Chmp1b2 (charged multivesicular body protein 1B2) - Rat Genome Database

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Gene: Chmp1b2 (charged multivesicular body protein 1B2) Rattus norvegicus
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Symbol: Chmp1b2
Name: charged multivesicular body protein 1B2
RGD ID: 1566265
Description: Predicted to be involved in endosome transport via multivesicular body sorting pathway; late endosome to vacuole transport; and protein transport. Predicted to be part of ESCRT III complex. Predicted to be active in multivesicular body. Orthologous to several human genes including CHMP1B (charged multivesicular body protein 1B); PARTICIPATES IN endocytosis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; oxaliplatin; paracetamol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Charged multivesicular body protein 1b-2-like; hypothetical protein LOC363487; LOC363487; RGD1566265; similar to RIKEN cDNA 2610002M06; uncharacterized protein LOC363487
RGD Orthologs
Human
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X76,933,194 - 76,974,018 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX76,933,204 - 76,974,032 (-)EnsemblGRCr8
mRatBN7.2X72,860,409 - 72,901,232 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX72,860,409 - 72,901,246 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX74,350,547 - 74,391,365 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X77,870,430 - 77,911,279 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X75,437,448 - 75,478,247 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X78,870,964 - 78,911,601 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX78,870,964 - 78,911,601 (-)Ensemblrn6Rnor6.0
Rnor_5.0X79,066,119 - 79,106,756 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X96,012,174 - 96,053,210 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX74,142,672 - 74,182,817 (-)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Chmp1b2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X76,933,194 - 76,974,018 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX76,933,204 - 76,974,032 (-)EnsemblGRCr8
mRatBN7.2X72,860,409 - 72,901,232 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX72,860,409 - 72,901,246 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX74,350,547 - 74,391,365 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X77,870,430 - 77,911,279 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X75,437,448 - 75,478,247 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X78,870,964 - 78,911,601 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX78,870,964 - 78,911,601 (-)Ensemblrn6Rnor6.0
Rnor_5.0X79,066,119 - 79,106,756 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X96,012,174 - 96,053,210 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX74,142,672 - 74,182,817 (-)NCBICelera
Cytogenetic MapXq22NCBI
CHMP1B2P
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X80,228,489 - 80,335,318 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX80,272,065 - 80,335,227 (-)Ensemblhg38GRCh38
GRCh38.p14 EnsemblX80,210,619 - 80,335,364 (-)Ensemblhg38GRCh38
GRCh37X79,483,988 - 79,590,817 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic MapXq21.1NCBI
HuRefX73,082,439 - 73,128,091 (-)NCBIHuRef
CHM1_1X79,431,573 - 79,459,189 (-)NCBICHM1_1
T2T-CHM13v2.0X78,661,052 - 78,768,028 (-)NCBIT2T-CHM13v2.0
Chmp1b2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X106,826,357 - 106,859,940 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX106,826,357 - 106,859,940 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X107,782,751 - 107,816,334 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX107,782,751 - 107,816,334 (-)Ensemblmm10GRCm38
MGSCv37X104,978,090 - 105,011,673 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X103,990,063 - 104,019,000 (-)NCBIMGSCv36mm8
CeleraX94,619,560 - 94,653,135 (-)NCBICelera
Cytogenetic MapXDNCBI
cM MapX47.62NCBI

Variants

.
Variants in Chmp1b2
82 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:92
Count of miRNA genes:71
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000003188
Prediction methods:Miranda, Pita, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X4493088389930883Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 66 165 91 90 59 92 59 6 355 191 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000003188   ⟹   ENSRNOP00000003188
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX76,933,204 - 76,974,032 (-)Ensembl
mRatBN7.2 EnsemblX72,860,419 - 72,901,246 (-)Ensembl
Rnor_6.0 EnsemblX78,870,964 - 78,911,601 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000105046   ⟹   ENSRNOP00000096279
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX76,933,638 - 76,974,032 (-)Ensembl
mRatBN7.2 EnsemblX72,860,409 - 72,892,165 (-)Ensembl
RefSeq Acc Id: NM_001134589   ⟹   NP_001128061
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X76,933,194 - 76,974,018 (-)NCBI
mRatBN7.2X72,860,409 - 72,901,232 (-)NCBI
Rnor_6.0X78,870,964 - 78,911,601 (-)NCBI
Rnor_5.0X79,066,119 - 79,106,756 (-)NCBI
RGSC_v3.4X96,012,174 - 96,053,210 (-)RGD
CeleraX74,142,672 - 74,182,817 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001128061 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM07109 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000003188
  ENSRNOP00000003188.5
  ENSRNOP00000096279.2
RefSeq Acc Id: NP_001128061   ⟸   NM_001134589
- UniProtKB: G3V6A6 (UniProtKB/TrEMBL),   A6IV71 (UniProtKB/TrEMBL),   A0A8I6AP66 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000003188   ⟸   ENSRNOT00000003188
Ensembl Acc Id: ENSRNOP00000096279   ⟸   ENSRNOT00000105046

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V6A6-F1-model_v2 AlphaFold G3V6A6 1-199 view protein structure

Transcriptome

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

Promoters
RGD ID:13701907
Promoter ID:EPDNEW_R12431
Type:initiation region
Name:RGD1566265_1
Description:similar to RIKEN cDNA 2610002M06
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_6.0X78,911,588 - 78,911,648EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566265 AgrOrtholog
BioCyc Gene G2FUF-1887 BioCyc
Ensembl Genes ENSRNOG00000002323 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003188 ENTREZGENE
  ENSRNOT00000003188.7 UniProtKB/TrEMBL
  ENSRNOT00000105046.2 UniProtKB/TrEMBL
Gene3D-CATH 6.10.140.1230 UniProtKB/TrEMBL
InterPro Snf7 UniProtKB/TrEMBL
KEGG Report rno:363487 UniProtKB/TrEMBL
NCBI Gene 363487 ENTREZGENE
PANTHER PTHR10476 UniProtKB/TrEMBL
Pfam Snf7 UniProtKB/TrEMBL
PhenoGen Chmp1b2 PhenoGen
RatGTEx ENSRNOG00000002323 RatGTEx
UniProt A0A8I6AP66 ENTREZGENE, UniProtKB/TrEMBL
  A6IV71 ENTREZGENE, UniProtKB/TrEMBL
  G3V6A6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-08-25 Chmp1b2  charged multivesicular body protein 1B2  RGD1566265  similar to RIKEN cDNA 2610002M06  Name and Symbol changed 629549 APPROVED
2008-04-30 RGD1566265  similar to RIKEN cDNA 2610002M06   RGD1566265_predicted  similar to RIKEN cDNA 2610002M06 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1566265_predicted  similar to RIKEN cDNA 2610002M06 (predicted)  LOC363487  similar to RIKEN cDNA 2610002M06  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC363487  similar to RIKEN cDNA 2610002M06      Symbol and Name status set to provisional 70820 PROVISIONAL