (-)NCBIUU_Cfam_GSD_1.0
Chmp2b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049712,282,396 - 2,320,530 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366102,281,066 - 2,321,211 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366102,282,925 - 2,320,554 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHMP2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13168,533,694 - 168,569,688 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113168,534,950 - 168,569,574 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213179,477,382 - 179,512,031 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CHMP2B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12289,672,043 - 89,701,801 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2289,672,022 - 89,701,897 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604177,021,098 - 77,060,029 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chmp2b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247893,557,797 - 3,587,703 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247893,557,811 - 3,587,814 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Chmp2b
50 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:68
Count of miRNA genes:59
Interacting mature miRNAs:66
Transcripts:ENSRNOT00000000904
Prediction methods: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
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)11121836709Rat
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11135331169Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat

Markers in Region
RH136671  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2113,338,669 - 3,338,884 (+)MAPPERmRatBN7.2
Rnor_6.0112,666,456 - 2,666,670NCBIRnor6.0
Rnor_5.0112,650,959 - 2,651,173UniSTSRnor5.0
RGSC_v3.4112,984,415 - 2,984,629UniSTSRGSC3.4
Celera113,315,694 - 3,315,908UniSTS
Cytogenetic Map11p12UniSTS
RH143770  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2113,363,910 - 3,364,011 (+)MAPPERmRatBN7.2
Rnor_6.0112,692,072 - 2,692,172NCBIRnor6.0
Rnor_5.0112,676,507 - 2,676,607UniSTSRnor5.0
RGSC_v3.4113,026,029 - 3,026,129UniSTSRGSC3.4
Celera113,339,878 - 3,339,978UniSTS
Cytogenetic Map11p12UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 56 40 19 40 6 7 74 35 41 11 6
Low 1 1 1 2 4 2
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000000904   ⟹   ENSRNOP00000000904
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl113,337,494 - 3,364,025 (-)Ensembl
Rnor_6.0 Ensembl112,665,285 - 2,692,198 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104960   ⟹   ENSRNOP00000089067
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl113,337,494 - 3,385,181 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117453   ⟹   ENSRNOP00000083221
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl113,337,499 - 3,364,030 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118130   ⟹   ENSRNOP00000078183
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl113,337,494 - 3,353,494 (-)Ensembl
RefSeq Acc Id: NM_001398813   ⟹   NP_001385742
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2113,337,478 - 3,364,015 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001385742 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL75910 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000000904
  ENSRNOP00000000904.6
  ENSRNOP00000078183.1
  ENSRNOP00000083221.1
  ENSRNOP00000089067.1
RefSeq Acc Id: ENSRNOP00000000904   ⟸   ENSRNOT00000000904
RefSeq Acc Id: ENSRNOP00000083221   ⟸   ENSRNOT00000117453
RefSeq Acc Id: ENSRNOP00000078183   ⟸   ENSRNOT00000118130
RefSeq Acc Id: ENSRNOP00000089067   ⟸   ENSRNOT00000104960
RefSeq Acc Id: NP_001385742   ⟸   NM_001398813
- UniProtKB: F1M8B7 (UniProtKB/TrEMBL),   A6K4X0 (UniProtKB/TrEMBL),   A0A8I5Y9Y9 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M8B7-F1-model_v2 AlphaFold F1M8B7 1-213 view protein structure

Transcriptome

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

Promoters
RGD ID:13698002
Promoter ID:EPDNEW_R8524
Type:initiation region
Name:Chmp2b_1
Description:charged multivesicular body protein 2B
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_6.0112,692,175 - 2,692,235EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306781 AgrOrtholog
BioCyc Gene G2FUF-22309 BioCyc
Ensembl Genes ENSRNOG00000040257 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000904 ENTREZGENE
  ENSRNOT00000000904.8 UniProtKB/TrEMBL
  ENSRNOT00000104960.1 UniProtKB/TrEMBL
  ENSRNOT00000117453.1 UniProtKB/TrEMBL
  ENSRNOT00000118130.1 UniProtKB/TrEMBL
Gene3D-CATH 6.10.140.1230 UniProtKB/TrEMBL
InterPro Snf7 UniProtKB/TrEMBL
KEGG Report rno:363720 UniProtKB/TrEMBL
NCBI Gene 363720 ENTREZGENE
PANTHER CHARGED MULTIVESICULAR BODY PROTEIN 2B UniProtKB/TrEMBL
  PTHR10476 UniProtKB/TrEMBL
Pfam Snf7 UniProtKB/TrEMBL
PhenoGen Chmp2b PhenoGen
RatGTEx ENSRNOG00000040257 RatGTEx
UniProt A0A8I5Y9Y9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZYY9_RAT UniProtKB/TrEMBL
  A0A8I6AB52_RAT UniProtKB/TrEMBL
  A6K4X0 ENTREZGENE, UniProtKB/TrEMBL
  F1M8B7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-09-29 Chmp2b  charged multivesicular body protein 2B  Chmp2b  chromatin modifying protein 2B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Chmp2b  chromatin modifying protein 2B  RGD1306781_predicted  similar to CGI-84 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1306781_predicted  similar to CGI-84 protein (predicted)  LOC363720_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC363720_predicted  similar to CGI-84 protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL