Ndufb6 (NADH:ubiquinone oxidoreductase subunit B6) - Rat Genome Database

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Gene: Ndufb6 (NADH:ubiquinone oxidoreductase subunit B6) Rattus norvegicus
Analyze
Symbol: Ndufb6
Name: NADH:ubiquinone oxidoreductase subunit B6
RGD ID: 1311354
Description: Predicted to be involved in mitochondrial ATP synthesis coupled electron transport and mitochondrial respiratory chain complex I assembly. Predicted to be located in mitochondrial inner membrane and nucleoplasm. Predicted to be part of mitochondrial respiratory chain complex I. Biomarker of obesity. Orthologous to human NDUFB6 (NADH:ubiquinone oxidoreductase subunit B6); PARTICIPATES IN Alzheimer's disease pathway; Huntington's disease pathway; oxidative phosphorylation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; aflatoxin B1.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: DD6C4-3; DD6C4-4; LOC297990; NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6; NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17kDa; NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
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
mRatBN7.2555,400,543 - 55,410,110 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl555,400,543 - 55,410,181 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx557,366,430 - 57,376,013 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0559,185,572 - 59,195,154 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0559,157,294 - 59,166,874 (-)NCBIRnor_WKY
Rnor_6.0556,567,109 - 56,576,676 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl556,567,109 - 56,576,676 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0561,110,999 - 61,120,566 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4557,677,225 - 57,687,302 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1557,677,435 - 57,687,478 (-)NCBI
Celera554,016,558 - 54,026,125 (-)NCBICelera
Cytogenetic Map5q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction 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. 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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. KEGG: Kyoto Encyclopedia of Genes and Genomes KEGG
4. A high-sucrose isocaloric pair-fed model induces obesity and impairs NDUFB6 gene function in rat adipose tissue. Lomba A, etal., J Nutrigenet Nutrigenomics. 2009;2(6):267-72. doi: 10.1159/000308465. Epub 2010 Jun 19.
5. Weight gain induced by an isocaloric pair-fed high fat diet: a nutriepigenetic study on FASN and NDUFB6 gene promoters. Lomba A, etal., Mol Genet Metab. 2010 Oct-Nov;101(2-3):273-8. doi: 10.1016/j.ymgme.2010.07.017. Epub 2010 Aug 3.
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12611891   PMID:14651853   PMID:17209039   PMID:17376863   PMID:18396137   PMID:18614015   PMID:24746669   PMID:27626371  


Genomics

Comparative Map Data
Ndufb6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2555,400,543 - 55,410,110 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl555,400,543 - 55,410,181 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx557,366,430 - 57,376,013 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0559,185,572 - 59,195,154 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0559,157,294 - 59,166,874 (-)NCBIRnor_WKY
Rnor_6.0556,567,109 - 56,576,676 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl556,567,109 - 56,576,676 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0561,110,999 - 61,120,566 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4557,677,225 - 57,687,302 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1557,677,435 - 57,687,478 (-)NCBI
Celera554,016,558 - 54,026,125 (-)NCBICelera
Cytogenetic Map5q22NCBI
NDUFB6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38932,553,001 - 32,573,159 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl932,553,001 - 32,573,184 (-)EnsemblGRCh38hg38GRCh38
GRCh37932,552,999 - 32,573,157 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36932,543,523 - 32,563,182 (-)NCBINCBI36Build 36hg18NCBI36
Build 34932,543,522 - 32,563,182NCBI
Celera932,484,729 - 32,504,395 (-)NCBICelera
Cytogenetic Map9p21.1NCBI
HuRef932,510,306 - 32,529,979 (-)NCBIHuRef
CHM1_1932,553,559 - 32,573,243 (-)NCBICHM1_1
T2T-CHM13v2.0932,569,166 - 32,589,354 (-)NCBIT2T-CHM13v2.0
Ndufb6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39440,270,591 - 40,279,421 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl440,270,591 - 40,279,421 (-)EnsemblGRCm39 Ensembl
GRCm38440,270,591 - 40,279,421 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl440,270,591 - 40,279,421 (-)EnsemblGRCm38mm10GRCm38
MGSCv37440,217,696 - 40,226,401 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36440,459,334 - 40,468,039 (-)NCBIMGSCv36mm8
Celera439,933,667 - 39,942,372 (-)NCBICelera
Cytogenetic Map4A5NCBI
Ndufb6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554723,054,154 - 3,064,433 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554723,054,026 - 3,064,530 (+)NCBIChiLan1.0ChiLan1.0
NDUFB6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1933,137,836 - 33,157,006 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl933,137,836 - 33,157,006 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0932,327,973 - 32,347,518 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
NDUFB6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11149,821,998 - 49,833,624 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl223,526,115 - 3,526,501 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1148,444,163 - 48,455,988 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01150,762,716 - 50,774,556 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1150,762,715 - 50,774,556 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11149,425,777 - 49,437,612 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01149,292,319 - 49,304,367 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01150,051,004 - 50,062,839 (-)NCBIUU_Cfam_GSD_1.0
Ndufb6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947164,684,163 - 164,696,201 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365241,231,852 - 1,243,659 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365241,231,744 - 1,243,783 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NDUFB6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1033,802,051 - 33,865,385 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11033,849,206 - 33,865,080 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21038,102,584 - 38,118,493 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NDUFB6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11247,682,066 - 47,701,467 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1247,682,192 - 47,701,273 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603844,574,190 - 44,593,784 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ndufb6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473637,223,153 - 37,235,027 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473637,223,046 - 37,235,144 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ndufb6
98 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:30
Count of miRNA genes:25
Interacting mature miRNAs:28
Transcripts:ENSRNOT00000029712
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
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52122674466226744Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52795544072955440Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52851548973515489Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52851548973515489Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53321566578215665Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53321566578215665Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53321566578215665Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641922Alcrsp8Alcohol response QTL 8alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)53518915368564008Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54372665686724018Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)54946360094463600Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)54946360094463600Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55098389595983895Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat


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: ENSRNOT00000029712   ⟹   ENSRNOP00000037051
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl555,400,610 - 55,410,181 (-)Ensembl
Rnor_6.0 Ensembl556,567,109 - 56,576,676 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103239   ⟹   ENSRNOP00000085453
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl555,400,543 - 55,410,013 (-)Ensembl
RefSeq Acc Id: NM_001106646   ⟹   NP_001100116
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2555,400,543 - 55,410,110 (-)NCBI
Rnor_6.0556,567,109 - 56,576,676 (-)NCBI
Rnor_5.0561,110,999 - 61,120,566 (-)NCBI
RGSC_v3.4557,677,225 - 57,687,302 (-)RGD
Celera554,016,558 - 54,026,125 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100116 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL98633 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100116   ⟸   NM_001106646
- UniProtKB: D3ZZ21 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000037051   ⟸   ENSRNOT00000029712
RefSeq Acc Id: ENSRNOP00000085453   ⟸   ENSRNOT00000103239

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZZ21-F1-model_v2 AlphaFold D3ZZ21 1-128 view protein structure

Transcriptome

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

Promoters
RGD ID:13693630
Promoter ID:EPDNEW_R4155
Type:initiation region
Name:Ndufb6_1
Description:NADH:ubiquinone oxidoreductase subunit B6
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_6.0556,576,640 - 56,576,700EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311354 AgrOrtholog
BioCyc Gene G2FUF-41601 BioCyc
BioCyc Pathway PWY-3781 [aerobic respiration I (cytochrome c)] BioCyc
Ensembl Genes ENSRNOG00000024539 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000037051 ENTREZGENE
  ENSRNOP00000037051.4 UniProtKB/TrEMBL
  ENSRNOP00000085453.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029712 ENTREZGENE
  ENSRNOT00000029712.5 UniProtKB/TrEMBL
  ENSRNOT00000103239.1 UniProtKB/TrEMBL
InterPro NADH_DH_UbQ_b-subcmplx_su6 UniProtKB/TrEMBL
KEGG Report rno:297990 UniProtKB/TrEMBL
NCBI Gene 297990 ENTREZGENE
PANTHER PTHR15083 UniProtKB/TrEMBL
Pfam NDUF_B6 UniProtKB/TrEMBL
PhenoGen Ndufb6 PhenoGen
UniProt A0A8I6GCX1_RAT UniProtKB/TrEMBL
  D3ZZ21 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-17 Ndufb6  NADH:ubiquinone oxidoreductase subunit B6  Ndufb6  NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Ndufb6  NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6   Ndufb6_predicted  NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Ndufb6_predicted  NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6 (predicted)    NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17kDa (predicted)  Name updated 1299863 APPROVED
2005-01-12 Ndufb6_predicted  NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17kDa (predicted)      Symbol and Name status set to approved 70820 APPROVED