Dhx38 (DEAH-box helicase 38) - Rat Genome Database

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Pathways
Gene: Dhx38 (DEAH-box helicase 38) Rattus norvegicus
Analyze
Symbol: Dhx38
Name: DEAH-box helicase 38
RGD ID: 1310345
Description: Predicted to enable 3'-5' RNA helicase activity and RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleus. Predicted to be part of catalytic step 2 spliceosome. Human ortholog(s) of this gene implicated in retinitis pigmentosa 84. Orthologous to human DHX38 (DEAH-box helicase 38); PARTICIPATES IN spliceosome pathway; INTERACTS WITH bisphenol A; furan; genistein.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: DEAH (Asp-Glu-Ala-His) box polypeptide 38; LOC292007; pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
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
GRCr81954,422,418 - 54,439,434 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1954,422,418 - 54,439,423 (-)EnsemblGRCr8
mRatBN7.21937,512,893 - 37,530,135 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1937,512,891 - 37,530,140 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1944,326,164 - 44,343,154 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01944,979,492 - 44,996,482 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01947,289,199 - 47,306,189 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01942,110,291 - 42,127,540 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1942,110,327 - 42,127,542 (+)Ensemblrn6Rnor6.0
Rnor_5.01952,935,420 - 52,952,669 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41939,416,281 - 39,433,530 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1936,917,971 - 36,935,220 (-)NCBICelera
RGSC_v3.11939,421,164 - 39,438,151 (-)NCBI
Cytogenetic Map19q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Functions of the DExD/H-box proteins in nuclear pre-mRNA splicing. Chang TH, etal., Biochim Biophys Acta. 2013 Aug;1829(8):764-74. doi: 10.1016/j.bbagrm.2013.02.006. Epub 2013 Feb 21.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
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:9524131   PMID:11991638   PMID:19946888   PMID:22681889  


Genomics

Comparative Map Data
Dhx38
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81954,422,418 - 54,439,434 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1954,422,418 - 54,439,423 (-)EnsemblGRCr8
mRatBN7.21937,512,893 - 37,530,135 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1937,512,891 - 37,530,140 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1944,326,164 - 44,343,154 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01944,979,492 - 44,996,482 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01947,289,199 - 47,306,189 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01942,110,291 - 42,127,540 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1942,110,327 - 42,127,542 (+)Ensemblrn6Rnor6.0
Rnor_5.01952,935,420 - 52,952,669 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41939,416,281 - 39,433,530 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1936,917,971 - 36,935,220 (-)NCBICelera
RGSC_v3.11939,421,164 - 39,438,151 (-)NCBI
Cytogenetic Map19q12NCBI
DHX38
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381672,093,847 - 72,112,912 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1672,093,613 - 72,112,912 (+)Ensemblhg38GRCh38
GRCh371672,127,746 - 72,146,811 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361670,685,116 - 70,704,312 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341670,685,115 - 70,704,311NCBI
Celera1656,441,736 - 56,460,927 (+)NCBICelera
Cytogenetic Map16q22.2NCBI
HuRef1657,894,449 - 57,913,646 (+)NCBIHuRef
CHM1_11673,540,965 - 73,560,161 (+)NCBICHM1_1
T2T-CHM13v2.01677,910,161 - 77,929,227 (+)NCBIT2T-CHM13v2.0
Dhx38
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398110,274,631 - 110,292,493 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8110,274,643 - 110,292,493 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm388109,547,999 - 109,565,861 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8109,548,011 - 109,565,861 (-)Ensemblmm10GRCm38
MGSCv378112,071,924 - 112,089,501 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv368112,437,153 - 112,454,730 (-)NCBIMGSCv36mm8
Celera8113,773,242 - 113,790,878 (-)NCBICelera
Cytogenetic Map8D3NCBI
cM Map857.09NCBI
Dhx38
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554844,752,834 - 4,770,843 (+)Ensembl
ChiLan1.0NW_0049554844,752,834 - 4,770,843 (+)NCBIChiLan1.0ChiLan1.0
DHX38
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21882,020,743 - 82,037,373 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11687,948,348 - 87,965,097 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01652,872,164 - 52,891,165 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11671,955,021 - 71,974,199 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1671,955,021 - 71,974,199 (+)EnsemblpanPan2panpan1.1
DHX38
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1577,810,853 - 77,830,020 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl577,811,041 - 77,830,015 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha577,772,505 - 77,791,748 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0578,250,159 - 78,269,404 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl578,250,397 - 78,269,404 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1578,070,301 - 78,089,544 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0577,893,070 - 77,912,098 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0578,392,435 - 78,411,679 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Dhx38
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934937,758,541 - 37,777,421 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647521,811,463 - 21,830,577 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647521,811,693 - 21,830,560 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DHX38
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl614,998,293 - 15,016,378 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1614,998,091 - 15,016,380 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2614,616,065 - 14,626,504 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DHX38
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1555,243,934 - 55,264,084 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl555,243,911 - 55,263,706 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604718,032,000 - 18,051,061 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Dhx38
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474614,301,922 - 14,337,152 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474614,301,921 - 14,319,649 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Dhx38
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11729,268,200 - 29,285,157 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Dhx38
219 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:75
Count of miRNA genes:66
Interacting mature miRNAs:72
Transcripts:ENSRNOT00000019810
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)194622677874246245Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194438513474246245Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)194072709254856850Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)194072709254856850Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)194072709254856850Rat

Markers in Region
RH140943  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21937,513,009 - 37,513,208 (-)MAPPERmRatBN7.2
Rnor_6.01942,127,223 - 42,127,421NCBIRnor6.0
Rnor_5.01952,952,352 - 52,952,550UniSTSRnor5.0
RGSC_v3.41939,416,400 - 39,416,598UniSTSRGSC3.4
Celera1936,918,090 - 36,918,288UniSTS
RH 3.4 Map19426.4UniSTS
Cytogenetic Map19q12UniSTS
D2S2154  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.296,943,970 - 6,944,119 (+)MAPPERmRatBN7.2
mRatBN7.2365,024,123 - 65,024,874 (+)MAPPERmRatBN7.2
mRatBN7.21937,525,934 - 37,527,508 (-)MAPPERmRatBN7.2
Rnor_6.0367,262,908 - 67,263,857NCBIRnor6.0
Rnor_6.01942,112,923 - 42,114,496NCBIRnor6.0
Rnor_5.01952,938,052 - 52,939,625UniSTSRnor5.0
Cytogenetic Map19q12UniSTS
Cytogenetic Map10q31UniSTS


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 67 160 91 90 59 92 59 6 356 192 11 139 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000019810   ⟹   ENSRNOP00000019810
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1954,422,418 - 54,439,423 (-)Ensembl
mRatBN7.2 Ensembl1937,512,891 - 37,530,140 (-)Ensembl
Rnor_6.0 Ensembl1942,110,327 - 42,127,542 (+)Ensembl
RefSeq Acc Id: NM_001399194   ⟹   NP_001386123
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81954,422,418 - 54,439,423 (-)NCBI
mRatBN7.21937,512,893 - 37,529,898 (-)NCBI
RefSeq Acc Id: XM_039097631   ⟹   XP_038953559
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81954,427,111 - 54,439,434 (-)NCBI
mRatBN7.21937,517,577 - 37,530,135 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001386123 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953559 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92497 (Get FASTA)   NCBI Sequence Viewer  
  EDL92498 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000019810
  ENSRNOP00000019810.9
Ensembl Acc Id: ENSRNOP00000019810   ⟸   ENSRNOT00000019810
RefSeq Acc Id: XP_038953559   ⟸   XM_039097631
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001386123   ⟸   NM_001399194
- UniProtKB: A6IZ19 (UniProtKB/TrEMBL),   D4A321 (UniProtKB/TrEMBL)
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A321-F1-model_v2 AlphaFold D4A321 1-1227 view protein structure

Transcriptome

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

Promoters
RGD ID:13701136
Promoter ID:EPDNEW_R11660
Type:initiation region
Name:Dhx38_1
Description:DEAH-box helicase 38
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_6.01942,110,407 - 42,110,467EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310345 AgrOrtholog
BioCyc Gene G2FUF-5732 BioCyc
Ensembl Genes ENSRNOG00000014619 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019810 ENTREZGENE
  ENSRNOT00000019810.9 UniProtKB/TrEMBL
Gene3D-CATH 1.20.120.1080 UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
InterPro DEAD-like_N UniProtKB/TrEMBL
  DNA/RNA_helicase_C UniProtKB/TrEMBL
  DNA/RNA_helicase_DEAD/DEAH_N UniProtKB/TrEMBL
  DNA/RNA_helicase_DEAH_CS UniProtKB/TrEMBL
  DUF1605 UniProtKB/TrEMBL
  HA2_WH UniProtKB/TrEMBL
  Helicase-assoc_dom UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
NCBI Gene 292007 ENTREZGENE
PANTHER ATP-DEPENDENT RNA HELICASE UniProtKB/TrEMBL
  PRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE PRP16 UniProtKB/TrEMBL
Pfam DEAD UniProtKB/TrEMBL
  DUF1605 UniProtKB/TrEMBL
  HA2 UniProtKB/TrEMBL
  HA2_C UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
PhenoGen Dhx38 PhenoGen
PROSITE DEAH_ATP_HELICASE UniProtKB/TrEMBL
  HELICASE_ATP_BIND_1 UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/TrEMBL
RatGTEx ENSRNOG00000014619 RatGTEx
SMART DEXDc UniProtKB/TrEMBL
  HA2 UniProtKB/TrEMBL
  HELICc UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A6IZ19 ENTREZGENE, UniProtKB/TrEMBL
  D4A321 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-13 Dhx38  DEAH-box helicase 38  Dhx38  DEAH (Asp-Glu-Ala-His) box polypeptide 38  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Dhx38  DEAH (Asp-Glu-Ala-His) box polypeptide 38   Dhx38_predicted  DEAH (Asp-Glu-Ala-His) box polypeptide 38 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Dhx38_predicted  DEAH (Asp-Glu-Ala-His) box polypeptide 38 (predicted)      Symbol and Name status set to approved 70820 APPROVED