Cyb561d2 (cytochrome b561 family, member D2) - Rat Genome Database

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Gene: Cyb561d2 (cytochrome b561 family, member D2) Rattus norvegicus
Analyze
Symbol: Cyb561d2
Name: cytochrome b561 family, member D2
RGD ID: 1359644
Description: Predicted to enable heme binding activity; transmembrane ascorbate ferrireductase activity; and transmembrane monodehydroascorbate reductase activity. Predicted to be involved in ascorbate homeostasis. Predicted to be located in endoplasmic reticulum and vesicle. Orthologous to human CYB561D2 (cytochrome b561 family member D2); INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cytochrome b-561 domain containing 2; cytochrome b561 domain-containing protein 2; MGC95239; putative tumor suppressor protein 101F6; similar to 101F6 protein; transmembrane ascorbate ferrireductase; transmembrane reductase CYB561D2
RGD Orthologs
Human
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28108,213,201 - 108,215,778 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8108,213,205 - 108,215,759 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8113,840,231 - 113,842,758 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08112,039,387 - 112,041,914 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08109,882,168 - 109,884,695 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08116,295,328 - 116,297,879 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8116,295,329 - 116,297,858 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08115,651,588 - 115,654,143 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48112,787,042 - 112,789,564 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18112,806,497 - 112,809,019 (-)NCBI
Celera8107,519,621 - 107,522,143 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. The 630-kb lung cancer homozygous deletion region on human chromosome 3p21.3: identification and evaluation of the resident candidate tumor suppressor genes. The International Lung Cancer Chromosome 3p21.3 Tumor Suppressor Gene Consortium. Lerman MI and Minna JD, Cancer Res 2000 Nov 1;60(21):6116-33.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. 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:15489334   PMID:17938141   PMID:19734123   PMID:19943161  


Genomics

Comparative Map Data
Cyb561d2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28108,213,201 - 108,215,778 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8108,213,205 - 108,215,759 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8113,840,231 - 113,842,758 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08112,039,387 - 112,041,914 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08109,882,168 - 109,884,695 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08116,295,328 - 116,297,879 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8116,295,329 - 116,297,858 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08115,651,588 - 115,654,143 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48112,787,042 - 112,789,564 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18112,806,497 - 112,809,019 (-)NCBI
Celera8107,519,621 - 107,522,143 (-)NCBICelera
Cytogenetic Map8q32NCBI
CYB561D2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38350,350,862 - 50,368,197 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl350,350,845 - 50,358,460 (+)EnsemblGRCh38hg38GRCh38
GRCh37350,388,293 - 50,405,628 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3p21.31NCBI
HuRef350,443,898 - 50,447,100 (+)NCBIHuRef
CHM1_1350,340,572 - 50,343,775 (+)NCBICHM1_1
T2T-CHM13v2.0350,380,585 - 50,397,917 (+)NCBIT2T-CHM13v2.0
Cyb561d2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399107,416,210 - 107,419,392 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9107,416,206 - 107,419,392 (-)EnsemblGRCm39 Ensembl
GRCm389107,539,005 - 107,542,193 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9107,539,007 - 107,542,193 (-)EnsemblGRCm38mm10GRCm38
MGSCv379107,441,342 - 107,444,196 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369107,397,112 - 107,399,966 (-)NCBIMGSCv36mm8
Celera9107,147,775 - 107,150,630 (-)NCBICelera
Cytogenetic Map9F1NCBI
cM Map958.12NCBI

Variants

.
Variants in Cyb561d2
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:62
Count of miRNA genes:46
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000031739
Prediction methods: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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088626Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)889265192114019816Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8100149864120994388Rat
631217Activ1Activity QTL 115.9voluntary movement trait (VT:0003491)number of photobeam interruptions in an experimental apparatus (CMO:0001517)8102370617108923645Rat

Markers in Region
BF396742  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28108,215,977 - 108,216,530 (+)MAPPERmRatBN7.2
Rnor_6.08116,298,105 - 116,298,657NCBIRnor6.0
Rnor_5.08115,654,365 - 115,654,917UniSTSRnor5.0
RGSC_v3.48112,789,819 - 112,790,371UniSTSRGSC3.4
Celera8107,522,398 - 107,522,950UniSTS
RH 3.4 Map81118.9UniSTS
Cytogenetic Map8q32UniSTS
RH140367  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28108,213,331 - 108,213,507 (+)MAPPERmRatBN7.2
Rnor_6.08116,295,459 - 116,295,634NCBIRnor6.0
Rnor_5.08115,651,719 - 115,651,894UniSTSRnor5.0
RGSC_v3.48112,787,173 - 112,787,348UniSTSRGSC3.4
Celera8107,519,752 - 107,519,927UniSTS
RH 3.4 Map81119.0UniSTS
Cytogenetic Map8q32UniSTS


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 13 7 14 7 59 23 23 9
Low 43 44 34 5 34 8 11 15 12 18 2 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000031739   ⟹   ENSRNOP00000033722
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8108,213,205 - 108,215,716 (-)Ensembl
Rnor_6.0 Ensembl8116,295,329 - 116,297,850 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082320   ⟹   ENSRNOP00000071082
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8108,213,206 - 108,215,759 (-)Ensembl
Rnor_6.0 Ensembl8116,295,410 - 116,297,858 (-)Ensembl
RefSeq Acc Id: NM_001007753   ⟹   NP_001007754
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,213,201 - 108,215,723 (-)NCBI
Rnor_6.08116,295,328 - 116,297,850 (-)NCBI
Rnor_5.08115,651,588 - 115,654,143 (-)NCBI
RGSC_v3.48112,787,042 - 112,789,564 (-)RGD
Celera8107,519,621 - 107,522,143 (-)RGD
Sequence:
RefSeq Acc Id: XM_006243804   ⟹   XP_006243866
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,213,201 - 108,215,778 (-)NCBI
Rnor_6.08116,295,328 - 116,297,879 (-)NCBI
Rnor_5.08115,651,588 - 115,654,143 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039081796   ⟹   XP_038937724
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,213,201 - 108,215,611 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001007754   ⟸   NM_001007753
- UniProtKB: Q641Y1 (UniProtKB/Swiss-Prot),   A6I2X3 (UniProtKB/TrEMBL),   A0A8L2QHT3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006243866   ⟸   XM_006243804
- Peptide Label: isoform X1
- UniProtKB: Q641Y1 (UniProtKB/Swiss-Prot),   A6I2X3 (UniProtKB/TrEMBL),   A0A8L2QHT3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000033722   ⟸   ENSRNOT00000031739
RefSeq Acc Id: ENSRNOP00000071082   ⟸   ENSRNOT00000082320
RefSeq Acc Id: XP_038937724   ⟸   XM_039081796
- Peptide Label: isoform X1
- UniProtKB: Q641Y1 (UniProtKB/Swiss-Prot),   A6I2X3 (UniProtKB/TrEMBL),   A0A8L2QHT3 (UniProtKB/TrEMBL)
Protein Domains
Cytochrome b561

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q641Y1-F1-model_v2 AlphaFold Q641Y1 1-222 view protein structure

Transcriptome

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

Promoters
RGD ID:13696267
Promoter ID:EPDNEW_R6791
Type:multiple initiation site
Name:Cyb561d2_1
Description:cytochrome b561 family, member D2
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_6.08116,297,837 - 116,297,897EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359644 AgrOrtholog
BioCyc Gene G2FUF-29201 BioCyc
Ensembl Genes ENSRNOG00000021887 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000031739.5 UniProtKB/TrEMBL
  ENSRNOT00000082320 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.120.1770 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7133078 IMAGE-MGC_LOAD
InterPro CYB561D1/2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_b561/ferric_Rdtase_TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:363137 UniProtKB/Swiss-Prot
MGC_CLONE MGC:95239 IMAGE-MGC_LOAD
NCBI Gene 363137 ENTREZGENE
PANTHER PTHR15422 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRANSMEMBRANE REDUCTASE CYB561D2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cytochrom_B561 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cyb561d2 PhenoGen
PROSITE CYTOCHROME_B561 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000021887 RatGTEx
SMART B561 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2QHT3 ENTREZGENE, UniProtKB/TrEMBL
  A6I2X3 ENTREZGENE, UniProtKB/TrEMBL
  C56D2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-20 Cyb561d2  cytochrome b561 family, member D2  Cyb561d2  cytochrome b-561 domain containing 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Cyb561d2  cytochrome b-561 domain containing 2  MGC95239  similar to 101F6 protein  Symbol and Name updated 1299863 APPROVED
2005-07-29 MGC95239  similar to 101F6 protein      Symbol and Name status set to provisional 70820 PROVISIONAL