Pyroxd1 (pyridine nucleotide-disulphide oxidoreductase domain 1) - Rat Genome Database

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Gene: Pyroxd1 (pyridine nucleotide-disulphide oxidoreductase domain 1) Rattus norvegicus
Analyze
Symbol: Pyroxd1
Name: pyridine nucleotide-disulphide oxidoreductase domain 1
RGD ID: 1303253
Description: Predicted to enable flavin adenine dinucleotide binding activity and oxidoreductase activity. Predicted to be involved in cellular response to oxidative stress. Predicted to be located in nucleus and sarcomere. Human ortholog(s) of this gene implicated in myofibrillar myopathy 8. Orthologous to human PYROXD1 (pyridine nucleotide-disulphide oxidoreductase domain 1); INTERACTS WITH bisphenol A; indole-3-methanol; paracetamol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MGC94881; pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1; similar to Recql 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
mRatBN7.24175,292,124 - 175,311,143 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4175,292,177 - 175,308,689 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4181,587,023 - 181,603,261 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04177,371,292 - 177,387,530 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04175,991,849 - 176,008,088 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04176,565,733 - 176,581,976 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4176,565,694 - 176,581,952 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04240,779,516 - 240,795,759 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44179,910,953 - 179,927,331 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14180,156,076 - 180,172,454 (+)NCBI
Celera4163,824,933 - 163,841,122 (+)NCBICelera
Cytogenetic Map4q44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (ISO,ISS)
nucleus  (IEA,ISO,ISS)
sarcomere  (IEA,ISO,ISS)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
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
4. 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.
Additional References at PubMed
PMID:21873635   PMID:27745833   PMID:30345904  


Genomics

Comparative Map Data
Pyroxd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24175,292,124 - 175,311,143 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4175,292,177 - 175,308,689 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4181,587,023 - 181,603,261 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04177,371,292 - 177,387,530 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04175,991,849 - 176,008,088 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04176,565,733 - 176,581,976 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4176,565,694 - 176,581,952 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04240,779,516 - 240,795,759 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44179,910,953 - 179,927,331 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14180,156,076 - 180,172,454 (+)NCBI
Celera4163,824,933 - 163,841,122 (+)NCBICelera
Cytogenetic Map4q44NCBI
PYROXD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381221,437,655 - 21,471,250 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1221,437,615 - 21,471,250 (+)EnsemblGRCh38hg38GRCh38
GRCh371221,590,589 - 21,624,184 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361221,481,878 - 21,514,567 (+)NCBINCBI36Build 36hg18NCBI36
Celera1226,745,930 - 26,779,563 (+)NCBICelera
Cytogenetic Map12p12.1NCBI
HuRef1221,364,639 - 21,398,217 (+)NCBIHuRef
CHM1_11221,556,189 - 21,589,812 (+)NCBICHM1_1
T2T-CHM13v2.01221,316,354 - 21,349,929 (+)NCBIT2T-CHM13v2.0
Pyroxd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396142,291,381 - 142,307,881 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6142,291,380 - 142,308,983 (+)EnsemblGRCm39 Ensembl
GRCm386142,345,627 - 142,362,729 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6142,345,654 - 142,363,257 (+)EnsemblGRCm38mm10GRCm38
MGSCv376142,294,217 - 142,311,144 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366142,302,894 - 142,319,258 (+)NCBIMGSCv36mm8
Celera6145,405,658 - 145,422,585 (+)NCBICelera
Cytogenetic Map6G2NCBI
cM Map673.9NCBI
Pyroxd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541317,097,859 - 17,115,148 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541317,097,859 - 17,115,148 (+)NCBIChiLan1.0ChiLan1.0
PYROXD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan11275,326,469 - 75,361,224 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01264,826,835 - 64,860,651 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11267,430,708 - 67,463,996 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1267,430,716 - 67,463,996 (-)Ensemblpanpan1.1panPan2
PYROXD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12726,234,503 - 26,257,328 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2726,234,777 - 26,257,528 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2720,194,447 - 20,221,893 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02726,560,004 - 26,587,581 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2726,560,007 - 26,587,543 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12726,423,276 - 26,450,836 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02726,401,954 - 26,429,406 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02719,899,333 - 19,926,966 (+)NCBIUU_Cfam_GSD_1.0
Pyroxd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494587,461,874 - 87,490,113 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365485,385,362 - 5,406,179 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365485,384,722 - 5,412,999 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PYROXD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl551,993,717 - 52,020,809 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1551,994,793 - 52,020,844 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2555,272,750 - 55,297,405 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PYROXD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11121,299,637 - 21,333,860 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1121,299,696 - 21,333,397 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606913,811,092 - 13,845,038 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pyroxd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475217,220,995 - 17,242,496 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475217,221,444 - 17,241,868 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pyroxd1
30 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:13
Count of miRNA genes:13
Interacting mature miRNAs:13
Transcripts:ENSRNOT00000016794
Prediction methods: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
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat

Markers in Region
RH130945  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24175,308,472 - 175,308,664 (+)MAPPERmRatBN7.2
Rnor_6.04176,582,028 - 176,582,219NCBIRnor6.0
Rnor_5.04240,795,811 - 240,796,002UniSTSRnor5.0
RGSC_v3.44179,927,388 - 179,927,579UniSTSRGSC3.4
Celera4163,841,179 - 163,841,370UniSTS
RH 3.4 Map41031.2UniSTS
Cytogenetic Map4q44UniSTS


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 18 32 16 19 16 1 1 74 35 38 11 1
Low 25 25 25 25 7 10 3 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016794   ⟹   ENSRNOP00000016794
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4175,292,177 - 175,308,413 (+)Ensembl
Rnor_6.0 Ensembl4176,565,694 - 176,581,952 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113178   ⟹   ENSRNOP00000083610
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4175,293,981 - 175,308,689 (+)Ensembl
RefSeq Acc Id: NM_001004234   ⟹   NP_001004234
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,292,177 - 175,308,416 (+)NCBI
Rnor_6.04176,565,733 - 176,581,971 (+)NCBI
Rnor_5.04240,779,516 - 240,795,759 (+)NCBI
RGSC_v3.44179,910,953 - 179,927,331 (+)RGD
Celera4163,824,933 - 163,841,122 (+)RGD
Sequence:
RefSeq Acc Id: XM_017592597   ⟹   XP_017448086
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,292,356 - 175,308,425 (+)NCBI
Rnor_6.04176,565,878 - 176,581,976 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039107464   ⟹   XP_038963392
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,292,124 - 175,311,143 (+)NCBI
RefSeq Acc Id: XM_039107465   ⟹   XP_038963393
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,292,124 - 175,307,274 (+)NCBI
RefSeq Acc Id: XR_005503206
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,292,124 - 175,307,194 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001004234   ⟸   NM_001004234
- UniProtKB: Q68FS6 (UniProtKB/Swiss-Prot),   F1LR31 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017448086   ⟸   XM_017592597
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZZN9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016794   ⟸   ENSRNOT00000016794
RefSeq Acc Id: XP_038963392   ⟸   XM_039107464
- Peptide Label: isoform X2
- UniProtKB: F1LR31 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038963393   ⟸   XM_039107465
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000083610   ⟸   ENSRNOT00000113178
Protein Domains
FAD/NAD(P)-binding   NADH-rubredoxin oxidoreductase C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q68FS6-F1-model_v2 AlphaFold Q68FS6 1-498 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:1303253 AgrOrtholog
BioCyc Gene G2FUF-42496 BioCyc
Ensembl Genes ENSRNOG00000012472 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016794 ENTREZGENE
  ENSRNOP00000016794.3 UniProtKB/TrEMBL
  ENSRNOP00000083610.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016794 ENTREZGENE
  ENSRNOT00000016794.6 UniProtKB/TrEMBL
  ENSRNOT00000113178.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.390.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.50.50.60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7110714 IMAGE-MGC_LOAD
InterPro FAD/NAD-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FAD/NAD-binding_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FAD/NAD-linked_Rdtase_dimer_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rubredoxin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:297708 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94881 IMAGE-MGC_LOAD
NCBI Gene 297708 ENTREZGENE
PANTHER PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE DOMAIN-CONTAINING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE DOMAIN-CONTAINING PROTEIN 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Pyr_redox_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rubredoxin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pyroxd1 PhenoGen
PRINTS FADPNR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF51905 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5ZZN9 ENTREZGENE, UniProtKB/TrEMBL
  F1LR31 ENTREZGENE, UniProtKB/TrEMBL
  PYRD1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Pyroxd1  pyridine nucleotide-disulphide oxidoreductase domain 1  MGC94881  similar to Recql protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-09-30 MGC94881        Symbol and Name status set to provisional 70820 PROVISIONAL