Rc3h1 (ring finger and CCCH-type domains 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Rc3h1 (ring finger and CCCH-type domains 1) Rattus norvegicus
Analyze
Symbol: Rc3h1
Name: ring finger and CCCH-type domains 1
RGD ID: 1563512
Description: Predicted to enable several functions, including CCR4-NOT complex binding activity; RNA binding activity; and zinc ion binding activity. Predicted to be involved in several processes, including P-body assembly; negative regulation of lymphocyte activation; and regulation of mRNA stability. Predicted to act upstream of or within several processes, including T cell activation; hematopoietic or lymphoid organ development; and lymphocyte homeostasis. Predicted to be located in P-body and cytoplasmic stress granule. Orthologous to human RC3H1 (ring finger and CCCH-type domains 1); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC304916; RGD1563512; RING CCCH (C3H) domains 1; ring finger and CCCH-type zinc finger domains 1; roquin-1; similar to mKIAA2025 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21373,174,075 - 73,245,762 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1373,173,946 - 73,238,839 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01378,723,028 - 78,794,663 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1378,722,763 - 78,789,266 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01383,619,665 - 83,689,320 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41376,493,343 - 76,530,107 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1372,962,695 - 73,034,187 (+)NCBICelera
Cytogenetic Map13q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15917799   PMID:18172933   PMID:19217324   PMID:20639877   PMID:22658674   PMID:22681889   PMID:23583643   PMID:25026077   PMID:25026078   PMID:25282160   PMID:25504471   PMID:25697406  
PMID:26000482   PMID:26255671   PMID:26489670  


Genomics

Comparative Map Data
Rc3h1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21373,174,075 - 73,245,762 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1373,173,946 - 73,238,839 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01378,723,028 - 78,794,663 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1378,722,763 - 78,789,266 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01383,619,665 - 83,689,320 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41376,493,343 - 76,530,107 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1372,962,695 - 73,034,187 (+)NCBICelera
Cytogenetic Map13q22NCBI
RC3H1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381173,931,084 - 174,022,357 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1173,931,084 - 174,022,357 (-)EnsemblGRCh38hg38GRCh38
GRCh371173,900,222 - 173,991,495 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361172,166,975 - 172,228,833 (-)NCBINCBI36Build 36hg18NCBI36
Celera1147,009,820 - 147,071,680 (-)NCBICelera
Cytogenetic Map1q25.1NCBI
HuRef1145,125,474 - 145,187,339 (-)NCBIHuRef
CHM1_11175,322,816 - 175,384,658 (-)NCBICHM1_1
T2T-CHM13v2.01173,289,302 - 173,380,290 (-)NCBIT2T-CHM13v2.0
Rc3h1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391160,733,981 - 160,802,546 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1160,733,988 - 160,802,548 (+)EnsemblGRCm39 Ensembl
GRCm381160,906,411 - 160,974,976 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1160,906,418 - 160,974,978 (+)EnsemblGRCm38mm10GRCm38
MGSCv371162,836,542 - 162,905,107 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361162,743,147 - 162,804,531 (+)NCBIMGSCv36mm8
Celera1163,345,875 - 163,414,502 (+)NCBICelera
Cytogenetic Map1H2.1NCBI
Rc3h1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540614,053,122 - 14,123,029 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540614,053,122 - 14,123,023 (-)NCBIChiLan1.0ChiLan1.0
RC3H1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11153,153,048 - 153,213,402 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1153,160,661 - 153,213,402 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01149,454,748 - 149,539,566 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
RC3H1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1725,265,836 - 25,312,417 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl725,233,235 - 25,305,174 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha724,766,202 - 24,845,548 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0724,983,310 - 25,063,044 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl724,983,031 - 25,055,836 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1724,903,636 - 24,982,946 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0724,985,200 - 25,064,573 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0725,130,410 - 25,209,772 (+)NCBIUU_Cfam_GSD_1.0
Rc3h1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934496,072,540 - 96,127,125 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648113,919,257 - 13,966,677 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493648113,919,006 - 13,973,868 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RC3H1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9116,208,799 - 116,292,381 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19116,204,807 - 116,292,455 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29127,839,470 - 127,927,237 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103230557
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12555,167,418 - 55,258,964 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2555,167,077 - 55,279,088 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236664807,917 - 55,965 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rc3h1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247717,837,547 - 7,948,217 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rc3h1
274 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:53
Count of miRNA genes:49
Interacting mature miRNAs:53
Transcripts:ENSRNOT00000003689
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 (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
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
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
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133228447177284471Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133453521879535218Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133726209282262092Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
4889861Pur29Proteinuria QTL 2913.80.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133741558480753406Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133741558482415584Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
12879444Bp397Blood pressure QTL 397arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134504940490049404Rat
12879471Bp398Blood pressure QTL 398arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134551471990514719Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134619797684753113Rat
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
2303028Bp329Blood pressure QTL 329arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135849787273485113Rat
724564Uae11Urinary albumin excretion QTL 115.7urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)135949252277046890Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)135987440885581182Rat
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
8655951Rf63Renal function QTL 6312.2blood urea nitrogen amount (VT:0005265)plasma urea nitrogen level (CMO:0000586)136906051977046890Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)136906051986800898Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)136906051986800898Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)136906051986800898Rat

Markers in Region
AA997206  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21373,238,692 - 73,238,842 (+)MAPPERmRatBN7.2
Rnor_6.01378,787,594 - 78,787,743NCBIRnor6.0
Rnor_5.01383,682,250 - 83,682,399UniSTSRnor5.0
RGSC_v3.41376,529,943 - 76,530,092UniSTSRGSC3.4
Celera1373,027,118 - 73,027,267UniSTS
RH 3.4 Map13440.5UniSTS
Cytogenetic Map13q22UniSTS


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 30 34 18 19 18 7 7 73 28 41 10 7
Low 3 13 23 23 23 1 4 1 7 1 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003689
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1373,173,946 - 73,238,839 (+)Ensembl
Rnor_6.0 Ensembl1378,722,763 - 78,789,266 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000075838
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1378,771,575 - 78,772,443 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076120
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1378,759,772 - 78,760,596 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076355
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1378,778,960 - 78,787,755 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076401
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1378,722,849 - 78,772,444 (+)Ensembl
RefSeq Acc Id: XM_008769698   ⟹   XP_008767920
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21373,174,075 - 73,245,762 (+)NCBI
Rnor_6.01378,723,028 - 78,794,663 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_008767920 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_008767920   ⟸   XM_008769698
- UniProtKB: A0A8I5ZR20 (UniProtKB/TrEMBL)
- Sequence:
Protein Domains
C3H1-type   RING-type

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:1563512 AgrOrtholog
BioCyc Gene G2FUF-17755 BioCyc
Ensembl Genes ENSRNOG00000002750 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000079488 ENTREZGENE
  ENSRNOP00000079488.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003689 ENTREZGENE
  ENSRNOT00000003689.9 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
InterPro RC3H1 UniProtKB/TrEMBL
  ROQ_II UniProtKB/TrEMBL
  Znf-RING_LisH UniProtKB/TrEMBL
  Znf_CCCH UniProtKB/TrEMBL
  Znf_CCCH_sf UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
  Znf_RING_CS UniProtKB/TrEMBL
NCBI Gene 680586 ENTREZGENE
PANTHER PTHR13139:SF6 UniProtKB/TrEMBL
Pfam ROQ_II UniProtKB/TrEMBL
  zf-RING_UBOX UniProtKB/TrEMBL
PhenoGen Rc3h1 PhenoGen
PROSITE ZF_C3H1 UniProtKB/TrEMBL
  ZF_RING_1 UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/TrEMBL
SMART RING UniProtKB/TrEMBL
  ZnF_C3H1 UniProtKB/TrEMBL
Superfamily-SCOP SSF90229 UniProtKB/TrEMBL
UniProt A0A8I5ZR20 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-10-28 Rc3h1  ring finger and CCCH-type domains 1  LOC680586  hypothetical protein LOC680586  Data Merged 737654 APPROVED
2011-08-02 Rc3h1  ring finger and CCCH-type domains 1  Rc3h1  ring finger and CCCH-type zinc finger domains 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 Rc3h1  ring finger and CCCH-type zinc finger domains 1  Rc3h1  RING CCCH (C3H) domains 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Rc3h1  RING CCCH (C3H) domains 1  RGD1563512_predicted  similar to mKIAA2025 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC680586  hypothetical protein LOC680586      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-07 RGD1563512_predicted  similar to mKIAA2025 protein (predicted)  LOC304916  similar to mKIAA2025 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC304916  similar to mKIAA2025 protein      Symbol and Name status set to provisional 70820 PROVISIONAL