Radx (RPA1 related single stranded DNA binding protein, X-linked) - Rat Genome Database

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Gene: Radx (RPA1 related single stranded DNA binding protein, X-linked) Rattus norvegicus
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Symbol: Radx
Name: RPA1 related single stranded DNA binding protein, X-linked
RGD ID: 1589413
Description: Predicted to enable single-stranded DNA binding activity. Predicted to be involved in negative regulation of double-strand break repair via homologous recombination. Predicted to be located in chromosome. Predicted to be active in replication fork. Orthologous to human RADX (RPA1 related single stranded DNA binding protein, X-linked); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; 17beta-estradiol (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC680663; LOC680663; MGC188110; RPA-related protein RADX; uncharacterized protein CXorf57 homolog
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X107,877,835 - 107,965,476 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX107,877,920 - 107,965,476 (+)EnsemblGRCr8
mRatBN7.2X103,089,284 - 103,176,840 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX103,089,284 - 103,176,838 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX105,221,800 - 105,309,354 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X108,720,548 - 108,808,099 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X106,291,959 - 106,382,595 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X110,670,037 - 110,782,420 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX110,670,119 - 110,782,284 (+)Ensemblrn6Rnor6.0
Rnor_5.0X110,810,982 - 110,822,582 (+)NCBIRnor_5.0Rnor_5.0rn5
Rnor_5.0X110,711,917 - 110,792,572 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X127,170,527 - 127,215,710 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX103,855,291 - 103,941,542 (+)NCBICelera
Cytogenetic MapXq32NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromosome  (IEA)
nuclear speck  (IEA,ISO)
replication fork  (IBA,IEA,ISO,ISS)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:22681889   PMID:28735897  


Genomics

Comparative Map Data
Radx
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X107,877,835 - 107,965,476 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX107,877,920 - 107,965,476 (+)EnsemblGRCr8
mRatBN7.2X103,089,284 - 103,176,840 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX103,089,284 - 103,176,838 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX105,221,800 - 105,309,354 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X108,720,548 - 108,808,099 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X106,291,959 - 106,382,595 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X110,670,037 - 110,782,420 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX110,670,119 - 110,782,284 (+)Ensemblrn6Rnor6.0
Rnor_5.0X110,810,982 - 110,822,582 (+)NCBIRnor_5.0Rnor_5.0rn5
Rnor_5.0X110,711,917 - 110,792,572 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X127,170,527 - 127,215,710 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX103,855,291 - 103,941,542 (+)NCBICelera
Cytogenetic MapXq32NCBI
RADX
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X106,611,978 - 106,679,439 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX106,611,930 - 106,679,439 (+)Ensemblhg38GRCh38
GRCh37X105,855,208 - 105,922,669 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X105,741,909 - 105,809,328 (+)NCBIBuild 36Build 36hg18NCBI36
CeleraX106,326,505 - 106,394,019 (+)NCBICelera
Cytogenetic MapXq22.3NCBI
HuRefX95,482,341 - 95,550,832 (+)NCBIHuRef
CHM1_1X105,765,982 - 105,833,494 (+)NCBICHM1_1
T2T-CHM13v2.0X105,048,421 - 105,115,882 (+)NCBIT2T-CHM13v2.0
Radx
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X138,381,116 - 138,455,333 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX138,381,116 - 138,455,331 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X139,480,367 - 139,554,584 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX139,480,367 - 139,554,582 (+)Ensemblmm10GRCm38
MGSCv37X136,014,906 - 136,089,119 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X134,826,807 - 134,900,944 (+)NCBIMGSCv36mm8
CeleraX122,741,905 - 122,816,200 (+)NCBICelera
Cytogenetic MapXF1NCBI
cM MapX61.35NCBI
RADX
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X106,097,529 - 106,164,854 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X106,101,130 - 106,168,455 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X95,714,600 - 95,781,853 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X106,092,394 - 106,159,716 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX106,092,340 - 106,159,772 (+)EnsemblpanPan2panpan1.1
RADX
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X80,146,335 - 80,234,732 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX80,146,040 - 80,235,739 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX66,262,981 - 66,351,404 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X81,780,985 - 81,869,803 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX81,780,959 - 81,869,801 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X79,251,983 - 79,340,421 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X80,960,658 - 81,049,418 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X80,740,823 - 80,829,269 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Radx
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X79,535,640 - 79,598,991 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364998,058,972 - 8,122,287 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364998,058,973 - 8,122,332 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RADX
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX87,025,603 - 87,103,501 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X87,025,603 - 87,103,503 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X101,460,402 - 101,480,736 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RADX
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X94,454,011 - 94,523,015 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX94,453,938 - 94,523,012 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606519,528,784 - 19,602,879 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Radx
81 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:280
Count of miRNA genes:184
Interacting mature miRNAs:201
Transcripts:ENSRNOT00000014811
Prediction methods:Miranda, Pita
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
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X97528096142528096Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX105359969157758123Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X80434318125434318Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX92979612117740458Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X105468858125434318Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
2302047Pia34Pristane induced arthritis QTL 345.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1996916163141916163Rat


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 11 54 151 85 84 53 36 53 6 264 117 8 126 70 92 31 12 12

Sequence


Ensembl Acc Id: ENSRNOT00000014811   ⟹   ENSRNOP00000014811
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX107,877,920 - 107,965,476 (+)Ensembl
mRatBN7.2 EnsemblX103,089,284 - 103,176,838 (+)Ensembl
Rnor_6.0 EnsemblX110,670,119 - 110,782,284 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000089579   ⟹   ENSRNOP00000071360
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX110,670,235 - 110,781,090 (+)Ensembl
RefSeq Acc Id: NM_001127377   ⟹   NP_001120849
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X107,877,920 - 107,965,476 (+)NCBI
mRatBN7.2X103,089,284 - 103,176,840 (+)NCBI
Rnor_6.0X110,670,119 - 110,782,286 (+)NCBI
Rnor_5.0X110,711,917 - 110,792,572 (+)NCBI
Rnor_5.0X110,810,982 - 110,822,582 (+)NCBI
RGSC_v3.4X127,170,527 - 127,215,710 (+)RGD
CeleraX103,855,291 - 103,941,542 (+)RGD
Sequence:
RefSeq Acc Id: XM_063280302   ⟹   XP_063136372
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X107,877,835 - 107,965,476 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001120849 (Get FASTA)   NCBI Sequence Viewer  
  XP_063136372 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI66523 (Get FASTA)   NCBI Sequence Viewer  
  B2GV47 (Get FASTA)   NCBI Sequence Viewer  
  EDL88019 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000014811
RefSeq Acc Id: NP_001120849   ⟸   NM_001127377
- UniProtKB: B2GV47 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000014811   ⟸   ENSRNOT00000014811
Ensembl Acc Id: ENSRNOP00000071360   ⟸   ENSRNOT00000089579
RefSeq Acc Id: XP_063136372   ⟸   XM_063280302
- Peptide Label: isoform X1
- UniProtKB: A0A8L2UIW5 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B2GV47-F1-model_v2 AlphaFold B2GV47 1-844 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:1589413 AgrOrtholog
BioCyc Gene G2FUF-1558 BioCyc
Ensembl Genes ENSRNOG00000011120 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000014811 ENTREZGENE
Gene3D-CATH 2.40.50.140 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7134576 IMAGE-MGC_LOAD
InterPro NA-bd_OB-fold UniProtKB/Swiss-Prot
  RADX UniProtKB/Swiss-Prot
KEGG Report rno:680663 UniProtKB/Swiss-Prot
MGC_CLONE MGC:188110 IMAGE-MGC_LOAD
NCBI Gene 680663 ENTREZGENE
PANTHER PTHR14944 UniProtKB/Swiss-Prot
  RPA-RELATED PROTEIN RADX UniProtKB/Swiss-Prot
Pfam DUF5521 UniProtKB/Swiss-Prot
PhenoGen Radx PhenoGen
RatGTEx ENSRNOG00000011120 RatGTEx
Superfamily-SCOP SSF50249 UniProtKB/Swiss-Prot
UniProt A0A8L2UIW5 ENTREZGENE, UniProtKB/TrEMBL
  B2GV47 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-09-17 Radx  RPA1 related single stranded DNA binding protein, X-linked  LOC680663  hypothetical protein LOC680663  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC680663  hypothetical protein LOC680663      Symbol and Name status set to provisional 70820 PROVISIONAL