Ccdc172 (coiled-coil domain containing 172) - Rat Genome Database
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Gene: Ccdc172 (coiled-coil domain containing 172) Rattus norvegicus
Analyze
Symbol: Ccdc172
Name: coiled-coil domain containing 172
RGD ID: 1359412
Description: Localizes to sperm midpiece. Orthologous to human CCDC172 (coiled-coil domain containing 172); INTERACTS WITH bisphenol A; acrylamide (ortholog); benzo[a]pyrene (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: coiled-coil domain-containing protein 172; hypothetical protein LOC361776; LOC361776; TEKT2-binding protein 1; UPF0628 protein C10orf96 homolog
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
Rnor_6.01279,633,655 - 279,699,234 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1279,633,671 - 279,676,909 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01286,995,694 - 287,041,588 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41264,938,299 - 264,981,620 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11265,149,399 - 265,192,664 (+)NCBI
Celera1253,289,322 - 253,332,261 (+)NCBICelera
Cytogenetic Map1q55NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Cellular Component
cytoplasm  (ISO,ISS)
sperm midpiece  (IDA)

Molecular Function

References


Genomics

Comparative Map Data
Ccdc172
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01279,633,655 - 279,699,234 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1279,633,671 - 279,676,909 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01286,995,694 - 287,041,588 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41264,938,299 - 264,981,620 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11265,149,399 - 265,192,664 (+)NCBI
Celera1253,289,322 - 253,332,261 (+)NCBICelera
Cytogenetic Map1q55NCBI
CCDC172
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl10116,324,448 - 116,380,029 (+)EnsemblGRCh38hg38GRCh38
GRCh3810116,324,097 - 116,380,029 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3710118,083,940 - 118,139,541 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3610118,073,930 - 118,129,531 (+)NCBINCBI36hg18NCBI36
Celera10111,813,149 - 111,868,738 (+)NCBI
Cytogenetic Map10q25.3NCBI
HuRef10111,711,013 - 111,766,601 (+)NCBIHuRef
CHM1_110118,367,061 - 118,422,663 (+)NCBICHM1_1
Ccdc172
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391958,500,416 - 58,546,504 (+)NCBIGRCm39mm39
GRCm381958,511,985 - 58,553,104 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1958,511,993 - 58,553,085 (+)EnsemblGRCm38mm10GRCm38
MGSCv371958,586,492 - 58,627,575 (+)NCBIGRCm37mm9NCBIm37
MGSCv361958,565,272 - 58,614,636 (+)NCBImm8
Celera1960,708,402 - 60,749,413 (+)NCBICelera
Cytogenetic Map19D2NCBI
Ccdc172
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543121,109,547 - 21,183,019 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543121,099,475 - 21,193,932 (+)NCBIChiLan1.0ChiLan1.0
CCDC172
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.110116,345,818 - 116,401,441 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl10116,345,394 - 116,401,441 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v010112,870,502 - 112,968,853 (+)NCBIMhudiblu_PPA_v0panPan3
CCDC172
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2826,954,022 - 27,011,998 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12826,953,945 - 27,013,600 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ccdc172
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364866,305,419 - 6,376,514 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC172
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14126,549,293 - 126,637,812 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114126,549,112 - 126,637,606 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214137,796,839 - 137,848,235 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC172
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.19109,138,300 - 109,192,883 (+)NCBI
ChlSab1.1 Ensembl9109,139,390 - 109,192,198 (+)Ensembl
Ccdc172
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473730,200,723 - 30,274,559 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1236795785281795785Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1245529606282763074Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1236265430281265430Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1243272341282763074Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1244401175282365384Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1235850810280850810Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1244992467282365384Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1252955158280632620Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1258132568282763074Rat
1581544Rf52Renal function QTL 520.05total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1252948438281795785Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1241482188281795785Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1191825895279986079Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1255728828282763074Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1238824734279986079Rat
1598839Rf56Renal function QTL 56renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1266793821279986079Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1259295704282763074Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1258709726281795785Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1244401175282365384Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1217054291281795785Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1244087148282763074Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1196395041282763074Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1249206242281795785Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1236795785281795785Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1163796316282763074Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1230420627282645769Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1236265430281265430Rat
7387289Uae45Urinary albumin excretion QTL 452.860.0021urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1244148899282763074Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1242302911282763074Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:47
Count of miRNA genes:39
Interacting mature miRNAs:47
Transcripts:ENSRNOT00000036012
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

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 13
Low 8 8 16
Below cutoff 6 3 3 5 3 2 2 12 8 9 2 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001014169 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760539 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760541 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760542 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017589457 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017589458 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017589459 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017589460 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001835441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001835442 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001835443 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07007078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01001035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01001036 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01001037 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01001038 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC079324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CV104909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000036012   ⟹   ENSRNOP00000029328
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1279,633,671 - 279,676,909 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091669   ⟹   ENSRNOP00000071660
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1279,633,727 - 279,676,909 (+)Ensembl
RefSeq Acc Id: NM_001014169   ⟹   NP_001014191
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01279,633,671 - 279,676,910 (+)NCBI
Rnor_5.01286,995,694 - 287,041,588 (+)NCBI
RGSC_v3.41264,938,299 - 264,981,620 (+)RGD
Celera1253,289,322 - 253,332,261 (+)RGD
Sequence:
RefSeq Acc Id: XM_008760539   ⟹   XP_008758761
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01279,633,655 - 279,683,620 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760541   ⟹   XP_008758763
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01279,633,655 - 279,676,910 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760542   ⟹   XP_008758764
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01279,633,655 - 279,679,524 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589457   ⟹   XP_017444946
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01279,633,655 - 279,699,234 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589458   ⟹   XP_017444947
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01279,633,655 - 279,699,047 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589459   ⟹   XP_017444948
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01279,633,655 - 279,697,309 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589460   ⟹   XP_017444949
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01279,633,655 - 279,699,047 (+)NCBI
Sequence:
RefSeq Acc Id: XR_001835441
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01279,633,655 - 279,699,047 (+)NCBI
Sequence:
RefSeq Acc Id: XR_001835442
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01279,633,655 - 279,699,047 (+)NCBI
Sequence:
RefSeq Acc Id: XR_001835443
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01279,633,655 - 279,699,047 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001014191   ⟸   NM_001014169
- UniProtKB: Q6AXT4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008758761   ⟸   XM_008760539
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008758764   ⟸   XM_008760542
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008758763   ⟸   XM_008760541
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017444946   ⟸   XM_017589457
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017444947   ⟸   XM_017589458
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017444949   ⟸   XM_017589460
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017444948   ⟸   XM_017589459
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000029328   ⟸   ENSRNOT00000036012
RefSeq Acc Id: ENSRNOP00000071660   ⟸   ENSRNOT00000091669

Transcriptome

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

Promoters
RGD ID:13691008
Promoter ID:EPDNEW_R1533
Type:multiple initiation site
Name:Ccdc172_1
Description:coiled-coil domain containing 172
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_6.01279,633,655 - 279,633,715EPDNEW

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)
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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)
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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
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 287010770 287010771 A G snv ACI/EurMcwi (MCW), Crl:SD (UDEL), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), SR/JrHsd (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), BUF/N (KNAW), DA/BklArbNsi (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), MNS/Gib (KNAW), SR/JrHsd (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 279633770 279633771 T C snv F344/NRrrc (MCW), LL/MavRrrc (RGD), WKY/Gcrc (RGD), ACI/N (MCW), WKY/NCrl (RGD), SS/JrHsdMcwi (RGD), SS/Jr (RGD), SR/JrHsd (RGD), WKY/NHsd (RGD), SHRSP/Gcrc (RGD), SBH/Ygl (RGD), CDS, MNS/Gib (RGD), MHS/Gib (RGD), CDR, MR/N (MCW), SBH/Ygl (MCW), WN/N (MCW), FHL/EurMcwi (RGD), ACI/EurMcwi (RGD), FHH/EurMcwi (MCW), BBDP/Wor (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), LE/Stm (RGD), FHL/EurMcwi (MCW), LEW/Crl (RGD), ACI/EurMcwi (MCW), LEW/NCrlBR (RGD), SR/JrHsd (MCW), LH/MavRrrc (RGD), SS/JrHsdMcwi (MCW), LN/MavRrrc (RGD), COP/CrCrl (MCW & UW)
1 279649099 279649100 A G snv WKY/NHsd (RGD), WKY/Gcrc (RGD), WKY/NCrl (RGD), SR/JrHsd (RGD), MNS/Gib (RGD), LL/MavRrrc (RGD), LN/MavRrrc (RGD), LH/MavRrrc (RGD), LEW/NCrlBR (RGD), LEW/Crl (RGD), ACI/EurMcwi (RGD), WKY/N (MCW), Buf/N (MCW), ACI/N (MCW), SR/JrHsd (MCW), ACI/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 264953697 264953698 A G snv ACI/N (KNAW), DA/BklArbNsi (ICAHN), WKY/N (KNAW), ACI/EurMcwi (MCW), SR/JrHsd (MCW), ACI/EurMcwi (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), MNS/Gib (ICL), SR/JrHsd (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), BUF/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359412 AgrOrtholog
Ensembl Genes ENSRNOG00000017656 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000029328 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000071660 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000036012 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000091669 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7135457 IMAGE-MGC_LOAD
InterPro CCDC172 UniProtKB/Swiss-Prot
KEGG Report rno:361776 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94503 IMAGE-MGC_LOAD
NCBI Gene 361776 ENTREZGENE
PANTHER PTHR22419 UniProtKB/Swiss-Prot
PhenoGen Ccdc172 PhenoGen
UniProt CC172_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-09-17 Ccdc172  coiled-coil domain containing 172  LOC361776  LOC361776  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 LOC361776  LOC361776      Symbol and Name status set to provisional 70820 PROVISIONAL