Rnf180 (ring finger protein 180) - Rat Genome Database

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Gene: Rnf180 (ring finger protein 180) Rattus norvegicus
Analyze
Symbol: Rnf180
Name: ring finger protein 180
RGD ID: 1595064
Description: Predicted to enable ubiquitin conjugating enzyme binding activity and ubiquitin protein ligase activity. Predicted to act upstream of or within several processes, including norepinephrine metabolic process; positive regulation of protein metabolic process; and serotonin metabolic process. Predicted to be located in endoplasmic reticulum membrane. Orthologous to human RNF180 (ring finger protein 180); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: E3 ubiquitin-protein ligase RNF180; hypothetical protein LOC685384; LOC685384; MGC188174
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
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2236,330,285 - 36,511,168 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl236,330,292 - 36,512,614 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx243,445,446 - 43,632,757 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0241,504,097 - 41,691,415 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0236,359,389 - 36,546,713 (-)NCBIRnor_WKY
Rnor_6.0235,718,100 - 35,892,578 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl235,718,889 - 35,870,578 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0254,840,702 - 55,009,539 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4236,186,010 - 36,253,660 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera232,280,890 - 32,455,843 (-)NCBICelera
Cytogenetic Map2q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15632090   PMID:18363970   PMID:23926250  


Genomics

Comparative Map Data
Rnf180
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2236,330,285 - 36,511,168 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl236,330,292 - 36,512,614 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx243,445,446 - 43,632,757 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0241,504,097 - 41,691,415 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0236,359,389 - 36,546,713 (-)NCBIRnor_WKY
Rnor_6.0235,718,100 - 35,892,578 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl235,718,889 - 35,870,578 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0254,840,702 - 55,009,539 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4236,186,010 - 36,253,660 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera232,280,890 - 32,455,843 (-)NCBICelera
Cytogenetic Map2q13NCBI
RNF180
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38564,165,351 - 64,372,869 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl564,165,843 - 64,372,869 (+)EnsemblGRCh38hg38GRCh38
GRCh37563,461,670 - 63,668,696 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36563,497,427 - 63,549,369 (+)NCBINCBI36Build 36hg18NCBI36
Build 34563,497,426 - 63,549,369NCBI
Celera560,458,571 - 60,665,603 (+)NCBICelera
Cytogenetic Map5q12.3NCBI
HuRef560,416,366 - 60,622,951 (+)NCBIHuRef
CHM1_1563,461,335 - 63,668,352 (+)NCBICHM1_1
T2T-CHM13v2.0564,985,947 - 65,192,972 (+)NCBIT2T-CHM13v2.0
Rnf180
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3913105,267,075 - 105,431,406 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl13105,266,509 - 105,431,323 (-)EnsemblGRCm39 Ensembl
GRCm3813105,130,567 - 105,294,818 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl13105,130,001 - 105,294,815 (-)EnsemblGRCm38mm10GRCm38
MGSCv3713105,937,574 - 106,083,094 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3613106,250,383 - 106,415,159 (-)NCBIMGSCv36mm8
Celera13109,539,891 - 109,686,561 (-)NCBICelera
Cytogenetic Map13D1NCBI
Rnf180
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554464,543,974 - 4,733,569 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554464,544,128 - 4,733,295 (-)NCBIChiLan1.0ChiLan1.0
RNF180
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1551,279,999 - 51,489,588 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl551,280,064 - 51,454,750 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0549,624,452 - 49,841,741 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
RNF180
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1250,166,987 - 50,353,694 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl250,197,137 - 50,352,946 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha247,123,982 - 47,310,531 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0250,652,171 - 50,838,819 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl250,583,194 - 50,838,812 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1247,713,305 - 47,899,710 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0248,504,093 - 48,695,296 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0249,398,273 - 49,582,944 (+)NCBIUU_Cfam_GSD_1.0
Rnf180
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213195,722,482 - 195,898,525 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364804,659,751 - 4,834,972 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049364804,809,103 - 4,834,977 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RNF180
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1642,723,065 - 42,953,592 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11642,686,225 - 42,951,928 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21645,753,323 - 46,078,166 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RNF180
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1460,340,926 - 60,555,932 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl460,340,804 - 60,557,227 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660498,946,267 - 9,171,918 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rnf180
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248155,432,991 - 5,622,914 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248155,433,057 - 5,621,833 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rnf180
1085 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:270
Count of miRNA genes:173
Interacting mature miRNAs:197
Transcripts:ENSRNOT00000066069
Prediction methods:Microtar, Miranda, Rnahybrid
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
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22699957143154682Rat
1643006Pain1Pain QTL 13.630.005mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)22699957148268661Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22715716072157160Rat
1300160Hrtrt3Heart rate QTL 33.62heart pumping trait (VT:2000009)absolute change in heart rate (CMO:0000534)22997159351729300Rat
10755434Coatc7Coat color QTL 70.04794coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23064806575648065Rat
731179Mamtr3Mammary tumor resistance QTL 30.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)23237377043665178Rat
10755436Coatc8Coat color QTL 80.02431coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23502311780023117Rat
61371Edpm1Estrogen-dependent pituitary mass QTL 140.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)23513484188029593Rat

Markers in Region
BE097076  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2236,330,296 - 36,330,503 (+)MAPPERmRatBN7.2
Rnor_6.0235,718,111 - 35,718,317NCBIRnor6.0
Rnor_5.0254,840,707 - 54,840,913UniSTSRnor5.0
RGSC_v3.4236,186,015 - 36,186,221UniSTSRGSC3.4
Celera232,280,895 - 32,281,101UniSTS
RH 3.4 Map2161.2UniSTS
Cytogenetic Map2q13UniSTS


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 1 56
Low 2 34 15 6 8 6 18 34 40 11
Below cutoff 9 31 25 10 25 7 9 1 1 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066069   ⟹   ENSRNOP00000059648
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl236,330,292 - 36,490,102 (-)Ensembl
Rnor_6.0 Ensembl235,718,889 - 35,870,578 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112277   ⟹   ENSRNOP00000083351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl236,330,292 - 36,512,614 (-)Ensembl
RefSeq Acc Id: NM_001134986   ⟹   NP_001128458
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2236,330,291 - 36,510,976 (-)NCBI
Rnor_6.0235,718,106 - 35,891,065 (-)NCBI
Rnor_5.0254,840,702 - 55,009,539 (-)NCBI
RGSC_v3.4236,186,010 - 36,253,660 (-)RGD
Celera232,280,890 - 32,455,843 (-)RGD
Sequence:
RefSeq Acc Id: XM_039103134   ⟹   XP_038959062
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2236,330,285 - 36,511,167 (-)NCBI
RefSeq Acc Id: XM_039103135   ⟹   XP_038959063
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2236,330,285 - 36,511,167 (-)NCBI
RefSeq Acc Id: XM_039103136   ⟹   XP_038959064
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2236,330,285 - 36,511,168 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001128458   ⟸   NM_001134986
- UniProtKB: B5DEG2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000059648   ⟸   ENSRNOT00000066069
RefSeq Acc Id: XP_038959064   ⟸   XM_039103136
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038959063   ⟸   XM_039103135
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038959062   ⟸   XM_039103134
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000083351   ⟸   ENSRNOT00000112277
Protein Domains
RING-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LRQ3-F1-model_v2 AlphaFold F1LRQ3 1-593 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:1595064 AgrOrtholog
BioCyc Gene G2FUF-54540 BioCyc
Ensembl Genes ENSRNOG00000043329 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059648 ENTREZGENE
  ENSRNOP00000059648.4 UniProtKB/TrEMBL
  ENSRNOP00000083351 ENTREZGENE
  ENSRNOP00000083351.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066069 ENTREZGENE
  ENSRNOT00000066069.4 UniProtKB/TrEMBL
  ENSRNOT00000112277 ENTREZGENE
  ENSRNOT00000112277.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
InterPro RNF180 UniProtKB/TrEMBL
  RNF180_C UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
  Znf_RING_CS UniProtKB/TrEMBL
KEGG Report rno:685384 UniProtKB/TrEMBL
NCBI Gene 685384 ENTREZGENE
PANTHER PTHR46717 UniProtKB/TrEMBL
Pfam RNF180_C UniProtKB/TrEMBL
PhenoGen Rnf180 PhenoGen
PROSITE ZF_RING_1 UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/TrEMBL
SMART RING UniProtKB/TrEMBL
UniProt A0A8I5ZZU5_RAT UniProtKB/TrEMBL
  B5DEG2 ENTREZGENE, UniProtKB/TrEMBL
  F1LRQ3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Rnf180  ring finger protein 180  LOC685384  hypothetical protein LOC685384  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC685384  hypothetical protein LOC685384      Symbol and Name status set to provisional 70820 PROVISIONAL