Psmd6 (proteasome 26S subunit, non-ATPase 6) - Rat Genome Database

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Gene: Psmd6 (proteasome 26S subunit, non-ATPase 6) Rattus norvegicus
Analyze
Symbol: Psmd6
Name: proteasome 26S subunit, non-ATPase 6
RGD ID: 735127
Description: Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be part of proteasome regulatory particle. Orthologous to human PSMD6 (proteasome 26S subunit, non-ATPase 6); PARTICIPATES IN ubiquitin/proteasome degradation pathway; INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 26S proteasome non-ATPase regulatory subunit 6; LOC103693817; MGC72968; P44s10; proteasome (prosome, macropain) 26S subunit, non-ATPase, 6; proteasome regulatory particle subunit p44S10; proteasome, 26S, non-ATPase regulatory subunit 6; uncharacterized LOC103693817; Unknown (protein for MGC:72968)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81513,532,675 - 13,542,682 (+)NCBIGRCr8
mRatBN7.21511,102,174 - 11,112,180 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1511,102,180 - 11,205,620 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1513,228,776 - 13,238,756 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01514,180,928 - 14,190,933 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01512,442,072 - 12,452,052 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01512,407,557 - 12,416,153 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1512,407,524 - 12,416,105 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01516,438,829 - 16,447,425 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41512,650,570 - 12,660,487 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11512,650,569 - 12,660,487 (+)NCBI
Celera1511,109,222 - 11,119,073 (+)NCBICelera
Cytogenetic Map15p16NCBI
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
(+)-schisandrin B  (EXP)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
1H-pyrazole  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-bromohexadecanoic acid  (ISO)
afimoxifene  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
C60 fullerene  (EXP)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
carbon nanotube  (ISO)
chromium(6+)  (ISO)
clobetasol  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
elemental selenium  (ISO)
ethanol  (ISO)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
ivermectin  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nefazodone  (EXP)
nickel atom  (ISO)
nimesulide  (EXP)
paracetamol  (EXP)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenacetin  (EXP)
phenylhydrazine  (EXP)
phlorizin  (ISO)
pirinixic acid  (ISO)
propiconazole  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
tetrachloromethane  (EXP,ISO)
thiram  (ISO)
trichloroethene  (ISO)
triphenyl phosphate  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

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. 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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
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:16857966   PMID:17323924   PMID:23376485  


Genomics

Comparative Map Data
Psmd6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81513,532,675 - 13,542,682 (+)NCBIGRCr8
mRatBN7.21511,102,174 - 11,112,180 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1511,102,180 - 11,205,620 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1513,228,776 - 13,238,756 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01514,180,928 - 14,190,933 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01512,442,072 - 12,452,052 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01512,407,557 - 12,416,153 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1512,407,524 - 12,416,105 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01516,438,829 - 16,447,425 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41512,650,570 - 12,660,487 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11512,650,569 - 12,660,487 (+)NCBI
Celera1511,109,222 - 11,119,073 (+)NCBICelera
Cytogenetic Map15p16NCBI
PSMD6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38364,010,551 - 64,024,007 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl364,010,550 - 64,024,010 (-)EnsemblGRCh38hg38GRCh38
GRCh37363,996,227 - 64,009,683 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36363,971,271 - 63,984,160 (-)NCBINCBI36Build 36hg18NCBI36
Celera364,013,003 - 64,025,892 (-)NCBICelera
Cytogenetic Map3p14.1NCBI
HuRef364,093,293 - 64,106,754 (-)NCBIHuRef
CHM1_1363,947,557 - 63,961,018 (-)NCBICHM1_1
T2T-CHM13v2.0364,054,166 - 64,067,621 (-)NCBIT2T-CHM13v2.0
Psmd6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39148,348,818 - 8,357,578 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl148,348,779 - 8,357,589 (+)EnsemblGRCm39 Ensembl
GRCm381414,112,185 - 14,120,945 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1414,112,174 - 14,120,984 (-)EnsemblGRCm38mm10GRCm38
MGSCv371414,944,699 - 14,953,418 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361412,905,452 - 12,914,171 (-)NCBIMGSCv36mm8
Celera149,775,803 - 9,784,442 (-)NCBICelera
Cytogenetic Map14A1NCBI
cM Map147.08NCBI
Psmd6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555171,874,874 - 1,886,480 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555171,874,874 - 1,886,480 (+)NCBIChiLan1.0ChiLan1.0
PSMD6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2263,930,332 - 63,943,839 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1363,935,120 - 63,948,632 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0363,912,457 - 63,925,443 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1365,291,810 - 65,304,861 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl365,291,696 - 65,304,861 (-)Ensemblpanpan1.1panPan2
PSMD6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12027,206,801 - 27,220,059 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2027,131,114 - 27,144,455 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02027,443,760 - 27,457,109 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2027,443,744 - 27,457,071 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12026,940,538 - 26,953,881 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02027,290,971 - 27,304,299 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02027,353,933 - 27,408,837 (+)NCBIUU_Cfam_GSD_1.0
Psmd6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118164,013,905 - 164,024,218 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366372,403,450 - 2,416,917 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366372,403,456 - 2,413,772 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PSMD6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1345,496,362 - 45,527,530 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11345,506,334 - 45,529,481 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21349,972,583 - 49,978,185 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PSMD6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12225,044,616 - 25,056,938 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2225,027,762 - 25,056,813 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041141,757,216 - 141,769,700 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Psmd6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248881,883,445 - 1,903,011 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248881,883,365 - 1,903,011 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Psmd6
46 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:121
Count of miRNA genes:97
Interacting mature miRNAs:105
Transcripts:ENSRNOT00000009249
Prediction methods:Microtar, 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
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15226636822711984Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15105825014481294Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat


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


RefSeq Acc Id: ENSRNOT00000009249   ⟹   ENSRNOP00000009249
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1511,102,180 - 11,205,620 (+)Ensembl
Rnor_6.0 Ensembl1512,407,524 - 12,416,105 (+)Ensembl
RefSeq Acc Id: NM_198730   ⟹   NP_942025
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81513,532,675 - 13,542,682 (+)NCBI
mRatBN7.21511,102,174 - 11,112,180 (+)NCBI
Rnor_6.01512,407,557 - 12,416,094 (+)NCBI
Rnor_5.01516,438,829 - 16,447,425 (+)NCBI
RGSC_v3.41512,650,570 - 12,660,487 (+)RGD
Celera1511,109,222 - 11,119,073 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_942025 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH59159 (Get FASTA)   NCBI Sequence Viewer  
  EDL94116 (Get FASTA)   NCBI Sequence Viewer  
  EDL94117 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000009249.3
RefSeq Acc Id: NP_942025   ⟸   NM_198730
- UniProtKB: Q6PCT9 (UniProtKB/TrEMBL),   F7FGV7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009249   ⟸   ENSRNOT00000009249
Protein Domains
PCI

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6PCT9-F1-model_v2 AlphaFold Q6PCT9 1-389 view protein structure

Transcriptome

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

Promoters
RGD ID:13699582
Promoter ID:EPDNEW_R10106
Type:initiation region
Name:Psmd6_1
Description:proteasome 26S subunit, non-ATPase 6
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_6.01512,407,540 - 12,407,600EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:735127 AgrOrtholog
BioCyc Gene G2FUF-14381 BioCyc
Ensembl Genes ENSRNOG00000006751 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009249.6 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.570 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6887177 IMAGE-MGC_LOAD
InterPro 26S_proteasome_reg_su-Rpn7 UniProtKB/TrEMBL
  PCI_dom UniProtKB/TrEMBL
  Rpn7_N UniProtKB/TrEMBL
  RPN7_PSMD6_C UniProtKB/TrEMBL
  TPR-like_helical_dom UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:289924 UniProtKB/TrEMBL
MGC_CLONE MGC:72968 IMAGE-MGC_LOAD
NCBI Gene 289924 ENTREZGENE
PANTHER PTHR14145 UniProtKB/TrEMBL
  PTHR14145:SF1 UniProtKB/TrEMBL
Pfam PCI UniProtKB/TrEMBL
  RPN7 UniProtKB/TrEMBL
  RPN7_PSMD6_C UniProtKB/TrEMBL
PhenoGen Psmd6 PhenoGen
PROSITE PCI UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006751 RatGTEx
SMART PINT UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
  SSF48452 UniProtKB/TrEMBL
UniProt A6K070_RAT UniProtKB/TrEMBL
  F7FGV7 ENTREZGENE, UniProtKB/TrEMBL
  Q6PCT9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Psmd6  proteasome 26S subunit, non-ATPase 6  LOC103693817  uncharacterized LOC103693817  Data merged from RGD:9476430 737654 PROVISIONAL
2015-08-19 Psmd6  proteasome 26S subunit, non-ATPase 6  Psmd6  proteasome (prosome, macropain) 26S subunit, non-ATPase, 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103693817  uncharacterized LOC103693817      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-30 Psmd6  proteasome (prosome, macropain) 26S subunit, non-ATPase, 6  P44s10  proteasome regulatory particle subunit p44S10  Symbol and Name updated 1299863 APPROVED
2005-07-08 P44s10  proteasome regulatory particle subunit p44S10  MGC72968  Unknown (protein for MGC:72968)  Symbol and Name updated 1299863 APPROVED