Ccdc121rt1 (coiled-coil domain containing 121, retrogene 1) - Rat Genome Database

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Gene: Ccdc121rt1 (coiled-coil domain containing 121, retrogene 1) Rattus norvegicus
Analyze
Symbol: Ccdc121rt1 (Ensembl: Ccdc121rt)
Name: coiled-coil domain containing 121, retrogene 1 (Ensembl:coiled-coil domain containing 121, retrotransposed)
RGD ID: 1566190
Description: Orthologous to human CCDC121 (coiled-coil domain containing 121).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Ccdc121; Ccdc121rt; coiled-coil domain containing 121; coiled-coil domain containing 121, retrotransposed; coiled-coil domain-containing protein 121-like; LOC289329; RGD1566190; similar to RIKEN cDNA 4930548H24
RGD Orthologs
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81395,785,468 - 95,787,135 (-)NCBIGRCr8
mRatBN7.21393,253,752 - 93,255,419 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1393,254,387 - 93,255,358 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01399,819,380 - 99,821,055 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1399,820,015 - 99,820,986 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013104,807,454 - 104,809,082 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41397,547,067 - 97,548,038 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1392,794,691 - 92,796,366 (-)NCBICelera
Cytogenetic Map13q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Ccdc121rt1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81395,785,468 - 95,787,135 (-)NCBIGRCr8
mRatBN7.21393,253,752 - 93,255,419 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1393,254,387 - 93,255,358 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01399,819,380 - 99,821,055 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1399,820,015 - 99,820,986 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013104,807,454 - 104,809,082 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41397,547,067 - 97,548,038 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1392,794,691 - 92,796,366 (-)NCBICelera
Cytogenetic Map13q26NCBI
Ccdc121rt1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391181,337,198 - 181,339,016 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1181,337,198 - 181,339,016 (-)EnsemblGRCm39 Ensembl
GRCm381181,509,633 - 181,511,451 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1181,509,633 - 181,511,451 (-)EnsemblGRCm38mm10GRCm38
MGSCv371183,439,764 - 183,441,582 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361183,346,306 - 183,348,126 (-)NCBIMGSCv36mm8
Celera1188,558,623 - 188,560,441 (-)NCBICelera
Cytogenetic Map1H4NCBI
cM Map184.69NCBI

Variants

.
Variants in Ccdc121rt1
13 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:63
Count of miRNA genes:61
Interacting mature miRNAs:62
Transcripts:ENSRNOT00000036629
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
8655959Pur32Proteinuria QTL 328.4urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137402391897213863Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat


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

endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 15 1 11 11
Below cutoff 7 1 2 1 3 3 28 9 13 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000036629   ⟹   ENSRNOP00000036570
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1393,254,387 - 93,255,358 (-)Ensembl
Rnor_6.0 Ensembl1399,820,015 - 99,820,986 (-)Ensembl
RefSeq Acc Id: NM_001408779   ⟹   NP_001395708
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81395,785,468 - 95,787,135 (-)NCBI
mRatBN7.21393,253,752 - 93,255,419 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001395708 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000036570
  ENSRNOP00000036570.5
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000036570   ⟸   ENSRNOT00000036629
RefSeq Acc Id: NP_001395708   ⟸   NM_001408779
- UniProtKB: F1LTT6 (UniProtKB/TrEMBL)
Protein Domains
DUF4515

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LTT6-F1-model_v2 AlphaFold F1LTT6 1-323 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566190 AgrOrtholog
BioCyc Gene G2FUF-17093 BioCyc
Ensembl Genes ENSRNOG00000022717 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000036629 ENTREZGENE
  ENSRNOT00000036629.6 UniProtKB/TrEMBL
InterPro DUF4515 UniProtKB/TrEMBL
KEGG Report rno:289329 UniProtKB/TrEMBL
NCBI Gene 289329 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING 121 UniProtKB/TrEMBL
  COILED-COIL DOMAIN-CONTAINING 166 UniProtKB/TrEMBL
Pfam DUF4515 UniProtKB/TrEMBL
PhenoGen Ccdc121rt1 PhenoGen
RatGTEx ENSRNOG00000022717 RatGTEx
UniProt F1LTT6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-08-21 Ccdc121rt1  coiled-coil domain containing 121, retrogene 1  Ccdc121  coiled-coil domain containing 121  Name and Symbol changed 629549 APPROVED
2023-05-25 Ccdc121  coiled-coil domain containing 121  Ccdc121rt  coiled-coil domain containing 121, retrotransposed  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2022-03-07 Ccdc121rt  coiled-coil domain containing 121, retrotransposed  Ccdc121  coiled-coil domain containing 121  Name and Symbol changed 629549 APPROVED
2008-03-07 Ccdc121  coiled-coil domain containing 121  RGD1566190_predicted  similar to RIKEN cDNA 4930548H24 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1566190_predicted  similar to RIKEN cDNA 4930548H24 (predicted)  LOC289329  similar to RIKEN cDNA 4930548H24  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC289329  similar to RIKEN cDNA 4930548H24      Symbol and Name status set to provisional 70820 PROVISIONAL