Chm (CHM Rab escort protein) - Rat Genome Database

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Gene: Chm (CHM Rab escort protein) Rattus norvegicus
Analyze
Symbol: Chm
Name: CHM Rab escort protein
RGD ID: 2340
Description: Exhibits small GTPase binding activity. Involved in protein geranylgeranylation. Localizes to Rab-protein geranylgeranyltransferase complex. Human ortholog(s) of this gene implicated in choroideremia. Orthologous to human CHM (CHM Rab escort protein); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CHM, Rab escort protein 1; choroideraemia protein homolog; Choroideremia; choroideremia (Rab escort protein 1); choroideremia protein homolog; choroidermia; rab escort protein 1; rab proteins geranylgeranyltransferase component A 1; REP-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X78,203,200 - 78,361,996 (-)NCBI
Rnor_6.0 EnsemblX84,666,900 - 84,821,775 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X84,666,900 - 84,821,775 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X84,610,339 - 84,767,421 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X101,753,857 - 101,927,941 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X101,827,289 - 102,001,374 (-)NCBI
CeleraX79,495,432 - 79,653,919 (-)NCBICelera
Cytogenetic MapXq31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA)
cytosol  (IBA,IEA,ISO,ISS)
nucleus  (IBA)
Rab-protein geranylgeranyltransferase complex  (IBA,IDA,IEA,IMP,ISO,ISS)

Molecular Function

References

Additional References at PubMed
PMID:1525821   PMID:7957092   PMID:15242790   PMID:18756270  


Genomics

Comparative Map Data
Chm
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X78,203,200 - 78,361,996 (-)NCBI
Rnor_6.0 EnsemblX84,666,900 - 84,821,775 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X84,666,900 - 84,821,775 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X84,610,339 - 84,767,421 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X101,753,857 - 101,927,941 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X101,827,289 - 102,001,374 (-)NCBI
CeleraX79,495,432 - 79,653,919 (-)NCBICelera
Cytogenetic MapXq31NCBI
CHM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX85,861,180 - 86,047,561 (-)EnsemblGRCh38hg38GRCh38
GRCh38X85,861,180 - 86,047,558 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X85,116,185 - 85,302,562 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X85,002,841 - 85,189,222 (-)NCBINCBI36hg18NCBI36
Build 34X84,925,656 - 85,108,711NCBI
CeleraX85,355,767 - 85,542,165 (-)NCBI
Cytogenetic MapXq21.2NCBI
HuRefX78,692,493 - 78,878,455 (-)NCBIHuRef
CHM1_1X85,009,817 - 85,196,134 (-)NCBICHM1_1
Chm
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X111,950,289 - 112,095,236 (-)NCBIGRCm39mm39
GRCm39 EnsemblX111,950,290 - 112,095,214 (-)Ensembl
GRCm38X113,040,592 - 113,185,539 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX113,040,593 - 113,185,517 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X110,154,201 - 110,299,124 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X109,158,373 - 109,302,459 (-)NCBImm8
CeleraX99,640,514 - 99,788,256 (-)NCBICelera
Cytogenetic MapXE1NCBI
Chm
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955525360,412 - 563,936 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955525359,393 - 563,930 (-)NCBIChiLan1.0ChiLan1.0
CHM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X85,038,154 - 85,224,741 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX85,038,154 - 85,224,761 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X74,928,576 - 75,115,733 (-)NCBIMhudiblu_PPA_v0panPan3
CHM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X66,636,003 - 66,880,256 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX66,639,095 - 66,880,209 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX57,393,834 - 57,644,452 (-)NCBI
ROS_Cfam_1.0X67,968,230 - 68,212,512 (-)NCBI
UMICH_Zoey_3.1X65,616,374 - 65,860,581 (-)NCBI
UNSW_CanFamBas_1.0X67,253,846 - 67,498,044 (-)NCBI
UU_Cfam_GSD_1.0X66,844,991 - 67,089,220 (-)NCBI
Chm
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X60,048,529 - 60,212,795 (-)NCBI
SpeTri2.0NW_0049365476,368,941 - 6,533,199 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX68,873,359 - 69,066,275 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X68,873,882 - 69,066,284 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X78,754,163 - 78,918,794 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CHM
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X74,626,531 - 74,810,560 (-)NCBI
ChlSab1.1 EnsemblX74,626,028 - 74,810,557 (-)Ensembl
Chm
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248522,270,647 - 2,514,864 (+)NCBI

Position Markers
DXWox24  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X84,797,610 - 84,797,775NCBIRnor6.0
Rnor_5.0X84,743,256 - 84,743,421UniSTSRnor5.0
RGSC_v3.4X101,907,635 - 101,907,800UniSTSRGSC3.4
CeleraX79,631,319 - 79,631,484UniSTS
Cytogenetic MapXq32UniSTS
DXWox25  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic MapXq32UniSTS
BF386272  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X84,766,431 - 84,766,584NCBIRnor6.0
CeleraX79,597,108 - 79,597,261UniSTS
RH 3.4 MapX747.0UniSTS
Cytogenetic MapXq32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X82930791127930791Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:387
Count of miRNA genes:209
Interacting mature miRNAs:273
Transcripts:ENSRNOT00000000174
Prediction methods:Miranda, Pita, 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.


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 1 27 30 14 18 14 2 2 74 33 34 11 2
Low 2 16 27 27 1 27 6 8 2 7 6
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000174   ⟹   ENSRNOP00000000174
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX84,666,900 - 84,821,775 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088570   ⟹   ENSRNOP00000075357
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX84,668,790 - 84,768,463 (-)Ensembl
RefSeq Acc Id: NM_017067   ⟹   NP_058763
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X78,204,553 - 78,361,943 (-)NCBI
Rnor_6.0X84,666,900 - 84,821,775 (-)NCBI
Rnor_5.0X84,610,339 - 84,767,421 (-)NCBI
RGSC_v3.4X101,753,857 - 101,927,941 (-)RGD
CeleraX79,495,432 - 79,653,919 (-)RGD
Sequence:
RefSeq Acc Id: XM_039099489   ⟹   XP_038955417
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X78,203,200 - 78,361,786 (-)NCBI
RefSeq Acc Id: XR_005497922
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X78,221,171 - 78,361,996 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_058763   ⟸   NM_017067
- UniProtKB: P37727 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000174   ⟸   ENSRNOT00000000174
RefSeq Acc Id: ENSRNOP00000075357   ⟸   ENSRNOT00000088570
RefSeq Acc Id: XP_038955417   ⟸   XM_039099489
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13701917
Promoter ID:EPDNEW_R12441
Type:multiple initiation site
Name:Chm_1
Description:CHM, Rab escort protein 1
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_6.0X84,821,792 - 84,821,852EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2340 AgrOrtholog
Ensembl Genes ENSRNOG00000000161 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000174 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075357 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000174 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000088570 UniProtKB/TrEMBL
Gene3D-CATH 3.50.50.60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro FAD/NAD-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GDP_dissociation_inhibitor UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rab_escort UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24942 UniProtKB/Swiss-Prot
NCBI Gene 24942 ENTREZGENE
PANTHER PTHR11787 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam GDI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Chm PhenoGen
PIRSF Rab_ger_ger_transf_A_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS RABESCORT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RABGDIREP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF51905 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2KAD5_RAT UniProtKB/TrEMBL
  G3V607_RAT UniProtKB/TrEMBL
  P37727 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-10 Chm  CHM Rab escort protein  Chm  CHM, Rab escort protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-01 Chm  CHM, Rab escort protein 1  Chm  choroideremia (Rab escort protein 1)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Chm  choroideremia (Rab escort protein 1)  Chm  choroidermia  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Chm  Choroideremia      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function binds prenylated Rabs and catalyzes geranylgeranyl transfer reaction 704419