Rchy1 (ring finger and CHY zinc finger domain containing 1) - Rat Genome Database

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Gene: Rchy1 (ring finger and CHY zinc finger domain containing 1) Rattus norvegicus
Analyze
Symbol: Rchy1
Name: ring finger and CHY zinc finger domain containing 1
RGD ID: 1359180
Description: Enables signaling receptor binding activity. Predicted to be involved in positive regulation of protein metabolic process; protein autoubiquitination; and ubiquitin-dependent protein catabolic process. Predicted to be located in cytosol and nucleoplasm. Predicted to be part of ubiquitin ligase complex. Predicted to be active in nucleus. Biomarker of sciatic neuropathy. Orthologous to human RCHY1 (ring finger and CHY zinc finger domain containing 1); PARTICIPATES IN p53 signaling pathway; measles pathway; ubiquitin/proteasome degradation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; Cuprizon.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MGC94651; Pirh2; ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase; RING finger and CHY zinc finger domain-containing protein 1
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
mRatBN7.21416,113,263 - 16,129,017 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1416,113,224 - 16,129,167 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1416,126,760 - 16,142,546 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01417,445,651 - 17,461,436 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01416,137,788 - 16,153,574 (+)NCBIRnor_WKY
Rnor_6.01417,615,968 - 17,631,715 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1417,615,968 - 17,631,714 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01417,533,357 - 17,548,694 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41417,683,377 - 17,698,982 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11417,683,376 - 17,698,981 (+)NCBI
Celera1415,505,664 - 15,521,436 (+)NCBICelera
Cytogenetic Map14p22NCBI
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

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Pirh2 interacts with and ubiquitylates signal recognition particle receptor beta subunit. Abe K, etal., Biomed Res. 2008 Feb;29(1):53-60.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Modes of p53 regulation. Kruse JP and Gu W, Cell. 2009 May 15;137(4):609-22. doi: 10.1016/j.cell.2009.04.050.
5. Pirh2, a p53-induced ubiquitin-protein ligase, promotes p53 degradation. Leng RP, etal., Cell 2003 Mar 21;112(6):779-91.
6. Dynamic changes of PIRH2 and p27kip1 expression in injured rat sciatic nerve. Li H, etal., Neurol Sci. 2012 Aug;33(4):749-57. doi: 10.1007/s10072-011-0809-8. Epub 2011 Sep 30.
7. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
8. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
9. GOA pipeline RGD automated data pipeline
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Comprehensive gene review and curation RGD comprehensive gene curation
12. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
13. Changes in Pirh2 and p27kip1 expression following traumatic brain injury in adult rats. Wu X, etal., J Mol Neurosci. 2012 Jan;46(1):184-91. doi: 10.1007/s12031-011-9572-9. Epub 2011 Jul 5.
Additional References at PubMed
PMID:15781263   PMID:19043414   PMID:19483087   PMID:25848801  


Genomics

Comparative Map Data
Rchy1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21416,113,263 - 16,129,017 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1416,113,224 - 16,129,167 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1416,126,760 - 16,142,546 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01417,445,651 - 17,461,436 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01416,137,788 - 16,153,574 (+)NCBIRnor_WKY
Rnor_6.01417,615,968 - 17,631,715 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1417,615,968 - 17,631,714 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01417,533,357 - 17,548,694 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41417,683,377 - 17,698,982 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11417,683,376 - 17,698,981 (+)NCBI
Celera1415,505,664 - 15,521,436 (+)NCBICelera
Cytogenetic Map14p22NCBI
RCHY1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38475,479,033 - 75,514,715 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl475,479,033 - 75,514,764 (-)EnsemblGRCh38hg38GRCh38
GRCh37476,404,243 - 76,439,925 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36476,623,371 - 76,658,652 (-)NCBINCBI36Build 36hg18NCBI36
Build 34476,761,535 - 76,796,807NCBI
Celera473,700,478 - 73,735,762 (-)NCBICelera
Cytogenetic Map4q21.1NCBI
HuRef472,150,764 - 72,186,444 (-)NCBIHuRef
CHM1_1476,381,206 - 76,416,667 (-)NCBICHM1_1
T2T-CHM13v2.0478,819,170 - 78,854,879 (-)NCBIT2T-CHM13v2.0
Rchy1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39592,096,701 - 92,111,004 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl592,096,763 - 92,110,927 (-)EnsemblGRCm39 Ensembl
GRCm38591,948,842 - 91,963,145 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl591,948,904 - 91,963,068 (-)EnsemblGRCm38mm10GRCm38
MGSCv37592,377,930 - 92,392,094 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36593,024,104 - 93,038,268 (-)NCBIMGSCv36mm8
Celera590,091,667 - 90,105,811 (-)NCBICelera
Cytogenetic Map5E2NCBI
Rchy1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554741,463,817 - 1,475,690 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554741,463,817 - 1,475,677 (-)NCBIChiLan1.0ChiLan1.0
RCHY1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1454,526,197 - 54,561,054 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl454,526,202 - 54,561,048 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0448,691,213 - 48,725,979 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
RCHY1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13267,136 - 94,053 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3267,509 - 93,987 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3241,788,013 - 41,814,963 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03289,116 - 116,022 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3289,053 - 115,956 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13286,184 - 113,092 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03239,247 - 66,189 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03240,106,164 - 40,133,080 (+)NCBIUU_Cfam_GSD_1.0
Rchy1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528511,927,449 - 12,003,857 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936598436,260 - 453,137 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936598436,559 - 453,137 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RCHY1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl871,162,840 - 71,181,919 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1871,155,388 - 71,182,020 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2875,355,281 - 75,368,606 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RCHY1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1723,989,028 - 24,025,151 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl723,989,745 - 24,025,437 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660372,311,593 - 2,352,613 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rchy1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624730322,448 - 342,454 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rchy1
100 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:187
Count of miRNA genes:134
Interacting mature miRNAs:142
Transcripts:ENSRNOT00000003470
Prediction methods:Microtar, Miranda
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
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14121760616960180Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14381307418274691Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14381307418274691Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat

Markers in Region
RH127475  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21416,128,680 - 16,128,830 (+)MAPPERmRatBN7.2
Rnor_6.01417,631,385 - 17,631,534NCBIRnor6.0
Rnor_5.01417,548,364 - 17,548,513UniSTSRnor5.0
RGSC_v3.41417,698,652 - 17,698,801UniSTSRGSC3.4
Celera1415,521,106 - 15,521,255UniSTS
Cytogenetic Map14p22UniSTS


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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003470   ⟹   ENSRNOP00000003470
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1416,113,224 - 16,129,005 (+)Ensembl
Rnor_6.0 Ensembl1417,615,968 - 17,631,714 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104798   ⟹   ENSRNOP00000084319
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1416,113,655 - 16,129,167 (+)Ensembl
RefSeq Acc Id: NM_001007618   ⟹   NP_001007619
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21416,113,263 - 16,129,011 (+)NCBI
Rnor_6.01417,615,968 - 17,631,715 (+)NCBI
Rnor_5.01417,533,357 - 17,548,694 (+)NCBI
RGSC_v3.41417,683,377 - 17,698,982 (+)RGD
Celera1415,505,664 - 15,521,436 (+)RGD
Sequence:
RefSeq Acc Id: XM_039091675   ⟹   XP_038947603
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21416,119,080 - 16,129,017 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001007619   ⟸   NM_001007618
- UniProtKB: Q5XIE4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003470   ⟸   ENSRNOT00000003470
RefSeq Acc Id: XP_038947603   ⟸   XM_039091675
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000084319   ⟸   ENSRNOT00000104798
Protein Domains
CHY-type   CTCHY-type   RING-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XIE4-F1-model_v2 AlphaFold Q5XIE4 1-261 view protein structure

Transcriptome

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

Promoters
RGD ID:13699218
Promoter ID:EPDNEW_R9743
Type:multiple initiation site
Name:Rchy1_1
Description:ring finger and CHY zinc finger domain containing 1
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_6.01417,615,931 - 17,615,991EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359180 AgrOrtholog
BioCyc Gene G2FUF-16238 BioCyc
Ensembl Genes ENSRNOG00000002546 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003470 ENTREZGENE
  ENSRNOP00000003470.3 UniProtKB/TrEMBL
  ENSRNOP00000084319.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003470 ENTREZGENE
  ENSRNOT00000003470.5 UniProtKB/TrEMBL
  ENSRNOT00000104798.1 UniProtKB/TrEMBL
Gene3D-CATH 2.20.28.10 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7191744 IMAGE-MGC_LOAD
InterPro RCHY1_zinc-ribbon UniProtKB/TrEMBL
  Znf_CHY UniProtKB/TrEMBL
  Znf_CHY_sf UniProtKB/TrEMBL
  Znf_CTCHY UniProtKB/TrEMBL
  Znf_CTCHY_sf UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:289508 UniProtKB/TrEMBL
MGC_CLONE MGC:94651 IMAGE-MGC_LOAD
NCBI Gene 289508 ENTREZGENE
PANTHER RING FINGER AND CHY ZINC FINGER DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
  RING FINGER AND CHY ZINC FINGER DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
Pfam zf-CHY UniProtKB/TrEMBL
  zf-RING_2 UniProtKB/TrEMBL
  zinc_ribbon_6 UniProtKB/TrEMBL
PhenoGen Rchy1 PhenoGen
PROSITE ZF_CHY UniProtKB/TrEMBL
  ZF_CTCHY UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/TrEMBL
SMART RING UniProtKB/TrEMBL
Superfamily-SCOP RING/U-box UniProtKB/TrEMBL
  SSF161219 UniProtKB/TrEMBL
  SSF161245 UniProtKB/TrEMBL
UniProt A0A8I5ZWY8_RAT UniProtKB/TrEMBL
  Q5XIE4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-21 Rchy1  ring finger and CHY zinc finger domain containing 1  Rchy1  ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-10 Rchy1  ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase  Rchy1  ring finger and CHY zinc finger domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Rchy1  ring finger and CHY zinc finger domain containing 1      Symbol and Name status set to approved 1299863 APPROVED
2005-07-29 Rchy1  ring finger and CHY zinc finger domain containing 1      Symbol and Name status set to provisional 70820 PROVISIONAL