Chchd2 (coiled-coil-helix-coiled-coil-helix domain containing 2) - Rat Genome Database

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Gene: Chchd2 (coiled-coil-helix-coiled-coil-helix domain containing 2) Rattus norvegicus
Analyze
Symbol: Chchd2
Name: coiled-coil-helix-coiled-coil-helix domain containing 2
RGD ID: 1309819
Description: Predicted to have sequence-specific DNA binding activity. Predicted to be involved in mitochondrion organization and positive regulation of transcription by RNA polymerase II. Predicted to localize to mitochondrion and nucleus. Human ortholog(s) of this gene implicated in Parkinson's disease 22. Orthologous to human CHCHD2 (coiled-coil-helix-coiled-coil-helix domain containing 2); INTERACTS WITH 17alpha-ethynylestradiol; alpha-hexachlorocyclohexane; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: coiled-coil-helix-coiled-coil-helix domain-containing protein 2; coiled-coil-helix-coiled-coil-helix domain-containing protein 2, mitochondrial; coiled-coil-helix-coiled-coil-helix domain-containing protein 2, mitochondrial-like; LOC100911516; LOC316643; MGC112750
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
mRatBN7.2994,500,439 - 94,501,110 (-)NCBI
Rnor_6.0 Ensembl9101,388,151 - 101,388,833 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09101,388,148 - 101,388,819 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.09101,018,487 - 101,019,158 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4927,858,760 - 28,053,369 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1993,460,637 - 93,461,304 (-)NCBI
Celera992,034,380 - 92,035,051 (-)NCBICelera
Cytogenetic Map9q36NCBI
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

Molecular Function

References

Additional References at PubMed
PMID:14651853   PMID:18614015   PMID:23303788   PMID:25662902  


Genomics

Comparative Map Data
Chchd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2994,500,439 - 94,501,110 (-)NCBI
Rnor_6.0 Ensembl9101,388,151 - 101,388,833 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09101,388,148 - 101,388,819 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.09101,018,487 - 101,019,158 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4927,858,760 - 28,053,369 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1993,460,637 - 93,461,304 (-)NCBI
Celera992,034,380 - 92,035,051 (-)NCBICelera
Cytogenetic Map9q36NCBI
CHCHD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl756,101,573 - 56,106,476 (-)EnsemblGRCh38hg38GRCh38
GRCh38756,101,573 - 56,106,476 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37756,169,266 - 56,174,169 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36756,136,760 - 56,141,681 (-)NCBINCBI36hg18NCBI36
Build 34755,943,476 - 55,948,396NCBI
Celera767,222,175 - 67,227,096 (-)NCBI
Cytogenetic Map7p11.2NCBI
HuRef755,983,486 - 55,988,171 (-)NCBIHuRef
CHM1_1756,172,283 - 56,177,351 (-)NCBICHM1_1
CRA_TCAGchr7v2756,173,513 - 56,178,434 (-)NCBI
Chchd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395129,910,002 - 129,916,311 (-)NCBIGRCm39mm39
GRCm39 Ensembl5129,909,997 - 129,916,311 (-)Ensembl
GRCm385129,881,161 - 129,887,470 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5129,881,156 - 129,887,470 (-)EnsemblGRCm38mm10GRCm38
MGSCv375130,357,032 - 130,363,340 (-)NCBIGRCm37mm9NCBIm37
MGSCv365130,165,865 - 130,172,173 (-)NCBImm8
Celera5126,880,556 - 126,886,855 (-)NCBICelera
Cytogenetic Map5G1.3NCBI
Chchd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554568,255,898 - 8,265,488 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554568,260,533 - 8,265,488 (-)NCBIChiLan1.0ChiLan1.0
CHCHD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1757,136,723 - 57,141,765 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl757,134,303 - 57,141,765 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0756,714,583 - 56,719,640 (-)NCBIMhudiblu_PPA_v0panPan3
CHCHD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.16581,276 - 585,367 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl6581,280 - 585,301 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha62,280,745 - 2,284,839 (-)NCBI
ROS_Cfam_1.06385,111 - 389,203 (-)NCBI
UMICH_Zoey_3.16328,861 - 332,963 (-)NCBI
UNSW_CanFamBas_1.06322,956 - 327,041 (-)NCBI
UU_Cfam_GSD_1.06494,144 - 498,243 (-)NCBI
Chchd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344126,172,517 - 126,175,918 (-)NCBI
SpeTri2.0NW_0049365437,860,432 - 7,864,050 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHCHD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1316,812,409 - 16,819,130 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2317,065,147 - 17,071,876 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CHCHD2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1212,675,522 - 2,680,406 (+)NCBI
Chchd2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247408,279,416 - 8,283,730 (-)NCBI

Position Markers
AV006093  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,533,326 - 30,533,459NCBIRnor6.0
Rnor_5.01232,475,094 - 32,475,227UniSTSRnor5.0
RGSC_v3.41227,962,835 - 27,962,968UniSTSRGSC3.4
Celera1228,617,568 - 28,617,701UniSTS
Cytogenetic Map12q13UniSTS
Cytogenetic Map9q36UniSTS
AI711004  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,460,977 - 30,461,161NCBIRnor6.0
Rnor_5.01232,403,406 - 32,403,590UniSTSRnor5.0
RGSC_v3.41228,032,769 - 28,032,953UniSTSRGSC3.4
Celera1228,555,625 - 28,555,809UniSTS
RH 3.4 Map12454.2UniSTS
Cytogenetic Map9q36UniSTS
Cytogenetic Map12q13UniSTS
BF399653  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,489,252 - 30,489,396NCBIRnor6.0
Rnor_5.01232,431,173 - 32,431,317UniSTSRnor5.0
RGSC_v3.41228,004,766 - 28,004,910UniSTSRGSC3.4
Celera1228,576,097 - 28,576,241UniSTS
RH 3.4 Map12452.3UniSTS
Cytogenetic Map12q13UniSTS
Cytogenetic Map9q36UniSTS
RH141085  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,570,898 - 30,571,089NCBIRnor6.0
Rnor_5.01232,511,526 - 32,511,717UniSTSRnor5.0
RGSC_v3.41227,923,155 - 27,923,346UniSTSRGSC3.4
Celera1228,654,579 - 28,654,770UniSTS
RH 3.4 Map12452.5UniSTS
Cytogenetic Map9q36UniSTS
Cytogenetic Map12q13UniSTS
RH141366  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,464,805 - 30,464,984NCBIRnor6.0
Rnor_5.01232,407,234 - 32,407,413UniSTSRnor5.0
RGSC_v3.41228,028,946 - 28,029,125UniSTSRGSC3.4
Celera1228,559,401 - 28,559,580UniSTS
RH 3.4 Map12446.6UniSTS
Cytogenetic Map12q13UniSTS
Cytogenetic Map9q36UniSTS
RH129042  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,526,329 - 30,526,525NCBIRnor6.0
Rnor_5.01232,468,097 - 32,468,293UniSTSRnor5.0
RGSC_v3.41227,969,774 - 27,969,970UniSTSRGSC3.4
Celera1228,610,569 - 28,610,765UniSTS
Cytogenetic Map9q36UniSTS
Cytogenetic Map12q13UniSTS
RH134402  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,491,507 - 30,491,698NCBIRnor6.0
Rnor_5.01232,433,428 - 32,433,619UniSTSRnor5.0
RGSC_v3.458,729,076 - 8,729,267UniSTSRGSC3.4
RGSC_v3.41228,002,464 - 28,002,655UniSTSRGSC3.4
Celera1228,578,352 - 28,578,543UniSTS
Cytogenetic Map12q13UniSTS
Cytogenetic Map9q36UniSTS
RH94823  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,450,052 - 30,450,306NCBIRnor6.0
Rnor_5.01232,392,481 - 32,392,735UniSTSRnor5.0
RGSC_v3.41228,043,624 - 28,043,878UniSTSRGSC3.4
Celera1228,544,700 - 28,544,954UniSTS
RH 3.4 Map12452.5UniSTS
Cytogenetic Map9q36UniSTS
Cytogenetic Map12q13UniSTS
RH142798  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,566,240 - 30,566,340NCBIRnor6.0
Rnor_5.01232,506,868 - 32,506,968UniSTSRnor5.0
RGSC_v3.41227,928,140 - 27,928,240UniSTSRGSC3.4
Celera1228,649,922 - 28,650,022UniSTS
RH 3.4 Map12446.6UniSTS
Cytogenetic Map12q13UniSTS
Cytogenetic Map9q36UniSTS
BE096988  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,441,321 - 30,441,499NCBIRnor6.0
Rnor_5.01232,383,750 - 32,383,928UniSTSRnor5.0
RGSC_v3.41228,052,897 - 28,053,075UniSTSRGSC3.4
Celera1228,535,293 - 28,535,471UniSTS
RH 3.4 Map12444.1UniSTS
Cytogenetic Map9q36UniSTS
BF387881  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,484,432 - 30,484,589NCBIRnor6.0
Rnor_5.01232,426,353 - 32,426,510UniSTSRnor5.0
RGSC_v3.41228,009,473 - 28,009,630UniSTSRGSC3.4
Celera1228,571,289 - 28,571,446UniSTS
RH 3.4 Map12446.2UniSTS
Cytogenetic Map12q13UniSTS
Cytogenetic Map9q36UniSTS
RH137104  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,533,283 - 30,533,483NCBIRnor6.0
Rnor_5.01232,475,051 - 32,475,251UniSTSRnor5.0
RGSC_v3.41227,962,811 - 27,963,011UniSTSRGSC3.4
Celera1228,617,525 - 28,617,725UniSTS
RH 3.4 Map12452.5UniSTS
Cytogenetic Map12q13UniSTS
Cytogenetic Map9q36UniSTS
RH138649  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,500,945 - 30,501,109NCBIRnor6.0
Rnor_5.01232,442,866 - 32,443,030UniSTSRnor5.0
RGSC_v3.41227,993,052 - 27,993,216UniSTSRGSC3.4
Celera1228,587,791 - 28,587,955UniSTS
RH 3.4 Map12453.1UniSTS
Cytogenetic Map9q36UniSTS
Cytogenetic Map12q13UniSTS
RH138684  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,563,491 - 30,563,614NCBIRnor6.0
Rnor_5.01232,504,119 - 32,504,242UniSTSRnor5.0
RGSC_v3.41227,930,866 - 27,930,989UniSTSRGSC3.4
Celera1228,647,171 - 28,647,294UniSTS
RH 3.4 Map12454.2UniSTS
Cytogenetic Map12q13UniSTS
Cytogenetic Map9q36UniSTS
RH138720  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,465,037 - 30,465,158NCBIRnor6.0
Rnor_5.01232,407,466 - 32,407,587UniSTSRnor5.0
RGSC_v3.41228,028,772 - 28,028,893UniSTSRGSC3.4
Celera1228,559,633 - 28,559,754UniSTS
RH 3.4 Map12449.1UniSTS
Cytogenetic Map12q13UniSTS
Cytogenetic Map9q36UniSTS
AU049267  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,514,883 - 30,515,040NCBIRnor6.0
Rnor_5.01232,456,522 - 32,456,679UniSTSRnor5.0
RGSC_v3.41227,983,406 - 27,983,563UniSTSRGSC3.4
Celera1228,597,455 - 28,597,612UniSTS
Cytogenetic Map9q36UniSTS
Cytogenetic Map12q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)970241351115241351Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)970942881115942881Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)981411073119983851Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)983686153111609081Rat
4889852Pur26Proteinuria QTL 26150.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)990024661107199079Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)990024661119983851Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)999041068107878528Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:182
Count of miRNA genes:140
Interacting mature miRNAs:157
Transcripts:ENSRNOT00000071424, ENSRNOT00000071817
Prediction methods:Microtar, Miranda, Rnahybrid
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
Low 20 14 14 1 14 36 6 19 1
Below cutoff 1 18 28 16 12 16 1 2 35 23 14 4 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071424   ⟹   ENSRNOP00000066780
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9101,106,892 - 101,107,575 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000071817   ⟹   ENSRNOP00000065307
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9101,388,151 - 101,388,833 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080892   ⟹   ENSRNOP00000069653
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9101,107,074 - 101,107,535 (-)Ensembl
RefSeq Acc Id: NM_001015019   ⟹   NP_001015019
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2994,500,439 - 94,501,110 (-)NCBI
Rnor_6.09101,388,148 - 101,388,819 (-)NCBI
Rnor_5.09101,018,487 - 101,019,158 (-)NCBI
RGSC_v3.4927,858,760 - 28,053,369 (-)RGD
Celera992,034,380 - 92,035,051 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001015019 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001015019   ⟸   NM_001015019
- UniProtKB: Q5BJB3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000065307   ⟸   ENSRNOT00000071817
RefSeq Acc Id: ENSRNOP00000066780   ⟸   ENSRNOT00000071424
RefSeq Acc Id: ENSRNOP00000069653   ⟸   ENSRNOT00000080892

Transcriptome

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

Promoters
RGD ID:13696885
Promoter ID:EPDNEW_R7409
Type:single initiation site
Name:LOC100911516_1
Description:coiled-coil-helix-coiled-coil-helix domain-containing protein2, mitochondrial-like
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_6.09101,388,833 - 101,388,893EPDNEW

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)
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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
FHH/EurMcwi (MCW)
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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)
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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
FHL/EurMcwi (MCW)
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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)
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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)
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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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (MCW)
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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)
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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)
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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
SHRSP/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
SR/JrHsd (MCW)
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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)
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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
SS/Jr (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
SS/JrHsdMcwi (MCW)
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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)
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
WKY/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
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)
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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309819 AgrOrtholog
  RGD:6492335 AgrOrtholog
Ensembl Genes ENSRNOG00000051180 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000051286 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065307 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000066780 UniProtKB/TrEMBL
  ENSRNOP00000069653 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071424 UniProtKB/TrEMBL
  ENSRNOT00000071817 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000080892 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7388574 IMAGE-MGC_LOAD
KEGG Report rno:100911516 UniProtKB/TrEMBL
  rno:316643 UniProtKB/TrEMBL
MGC_CLONE MGC:112750 IMAGE-MGC_LOAD
NCBI Gene 316643 ENTREZGENE
PhenoGen Chchd2 PhenoGen
UniProt M0R785_RAT UniProtKB/TrEMBL
  Q5BJB3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Chchd2  coiled-coil-helix-coiled-coil-helix domain containing 2  LOC100911516  coiled-coil-helix-coiled-coil-helix domain-containing protein 2, mitochondrial-like  Data Merged 737654 PROVISIONAL
2012-07-05 LOC100911516  coiled-coil-helix-coiled-coil-helix domain-containing protein 2, mitochondrial-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-12-06 Chchd2  coiled-coil-helix-coiled-coil-helix domain containing 2  Chchd2_predicted  coiled-coil-helix-coiled-coil-helix domain containing 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Chchd2_predicted  coiled-coil-helix-coiled-coil-helix domain containing 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED