Ccdc138 (coiled-coil domain containing 138) - Rat Genome Database
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Gene: Ccdc138 (coiled-coil domain containing 138) Rattus norvegicus
Analyze
Symbol: Ccdc138
Name: coiled-coil domain containing 138
RGD ID: 1566050
Description: Orthologous to human CCDC138 (coiled-coil domain containing 138); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; endosulfan.
Type: protein-coding
RefSeq Status: MODEL
Also known as: coiled-coil domain-containing protein 138; LOC499442; RGD1566050; similar to hypothetical protein FLJ32745
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
mRatBN7.22026,493,624 - 26,572,367 (+)NCBI
Rnor_6.0 Ensembl2028,078,500 - 28,157,071 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02028,076,784 - 28,158,053 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02029,897,919 - 29,975,893 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42037,181,926 - 37,269,631 (-)NCBIRGSC3.4rn4RGSC3.4
Celera2027,943,945 - 28,023,299 (+)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References


Genomics

Comparative Map Data
Ccdc138
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22026,493,624 - 26,572,367 (+)NCBI
Rnor_6.0 Ensembl2028,078,500 - 28,157,071 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02028,076,784 - 28,158,053 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02029,897,919 - 29,975,893 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42037,181,926 - 37,269,631 (-)NCBIRGSC3.4rn4RGSC3.4
Celera2027,943,945 - 28,023,299 (+)NCBICelera
Cytogenetic Map20q11NCBI
CCDC138
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2108,786,757 - 108,885,477 (+)EnsemblGRCh38hg38GRCh38
GRCh382108,786,733 - 108,885,485 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372109,403,208 - 109,493,047 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh372109,403,206 - 109,501,941 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362108,769,651 - 108,859,279 (+)NCBINCBI36hg18NCBI36
Celera2103,713,196 - 103,802,791 (+)NCBI
Cytogenetic Map2q13NCBI
HuRef2103,001,686 - 103,091,278 (+)NCBIHuRef
CHM1_12109,407,534 - 109,497,317 (+)NCBICHM1_1
Ccdc138
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391058,333,523 - 58,412,066 (+)NCBIGRCm39mm39
GRCm381058,497,699 - 58,576,244 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1058,497,948 - 58,576,244 (+)EnsemblGRCm38mm10GRCm38
MGSCv371057,960,685 - 58,038,992 (+)NCBIGRCm37mm9NCBIm37
MGSCv361057,893,327 - 57,971,601 (+)NCBImm8
MGSCv361058,477,854 - 58,557,364 (+)NCBImm8
Cytogenetic Map10B4NCBI
Ccdc138
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547012,251,682 - 12,305,973 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495547012,249,279 - 12,305,099 (+)NCBIChiLan1.0ChiLan1.0
CCDC138
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A110,041,114 - 110,128,383 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A110,041,000 - 110,128,234 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A95,030,440 - 95,126,627 (+)NCBIMhudiblu_PPA_v0panPan3
CCDC138
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1034,976,670 - 35,086,297 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11034,976,341 - 35,086,080 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ccdc138
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936829335,977 - 397,252 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC138
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl347,470,706 - 47,523,536 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1347,470,649 - 47,525,606 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2349,632,032 - 49,688,845 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC138
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11412,320,653 - 12,412,191 (+)NCBI
ChlSab1.1 Ensembl1412,320,719 - 12,411,855 (+)Ensembl
Ccdc138
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474911,924,869 - 11,974,072 (+)NCBI

Position Markers
RH131887  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02028,077,131 - 28,077,280NCBIRnor6.0
Rnor_5.02029,896,616 - 29,896,765UniSTSRnor5.0
RGSC_v3.42037,270,851 - 37,271,000UniSTSRGSC3.4
Celera2027,944,292 - 27,944,441UniSTS
Cytogenetic Map20q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201887215049108956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:13
Count of miRNA genes:11
Interacting mature miRNAs:13
Transcripts:ENSRNOT00000030005
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.


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 25 21 30 4
Low 3 40 57 41 19 41 8 9 49 14 11 7 8
Below cutoff 3 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000030005   ⟹   ENSRNOP00000031531
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2028,078,500 - 28,157,071 (+)Ensembl
RefSeq Acc Id: XM_001053950   ⟹   XP_001053950
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2027,943,945 - 28,023,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006223889   ⟹   XP_006223951
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2027,945,661 - 28,023,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006223890   ⟹   XP_006223952
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2027,946,959 - 28,023,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256400   ⟹   XP_006256462
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,493,624 - 26,572,367 (+)NCBI
Rnor_6.02028,078,500 - 28,158,053 (+)NCBI
Rnor_5.02029,897,919 - 29,975,893 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256401   ⟹   XP_006256463
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,496,710 - 26,572,367 (+)NCBI
Rnor_6.02028,080,881 - 28,158,053 (+)NCBI
Rnor_5.02029,897,919 - 29,975,893 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588057   ⟹   XP_017443546
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2027,945,665 - 28,023,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588058   ⟹   XP_017443547
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2027,945,665 - 28,023,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588060   ⟹   XP_017443549
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2027,945,665 - 28,023,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588061   ⟹   XP_017443550
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2027,946,960 - 28,023,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588062   ⟹   XP_017443551
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2027,946,959 - 28,023,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588063   ⟹   XP_017443552
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2027,965,125 - 28,023,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601797   ⟹   XP_017457286
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02028,078,504 - 28,158,053 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601798   ⟹   XP_017457287
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02028,078,504 - 28,158,053 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601799   ⟹   XP_017457288
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,493,624 - 26,572,367 (+)NCBI
Rnor_6.02028,078,504 - 28,158,053 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601800   ⟹   XP_017457289
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,493,624 - 26,572,367 (+)NCBI
Rnor_6.02028,079,799 - 28,158,053 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601801   ⟹   XP_017457290
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,496,656 - 26,572,367 (+)NCBI
Rnor_6.02028,086,928 - 28,158,053 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601802   ⟹   XP_017457291
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,512,897 - 26,572,367 (+)NCBI
Rnor_6.02028,098,121 - 28,158,053 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099228   ⟹   XP_038955156
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,493,624 - 26,572,367 (+)NCBI
RefSeq Acc Id: XM_574765   ⟹   XP_574765
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,493,624 - 26,572,367 (+)NCBI
Rnor_6.02028,076,784 - 28,158,053 (+)NCBI
Rnor_5.02029,897,919 - 29,975,893 (+)NCBI
RGSC_v3.42037,181,926 - 37,269,631 (-)RGD
Sequence:
RefSeq Acc Id: XR_005497585
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,493,624 - 26,571,957 (+)NCBI
RefSeq Acc Id: XR_005497586
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,493,624 - 26,543,012 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_001053950   ⟸   XM_001053950
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_574765   ⟸   XM_574765
- Peptide Label: isoform X1
- UniProtKB: D3ZGR6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006223951   ⟸   XM_006223889
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006223952   ⟸   XM_006223890
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006256462   ⟸   XM_006256400
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006256463   ⟸   XM_006256401
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017443546   ⟸   XM_017588057
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017443547   ⟸   XM_017588058
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017443549   ⟸   XM_017588060
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017443551   ⟸   XM_017588062
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017443550   ⟸   XM_017588061
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017443552   ⟸   XM_017588063
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017457286   ⟸   XM_017601797
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017457287   ⟸   XM_017601798
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017457288   ⟸   XM_017601799
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017457289   ⟸   XM_017601800
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017457290   ⟸   XM_017601801
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017457291   ⟸   XM_017601802
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000031531   ⟸   ENSRNOT00000030005
RefSeq Acc Id: XP_038955156   ⟸   XM_039099228
- Peptide Label: isoform X4

Transcriptome

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

Promoters
RGD ID:13701584
Promoter ID:EPDNEW_R12106
Type:multiple initiation site
Name:Ccdc138_1
Description:coiled-coil domain containing 138
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_6.02028,078,485 - 28,078,545EPDNEW

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)
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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)
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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
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)
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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
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:1566050 AgrOrtholog
Ensembl Genes ENSRNOG00000028581 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000031531 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030005 UniProtKB/TrEMBL
InterPro CCDC138 UniProtKB/TrEMBL
KEGG Report rno:499442 UniProtKB/TrEMBL
NCBI Gene 499442 ENTREZGENE
PANTHER PTHR34523 UniProtKB/TrEMBL
PhenoGen Ccdc138 PhenoGen
UniProt D3ZGR6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-12 Ccdc138  coiled-coil domain containing 138  RGD1566050  similar to hypothetical protein FLJ32745  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1566050  similar to hypothetical protein FLJ32745   RGD1566050_predicted  similar to hypothetical protein FLJ32745 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1566050_predicted  similar to hypothetical protein FLJ32745 (predicted)  LOC499442  similar to hypothetical protein FLJ32745  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499442  similar to hypothetical protein FLJ32745      Symbol and Name status set to provisional 70820 PROVISIONAL