R3hdm4 (R3H domain containing 4) - Rat Genome Database

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Gene: R3hdm4 (R3H domain containing 4) Rattus norvegicus
Analyze
Symbol: R3hdm4
Name: R3H domain containing 4
RGD ID: 1307067
Description: Predicted to enable nucleic acid binding activity. Orthologous to human R3HDM4 (R3H domain containing 4); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC362840; LOC362840; R3H domain-containing protein 4; RGD1307067; uncharacterized protein LOC362840
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
GRCr8710,441,032 - 10,448,143 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl710,440,772 - 10,448,143 (+)EnsemblGRCr8
mRatBN7.279,790,401 - 9,797,512 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl79,790,322 - 9,797,512 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx712,672,377 - 12,679,525 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0714,547,697 - 14,554,842 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0712,408,881 - 12,416,016 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0712,611,476 - 12,618,586 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,611,468 - 12,618,586 (+)Ensemblrn6Rnor6.0
Rnor_5.0712,781,198 - 12,788,308 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4711,302,975 - 11,309,973 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera77,965,345 - 7,972,285 (+)NCBICelera
RGSC_v3.1711,301,478 - 11,309,971 (+)NCBI
Cytogenetic Map7q11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
R3hdm4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8710,441,032 - 10,448,143 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl710,440,772 - 10,448,143 (+)EnsemblGRCr8
mRatBN7.279,790,401 - 9,797,512 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl79,790,322 - 9,797,512 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx712,672,377 - 12,679,525 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0714,547,697 - 14,554,842 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0712,408,881 - 12,416,016 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0712,611,476 - 12,618,586 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,611,468 - 12,618,586 (+)Ensemblrn6Rnor6.0
Rnor_5.0712,781,198 - 12,788,308 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4711,302,975 - 11,309,973 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera77,965,345 - 7,972,285 (+)NCBICelera
RGSC_v3.1711,301,478 - 11,309,971 (+)NCBI
Cytogenetic Map7q11NCBI
R3HDM4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3819896,503 - 913,219 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl19896,503 - 913,245 (-)Ensemblhg38GRCh38
GRCh3719896,503 - 913,219 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3619847,503 - 864,200 (-)NCBIBuild 36Build 36hg18NCBI36
Build 3419847,502 - 864,200NCBI
Celera19828,869 - 845,586 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef19670,513 - 686,876 (-)NCBIHuRef
CHM1_119895,123 - 912,814 (-)NCBICHM1_1
T2T-CHM13v2.019859,232 - 875,957 (-)NCBIT2T-CHM13v2.0
R3hdm4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391079,745,886 - 79,752,764 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1079,745,886 - 79,757,042 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381079,910,052 - 79,916,930 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1079,910,052 - 79,921,208 (-)Ensemblmm10GRCm38
MGSCv371079,372,798 - 79,379,675 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361079,313,181 - 79,320,040 (-)NCBIMGSCv36mm8
Celera1080,924,863 - 80,931,740 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
R3hdm4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554956,919,236 - 6,936,128 (+)Ensembl
ChiLan1.0NW_0049554956,926,619 - 6,936,128 (+)NCBIChiLan1.0ChiLan1.0
R3HDM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2205,227,576 - 5,244,164 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1194,466,969 - 4,483,481 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v019219,000 - 235,541 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.119868,192 - 874,301 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl19868,192 - 877,925 (-)EnsemblpanPan2panpan1.1
R3HDM4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12057,761,100 - 57,769,656 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2057,760,909 - 57,769,105 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2057,563,079 - 57,571,673 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02058,503,366 - 58,511,900 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2058,503,160 - 58,511,349 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12057,558,210 - 57,566,745 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02058,037,856 - 58,046,464 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02058,240,857 - 58,249,400 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
R3hdm4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118217,453,435 - 217,461,602 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936588372,971 - 378,538 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936588373,177 - 382,018 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
R3HDM4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl277,479,273 - 77,489,105 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1277,479,259 - 77,489,106 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2277,508,534 - 77,518,363 (-)NCBISscrofa10.2Sscrofa10.2susScr3
R3HDM4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.16643,058 - 662,407 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl6644,005 - 662,338 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660818,255,189 - 8,272,039 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
R3hdm4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248287,682,754 - 7,692,778 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248287,682,770 - 7,691,215 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
R3hdm4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11154,958,671 - 154,965,725 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in R3hdm4
62 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:298
Count of miRNA genes:158
Interacting mature miRNAs:177
Transcripts:ENSRNOT00000015869
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7166965846669658Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7123748937Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7721609752216097Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)71011291699900612Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)7131777942Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)71104117804Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7170952746709527Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7132612984Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71011291660150541Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7946087754460877Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7129716167Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134650782Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7132612984Rat


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 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000015869   ⟹   ENSRNOP00000015869
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl710,440,772 - 10,448,143 (+)Ensembl
mRatBN7.2 Ensembl79,790,426 - 9,797,512 (+)Ensembl
Rnor_6.0 Ensembl712,611,468 - 12,618,586 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000093610
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl712,616,442 - 12,616,847 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000094419   ⟹   ENSRNOP00000094170
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,790,322 - 9,797,512 (+)Ensembl
RefSeq Acc Id: NM_001173974   ⟹   NP_001167445
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8710,441,032 - 10,448,143 (+)NCBI
mRatBN7.279,790,401 - 9,797,512 (+)NCBI
Rnor_6.0712,611,476 - 12,618,586 (+)NCBI
Rnor_5.0712,781,198 - 12,788,308 (+)NCBI
Celera77,965,345 - 7,972,285 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001167445 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI61971 (Get FASTA)   NCBI Sequence Viewer  
  EDL89369 (Get FASTA)   NCBI Sequence Viewer  
  EDL89370 (Get FASTA)   NCBI Sequence Viewer  
  EDL89371 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000015869
  ENSRNOP00000015869.9
RefSeq Acc Id: NP_001167445   ⟸   NM_001173974
- UniProtKB: B1WC19 (UniProtKB/TrEMBL),   F7EW14 (UniProtKB/TrEMBL),   A0A8J8XLF6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000015869   ⟸   ENSRNOT00000015869
Ensembl Acc Id: ENSRNOP00000094170   ⟸   ENSRNOT00000094419
Protein Domains
R3H

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1WC19-F1-model_v2 AlphaFold B1WC19 1-263 view protein structure

Transcriptome

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

Promoters
RGD ID:13695041
Promoter ID:EPDNEW_R5565
Type:multiple initiation site
Name:R3hdm4_1
Description:R3H domain containing 4
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_6.0712,611,480 - 12,611,540EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307067 AgrOrtholog
BioCyc Gene G2FUF-34900 BioCyc
Ensembl Genes ENSRNOG00000011489 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015869 ENTREZGENE
  ENSRNOT00000015869.10 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1370.50 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9028992 IMAGE-MGC_LOAD
InterPro R3H-assoc_dom UniProtKB/TrEMBL
  R3H_dom_sf UniProtKB/TrEMBL
  R3H_ss_bd UniProtKB/TrEMBL
  R3HDM4 UniProtKB/TrEMBL
KEGG Report rno:362840 UniProtKB/TrEMBL
MGC_CLONE MGC:187780 IMAGE-MGC_LOAD
NCBI Gene 362840 ENTREZGENE
PANTHER PTHR32019 UniProtKB/TrEMBL
  R3H DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
Pfam R3H UniProtKB/TrEMBL
  R3H-assoc UniProtKB/TrEMBL
PhenoGen R3hdm4 PhenoGen
PROSITE R3H UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011489 RatGTEx
Superfamily-SCOP SSF82708 UniProtKB/TrEMBL
UniProt A0A8J8XLF6 ENTREZGENE, UniProtKB/TrEMBL
  B1WC19 ENTREZGENE, UniProtKB/TrEMBL
  F7EW14 ENTREZGENE
UniProt Secondary F7EW14 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-12-06 R3hdm4  R3H domain containing 4  RGD1307067  LOC362840  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1307067  LOC362840   RGD1307067_predicted  LOC362840 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1307067_predicted  LOC362840 (predicted)  LOC362840_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC362840_predicted  LOC362840 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL