Shisa4 (shisa family member 4) - Rat Genome Database

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Gene: Shisa4 (shisa family member 4) Rattus norvegicus
Analyze
Symbol: Shisa4
Name: shisa family member 4
RGD ID: 1312041
Description: Predicted to be located in membrane. Orthologous to human SHISA4 (shisa family member 4); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC360848; Prmp; proline rich membrane protein; protein shisa-4; RGD1312041; shisa homolog 4; shisa homolog 4 (Xenopus laevis); similar to scotin; Tmem58; transmembrane protein 58
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
GRCr81349,351,518 - 49,355,599 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1349,351,518 - 49,356,227 (-)EnsemblGRCr8
mRatBN7.21346,799,735 - 46,803,816 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1346,799,772 - 46,803,998 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1349,408,140 - 49,411,393 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01350,696,215 - 50,699,469 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01347,960,188 - 47,963,410 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01352,193,989 - 52,197,205 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1352,193,989 - 52,197,205 (-)Ensemblrn6Rnor6.0
Rnor_5.01357,244,749 - 57,248,270 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41348,368,910 - 48,372,126 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1347,120,498 - 47,123,714 (-)NCBICelera
RGSC_v3.11348,382,485 - 48,386,271 (-)NCBI
Cytogenetic Map13q13NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:17005852  


Genomics

Comparative Map Data
Shisa4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81349,351,518 - 49,355,599 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1349,351,518 - 49,356,227 (-)EnsemblGRCr8
mRatBN7.21346,799,735 - 46,803,816 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1346,799,772 - 46,803,998 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1349,408,140 - 49,411,393 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01350,696,215 - 50,699,469 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01347,960,188 - 47,963,410 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01352,193,989 - 52,197,205 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1352,193,989 - 52,197,205 (-)Ensemblrn6Rnor6.0
Rnor_5.01357,244,749 - 57,248,270 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41348,368,910 - 48,372,126 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1347,120,498 - 47,123,714 (-)NCBICelera
RGSC_v3.11348,382,485 - 48,386,271 (-)NCBI
Cytogenetic Map13q13NCBI
SHISA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381201,888,677 - 201,892,587 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1201,888,679 - 201,892,587 (+)Ensemblhg38GRCh38
GRCh371201,857,805 - 201,861,715 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361200,124,655 - 200,128,050 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341198,589,688 - 198,593,083NCBI
Celera1174,981,622 - 174,985,540 (+)NCBICelera
Cytogenetic Map1q32.1NCBI
HuRef1173,023,711 - 173,027,629 (+)NCBIHuRef
CHM1_11203,280,041 - 203,283,959 (+)NCBICHM1_1
T2T-CHM13v2.01201,146,432 - 201,150,342 (+)NCBIT2T-CHM13v2.0
Shisa4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391135,298,578 - 135,302,812 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1135,298,795 - 135,302,975 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381135,371,057 - 135,375,298 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1135,371,057 - 135,375,237 (-)Ensemblmm10GRCm38
MGSCv371137,268,033 - 137,271,640 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361137,187,867 - 137,191,474 (-)NCBIMGSCv36mm8
Celera1137,999,630 - 138,003,194 (-)NCBICelera
Cytogenetic Map1E4NCBI
cM Map158.58NCBI
Shisa4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540637,957,326 - 37,962,468 (+)Ensembl
ChiLan1.0NW_00495540637,959,156 - 37,961,972 (+)NCBIChiLan1.0ChiLan1.0
SHISA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2147,490,302 - 47,493,931 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1147,455,003 - 47,458,630 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01177,485,825 - 177,489,458 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11181,787,839 - 181,791,472 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1181,787,839 - 181,791,472 (+)EnsemblpanPan2panpan1.1
SHISA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.171,064,833 - 1,066,591 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha71,107,595 - 1,118,535 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.071,063,795 - 1,074,775 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl71,067,011 - 1,075,299 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.171,051,763 - 1,062,699 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.071,168,297 - 1,170,899 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.071,183,975 - 1,194,940 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Shisa4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934473,365,516 - 73,369,475 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365672,600,556 - 2,604,180 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365672,600,309 - 2,604,201 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHISA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1024,158,688 - 24,162,063 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11024,158,648 - 24,161,504 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SHISA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12527,517,915 - 27,521,536 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2527,518,369 - 27,521,219 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605528,300,411 - 28,304,194 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Shisa4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248078,881,767 - 8,888,534 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248078,884,641 - 8,888,164 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Shisa4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v110346,322 - 350,544 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Shisa4
25 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:385
Count of miRNA genes:195
Interacting mature miRNAs:239
Transcripts:ENSRNOT00000009712
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134863963493639634Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133721624190057603Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)131186625456866254Rat
6893344Cm79Cardiac mass QTL 791.50.04heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)134627292251216694Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1338975045103588154Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133992469384924693Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134874981487285480Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132485392569853925Rat
4889861Pur29Proteinuria QTL 2913.80.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133996821183286298Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131238432057384320Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131746828262468282Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131238432057384320Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)13742179187286911Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)132433543255601132Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133708798382087983Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13600200888706694Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)134098358585983585Rat
724564Uae11Urinary albumin excretion QTL 115.7urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)134735425894285672Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1321120177109350286Rat
4145117Mcs27Mammary carcinoma susceptibility QTL 270.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)134599007750392939Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132624480871244808Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133379409678794096Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133992469384924693Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133483494779834947Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1311081740103588154Rat
2301962Cm72Cardiac mass QTL 724.12heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)133379409660914504Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13600200888706694Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133981472684814726Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133996821184968211Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132624480871244808Rat
12879472Bp399Blood pressure QTL 399arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134778041850392939Rat
11530006Niddm72Non-insulin dependent diabetes mellitus QTL 720.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)133828629883286298Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131103588154Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)131771133662711336Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)131186625456866254Rat

Markers in Region
RH143294  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21346,799,760 - 46,799,984 (+)MAPPERmRatBN7.2
Rnor_6.01352,193,263 - 52,193,486NCBIRnor6.0
Rnor_5.01357,244,023 - 57,244,246UniSTSRnor5.0
RGSC_v3.41348,368,184 - 48,368,407UniSTSRGSC3.4
Celera1347,119,772 - 47,119,995UniSTS
RH 3.4 Map13197.2UniSTS
Cytogenetic Map13q13UniSTS


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 90 89 58 54 58 6 317 154 11 139 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000009712   ⟹   ENSRNOP00000009712
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1349,351,812 - 49,356,227 (-)Ensembl
mRatBN7.2 Ensembl1346,800,023 - 46,803,542 (-)Ensembl
Rnor_6.0 Ensembl1352,193,989 - 52,197,205 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000106579   ⟹   ENSRNOP00000079579
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1349,351,518 - 49,355,599 (-)Ensembl
mRatBN7.2 Ensembl1346,799,772 - 46,803,998 (-)Ensembl
RefSeq Acc Id: NM_001077826   ⟹   NP_001071294
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81349,351,518 - 49,355,599 (-)NCBI
mRatBN7.21346,799,735 - 46,803,816 (-)NCBI
Rnor_6.01352,193,989 - 52,197,205 (-)NCBI
Rnor_5.01357,244,749 - 57,248,270 (-)NCBI
RGSC_v3.41348,368,910 - 48,372,126 (-)RGD
Celera1347,120,498 - 47,123,714 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001071294 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI58558 (Get FASTA)   NCBI Sequence Viewer  
  ABK41474 (Get FASTA)   NCBI Sequence Viewer  
  EDM09697 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000009712.7
  ENSRNOP00000079579
  ENSRNOP00000079579.1
RefSeq Acc Id: NP_001071294   ⟸   NM_001077826
- Peptide Label: precursor
- UniProtKB: A0MV40 (UniProtKB/TrEMBL),   A6ICF0 (UniProtKB/TrEMBL),   F7F9R9 (UniProtKB/TrEMBL),   A0A8I5ZNJ8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000009712   ⟸   ENSRNOT00000009712
Ensembl Acc Id: ENSRNOP00000079579   ⟸   ENSRNOT00000106579
Protein Domains
Shisa N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0MV40-F1-model_v2 AlphaFold A0MV40 1-197 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:1312041 AgrOrtholog
BioCyc Gene G2FUF-18207 BioCyc
Ensembl Genes ENSRNOG00000007369 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009712.8 UniProtKB/TrEMBL
  ENSRNOT00000106579 ENTREZGENE
  ENSRNOT00000106579.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7313337 IMAGE-MGC_LOAD
InterPro Shisa UniProtKB/TrEMBL
  Shisa_N UniProtKB/TrEMBL
KEGG Report rno:360848 UniProtKB/TrEMBL
MGC_CLONE MGC:187232 IMAGE-MGC_LOAD
NCBI Gene 360848 ENTREZGENE
PANTHER PROTEIN SHISA-4 UniProtKB/TrEMBL
  PTHR31395 UniProtKB/TrEMBL
Pfam Shisa UniProtKB/TrEMBL
PhenoGen Shisa4 PhenoGen
RatGTEx ENSRNOG00000007369 RatGTEx
UniProt A0A8I5ZNJ8 ENTREZGENE, UniProtKB/TrEMBL
  A0MV40 ENTREZGENE, UniProtKB/TrEMBL
  A6ICF0 ENTREZGENE
  F7F9R9 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A6ICF0 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-07 Shisa4  shisa family member 4  Shisa4  shisa homolog 4 (Xenopus laevis)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-02 Shisa4  shisa homolog 4 (Xenopus laevis)  Tmem58  transmembrane protein 58   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Tmem58  transmembrane protein 58   Tmem58_predicted  transmembrane protein 58 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Tmem58_predicted  transmembrane protein 58 (predicted)  RGD1312041_predicted  similar to scotin (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1312041_predicted  similar to scotin (predicted)  LOC360848_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC360848_predicted  similar to scotin (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL