Ccdc9b (coiled-coil domain containing 9B) - Rat Genome Database

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Gene: Ccdc9b (coiled-coil domain containing 9B) Rattus norvegicus
Analyze
Symbol: Ccdc9b
Name: coiled-coil domain containing 9B
RGD ID: 1565536
Description: Orthologous to human CCDC9B (coiled-coil domain containing 9B); INTERACTS WITH aconitine; aflatoxin B1; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: coiled-coil domain-containing protein 9B; LOC311323; RGD1565536; similar to hypothetical protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83126,190,039 - 126,198,931 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3126,192,232 - 126,199,580 (-)EnsemblGRCr8
mRatBN7.23105,736,120 - 105,745,039 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3105,739,174 - 105,744,697 (-)EnsemblmRatBN7.2
Rnor_6.03110,548,238 - 110,557,096 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3110,551,233 - 110,556,813 (-)Ensemblrn6Rnor6.0
Rnor_5.03117,088,852 - 117,097,427 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43105,260,699 - 105,266,052 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3104,650,266 - 104,659,124 (-)NCBICelera
Cytogenetic Map3q35NCBI
JBrowse:




References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:22658674  


Genomics

Comparative Map Data
Ccdc9b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83126,190,039 - 126,198,931 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3126,192,232 - 126,199,580 (-)EnsemblGRCr8
mRatBN7.23105,736,120 - 105,745,039 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3105,739,174 - 105,744,697 (-)EnsemblmRatBN7.2
Rnor_6.03110,548,238 - 110,557,096 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3110,551,233 - 110,556,813 (-)Ensemblrn6Rnor6.0
Rnor_5.03117,088,852 - 117,097,427 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43105,260,699 - 105,266,052 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3104,650,266 - 104,659,124 (-)NCBICelera
Cytogenetic Map3q35NCBI
CCDC9B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381540,331,452 - 40,340,939 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1540,331,452 - 40,340,939 (-)Ensemblhg38GRCh38
GRCh371540,623,653 - 40,633,140 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361538,410,945 - 38,420,460 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1517,389,636 - 17,399,151 (-)NCBICelera
Cytogenetic Map15q15.1NCBI
HuRef1517,467,024 - 17,476,543 (-)NCBIHuRef
CHM1_11540,743,516 - 40,753,031 (-)NCBICHM1_1
T2T-CHM13v2.01538,138,324 - 38,147,811 (-)NCBIT2T-CHM13v2.0
Ccdc9b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392118,584,626 - 118,593,421 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2118,584,639 - 118,593,142 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm382118,754,145 - 118,762,947 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2118,754,158 - 118,762,661 (-)Ensemblmm10GRCm38
MGSCv372118,579,881 - 118,588,397 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv362118,445,599 - 118,453,107 (-)NCBIMGSCv36mm8
Celera2119,908,822 - 119,917,331 (-)NCBICelera
Cytogenetic Map2E5NCBI
cM Map259.45NCBI
Ccdc9b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554167,257,232 - 7,267,171 (-)Ensembl
ChiLan1.0NW_0049554167,258,446 - 7,268,342 (-)NCBIChiLan1.0ChiLan1.0
CCDC9B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21629,565,417 - 29,574,915 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11533,716,865 - 33,726,375 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01519,265,502 - 19,275,023 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11537,520,475 - 37,529,968 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1537,520,475 - 37,529,968 (-)EnsemblpanPan2panpan1.1
CCDC9B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1307,514,029 - 7,523,076 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl307,516,710 - 7,523,357 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha307,567,936 - 7,576,983 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0307,639,833 - 7,648,881 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl307,639,833 - 7,648,874 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1307,564,367 - 7,573,415 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0307,670,318 - 7,679,353 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0307,799,099 - 7,808,147 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ccdc9b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864085,947,901 - 85,956,972 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364713,795,343 - 3,805,010 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364713,795,964 - 3,805,023 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC9B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1130,974,664 - 130,983,971 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11130,974,635 - 130,983,973 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21146,059,846 - 146,069,050 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC9B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12642,647,463 - 42,683,869 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2642,674,301 - 42,680,175 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604898,280,644 - 98,290,293 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc9b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248047,636,587 - 7,642,103 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248047,633,390 - 7,642,451 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ccdc9b
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1596,908,238 - 96,920,114 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ccdc9b
52 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:46
Count of miRNA genes:44
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000045362
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)396509147141509147Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)373592512136118980Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)367641776167835660Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)358601291153936591Rat
1582216Bw65Body weight QTL 656.3body mass (VT:0001259)body weight (CMO:0000012)3122654702136118980Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)349872657138829559Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1582219Bw63Body weight QTL 633.80.001body mass (VT:0001259)body weight (CMO:0000012)3116582412136118980Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)385062224136118980Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)385062224136118980Rat
7387306Bw124Body weight QTL 1243.20.0003body mass (VT:0001259)body weight (CMO:0000012)3104545086149545086Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)381425008141509147Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)370845569136091483Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)393829559138829559Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)3112250810157250810Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3101255536134750886Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)379649560177741895Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)396509147141509147Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3117537367162537367Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3125116475170116475Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3110225882155225882Rat
631200Cm25Cardiac mass QTL 254.80.0001heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)381541464126563126Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)390755164141509147Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3122395989167395989Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)398651826167012663Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)3125814931139636791Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3110634702155634702Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3116188400161188400Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 83 59 6 347 183 11 140 81 92 31 16 16

Sequence


Ensembl Acc Id: ENSRNOT00000045362   ⟹   ENSRNOP00000046560
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3126,193,233 - 126,198,571 (-)Ensembl
mRatBN7.2 Ensembl3105,739,316 - 105,744,697 (-)Ensembl
Rnor_6.0 Ensembl3110,551,432 - 110,556,813 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000092158   ⟹   ENSRNOP00000070443
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3126,192,232 - 126,199,580 (-)Ensembl
mRatBN7.2 Ensembl3105,739,174 - 105,744,697 (-)Ensembl
Rnor_6.0 Ensembl3110,551,233 - 110,556,808 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000094242   ⟹   ENSRNOP00000079722
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3105,739,316 - 105,744,626 (-)Ensembl
RefSeq Acc Id: XM_056985387   ⟹   XP_056841367
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83126,190,039 - 126,198,928 (-)NCBI
mRatBN7.23105,736,120 - 105,745,039 (-)NCBI
RefSeq Acc Id: XM_056985388   ⟹   XP_056841368
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83126,190,039 - 126,197,711 (-)NCBI
mRatBN7.23105,736,120 - 105,743,800 (-)NCBI
RefSeq Acc Id: XM_056985389   ⟹   XP_056841369
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83126,190,039 - 126,198,931 (-)NCBI
mRatBN7.23105,736,120 - 105,745,039 (-)NCBI
RefSeq Acc Id: XM_063285305   ⟹   XP_063141375
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83126,190,039 - 126,198,931 (-)NCBI
RefSeq Acc Id: XM_063285306   ⟹   XP_063141376
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83126,190,039 - 126,197,334 (-)NCBI
RefSeq Acc Id: XR_010065344
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83126,193,679 - 126,198,928 (-)NCBI
RefSeq Acc Id: XR_010065345
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83126,194,618 - 126,198,928 (-)NCBI
Ensembl Acc Id: ENSRNOP00000070443   ⟸   ENSRNOT00000092158
Ensembl Acc Id: ENSRNOP00000046560   ⟸   ENSRNOT00000045362
Ensembl Acc Id: ENSRNOP00000079722   ⟸   ENSRNOT00000094242
RefSeq Acc Id: XP_056841369   ⟸   XM_056985389
- Peptide Label: isoform X5
RefSeq Acc Id: XP_056841367   ⟸   XM_056985387
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZNP2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_056841368   ⟸   XM_056985388
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZNP2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063141375   ⟸   XM_063285305
- Peptide Label: isoform X3
- UniProtKB: A0A8I5ZNP2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063141376   ⟸   XM_063285306
- Peptide Label: isoform X4

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZKN0-F1-model_v2 AlphaFold D3ZKN0 1-538 view protein structure

Transcriptome

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

Promoters
RGD ID:13692318
Promoter ID:EPDNEW_R2836
Type:initiation region
Name:Ccdc9b_1
Description:coiled-coil domain containing 9B
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_6.03110,556,794 - 110,556,854EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565536 AgrOrtholog
BioCyc Gene G2FUF-48231 BioCyc
Ensembl Genes ENSRNOG00000028910 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000045362.6 UniProtKB/TrEMBL
  ENSRNOT00000092158 ENTREZGENE
  ENSRNOT00000092158.3 UniProtKB/TrEMBL
InterPro DUF4594 UniProtKB/TrEMBL
NCBI Gene 311323 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 9B UniProtKB/TrEMBL
  PTHR15635 UniProtKB/TrEMBL
Pfam DUF4594 UniProtKB/TrEMBL
PhenoGen Ccdc9b PhenoGen
RatGTEx ENSRNOG00000028910 RatGTEx
UniProt A0A0G2JXY0_RAT UniProtKB/TrEMBL
  A0A8I5ZNP2 ENTREZGENE
  D3ZKN0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-10-23 Ccdc9b  coiled-coil domain containing 9B  RGD1565536  similar to hypothetical protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1565536  similar to hypothetical protein   RGD1565536_predicted  similar to hypothetical protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1565536_predicted  similar to hypothetical protein (predicted)  LOC311323  similar to hypothetical protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC311323  similar to hypothetical protein      Symbol and Name status set to provisional 70820 PROVISIONAL