Cfap36 (cilia and flagella associated protein 36) - Rat Genome Database

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Pathways
Gene: Cfap36 (cilia and flagella associated protein 36) Rattus norvegicus
Analyze
Symbol: Cfap36
Name: cilia and flagella associated protein 36
RGD ID: 1311732
Description: Predicted to be located in ciliary transition zone. Predicted to be active in axoneme and ciliary base. Orthologous to human CFAP36 (cilia and flagella associated protein 36); INTERACTS WITH 4,4'-sulfonyldiphenol; bisphenol A; bisphenol F.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Ccdc104; cilia- and flagella-associated protein 36; coiled-coil domain containing 104; coiled-coil domain-containing protein 104; LOC289859; MGC114472; RGD1311732; similar to hypothetical protein MGC15407
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
GRCr814107,166,932 - 107,192,531 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl14107,166,947 - 107,192,406 (-)EnsemblGRCr8
mRatBN7.214102,966,006 - 102,991,693 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl14102,966,001 - 102,991,555 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx14107,300,956 - 107,326,368 (-)NCBIUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014108,537,722 - 108,563,096 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.014105,010,140 - 105,035,514 (-)NCBIUTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd14107,670,998 - 107,696,371 (-)NCBI
Lyon_Normotensive14106,304,173 - 106,329,581 (-)NCBI
Lyon_Hypertensive14107,850,288 - 107,875,696 (-)NCBI
F344_StmMcwi14106,672,784 - 106,698,190 (-)NCBI
Rnor_6.014113,618,954 - 113,644,874 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14113,618,964 - 113,644,779 (-)EnsemblRnor_6.0 Ensemblrn6Rnor6.0
Rnor_5.014113,294,058 - 113,319,619 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.414110,220,114 - 110,245,524 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera14101,851,515 - 101,876,871 (-)NCBICelera
RGSC_v3.114110,246,470 - 110,271,871 (-)NCBI
Cytogenetic Map14q22NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
axoneme  (IBA)
ciliary base  (IBA,IEA,ISO)
ciliary transition zone  (IEA,ISO)
cilium  (IEA)
cytoplasm  (IEA,ISS)
motile cilium  (IEA)
nucleus  (IEA,ISS)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:26455799  


Genomics

Comparative Map Data
Cfap36
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr814107,166,932 - 107,192,531 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl14107,166,947 - 107,192,406 (-)EnsemblGRCr8
mRatBN7.214102,966,006 - 102,991,693 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl14102,966,001 - 102,991,555 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx14107,300,956 - 107,326,368 (-)NCBIUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014108,537,722 - 108,563,096 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.014105,010,140 - 105,035,514 (-)NCBIUTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd14107,670,998 - 107,696,371 (-)NCBI
Lyon_Normotensive14106,304,173 - 106,329,581 (-)NCBI
Lyon_Hypertensive14107,850,288 - 107,875,696 (-)NCBI
F344_StmMcwi14106,672,784 - 106,698,190 (-)NCBI
Rnor_6.014113,618,954 - 113,644,874 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14113,618,964 - 113,644,779 (-)EnsemblRnor_6.0 Ensemblrn6Rnor6.0
Rnor_5.014113,294,058 - 113,319,619 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.414110,220,114 - 110,245,524 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera14101,851,515 - 101,876,871 (-)NCBICelera
RGSC_v3.114110,246,470 - 110,271,871 (-)NCBI
Cytogenetic Map14q22NCBI
CFAP36
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38255,519,718 - 55,545,079 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl255,519,559 - 55,545,501 (+)EnsemblGRCh38.p14 Ensemblhg38GRCh38
GRCh37255,746,854 - 55,772,215 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36255,600,244 - 55,625,720 (+)NCBIBuild 36Build 36hg18NCBI36
Celera255,587,129 - 55,612,615 (+)NCBICelera
Cytogenetic Map2p16.1NCBI
HuRef255,481,985 - 55,507,473 (+)NCBIHuRef
CHM1_1255,677,331 - 55,702,834 (+)NCBICHM1_1
T2T-CHM13v2.0255,516,894 - 55,542,266 (+)NCBIT2T-CHM13v2.0
Cfap36
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391129,168,912 - 29,197,317 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1129,165,912 - 29,197,443 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381129,218,918 - 29,247,317 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1129,221,532 - 29,247,409 (-)EnsemblGRCm38.p6 Ensemblmm10GRCm38
MGSCv371129,121,536 - 29,147,272 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361129,121,536 - 29,147,272 (-)NCBIMGSCv36mm8
Celera1131,587,363 - 31,614,826 (-)NCBICelera
Cytogenetic Map11A3.3NCBI
cM Map1116.46NCBI
Cfap36
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542427,522,324 - 27,547,437 (-)EnsemblChiLan1.0 Ensembl
ChiLan1.0NW_00495542427,522,324 - 27,547,437 (-)NCBIChiLan1.0ChiLan1.0
CFAP36
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21270,781,642 - 70,807,158 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A70,785,593 - 70,811,070 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A55,675,944 - 55,701,411 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A56,815,462 - 56,840,695 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A56,815,462 - 56,840,695 (+)EnsemblPanPan1.1 EnsemblpanPan2panpan1.1
CFAP36
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11056,373,995 - 56,403,121 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1056,373,996 - 56,403,120 (+)EnsemblCanFam3.1 EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1056,330,418 - 56,359,565 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01057,377,932 - 57,407,087 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1057,377,950 - 57,409,771 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11057,079,732 - 57,108,861 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01057,358,901 - 57,388,035 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01057,649,755 - 57,678,902 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cfap36
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mIctTri1.hap11276,703,483 - 76,734,388 (-)NCBImIctTri1.hap1
HiC_Itri_2NW_02440629226,653,806 - 26,687,213 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364911,884,020 - 1,916,927 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364911,884,071 - 1,915,127 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CFAP36
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl385,709,784 - 85,742,436 (-)EnsemblSscrofa11.1 EnsemblsusScr11Sscrofa11.1
Sscrofa11.1385,712,377 - 85,742,429 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2390,513,265 - 90,543,452 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CFAP36
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mChlSab1.0.hap11455,442,163 - 55,470,604 (+)NCBImChlSab1.0.hap1
Vero_WHO_p1.0NW_02366604560,334,247 - 60,360,723 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
ChlSab1.11451,360,320 - 51,386,815 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1451,360,391 - 51,386,854 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Cfap36
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248336,009,569 - 6,034,550 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
HetGla_female_1.0 EnsemblNW_0046248336,010,926 - 6,034,560 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
Naked mole-rat maternal Ensembl486,047,860 - 86,071,808 (+)Ensembl
Cfap36
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11196,839,106 - 96,864,580 (-)NCBIRrattus_CSIRO_v1Rrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:37
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000005306
Prediction methods:Miranda, Rnahybrid
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
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1462398852107398852Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1474255551109089856Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1474255551109089856Rat

Markers in Region
RH130876  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr814107,167,823 - 107,168,173 (+)Marker Load Pipeline
mRatBN7.214102,966,892 - 102,967,242 (+)MAPPERmRatBN7.2
Rnor_6.014113,619,841 - 113,620,190NCBIRnor6.0
Rnor_5.014113,294,945 - 113,295,294UniSTSRnor5.0
RGSC_v3.414110,221,001 - 110,221,350UniSTSRGSC3.4
Celera14101,852,402 - 101,852,751UniSTS
Cytogenetic Map14q22UniSTS
RH144376  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214102,976,469 - 102,976,587 (+)MAPPERmRatBN7.2
Rnor_6.014113,629,418 - 113,629,535NCBIRnor6.0
Rnor_5.014113,304,522 - 113,304,639UniSTSRnor5.0
RGSC_v3.414110,230,578 - 110,230,695UniSTSRGSC3.4
Celera14101,861,999 - 101,862,116UniSTS
Cytogenetic Map14q22UniSTS
RH140573  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214102,988,314 - 102,988,494 (+)MAPPERmRatBN7.2
Rnor_6.014113,641,619 - 113,641,798NCBIRnor6.0
Rnor_5.014113,316,386 - 113,316,565UniSTSRnor5.0
RGSC_v3.414110,242,364 - 110,242,543UniSTSRGSC3.4
Celera14101,873,711 - 101,873,890UniSTS
Cytogenetic Map14q22UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
pharyngeal arch
renal system
reproductive system
respiratory system
sensory system
visual system
277 156 729 1590 4066 1009 1724 133 872 489 854 156 5386 2589 448 3979 38 1392 741 907 160 158

Sequence


Ensembl Acc Id: ENSRNOT00000005306   ⟹   ENSRNOP00000005306
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl14107,166,947 - 107,192,406 (-)Ensembl
mRatBN7.2 Ensembl14102,966,001 - 102,991,555 (-)Ensembl
Rnor_6.0 Ensembl14113,618,964 - 113,644,779 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000099701   ⟹   ENSRNOP00000081264
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl14107,166,947 - 107,190,682 (-)Ensembl
mRatBN7.2 Ensembl14102,966,001 - 102,991,482 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000118027   ⟹   ENSRNOP00000095466
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl14107,166,947 - 107,192,406 (-)Ensembl
mRatBN7.2 Ensembl14102,966,001 - 102,991,555 (-)Ensembl
RefSeq Acc Id: NM_001024866   ⟹   NP_001020037
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814107,166,937 - 107,192,406 (-)NCBI
mRatBN7.214102,966,006 - 102,991,475 (-)NCBI
Dahl_SR_JrHsd14107,670,998 - 107,696,371 (-)NCBI
Lyon_Normotensive14106,304,173 - 106,329,581 (-)NCBI
Lyon_Hypertensive14107,850,288 - 107,875,696 (-)NCBI
F344_StmMcwi14106,672,784 - 106,698,190 (-)NCBI
Rnor_6.014113,618,954 - 113,644,779 (-)NCBI
Rnor_5.014113,294,058 - 113,319,619 (-)NCBI
RGSC_v3.414110,220,114 - 110,245,524 (-)RGD
Celera14101,851,515 - 101,876,871 (-)RGD
Sequence:
RefSeq Acc Id: XM_006251598   ⟹   XP_006251660
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814107,166,932 - 107,192,514 (-)NCBI
mRatBN7.214102,966,011 - 102,991,556 (-)NCBI
Rnor_6.014113,618,959 - 113,644,874 (-)NCBI
Rnor_5.014113,294,058 - 113,319,619 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091776   ⟹   XP_038947704
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814107,166,932 - 107,192,531 (-)NCBI
mRatBN7.214102,966,006 - 102,991,693 (-)NCBI
RefSeq Acc Id: NP_001020037   ⟸   NM_001024866
- UniProtKB: Q4V8E4 (UniProtKB/Swiss-Prot),   A0ACJ1L2T0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251660   ⟸   XM_006251598
- Peptide Label: isoform X1
- UniProtKB: A0A8I6ATJ2 (UniProtKB/TrEMBL),   A0ACJ1L2T0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000005306   ⟸   ENSRNOT00000005306
RefSeq Acc Id: XP_038947704   ⟸   XM_039091776
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000095466   ⟸   ENSRNOT00000118027
Ensembl Acc Id: ENSRNOP00000081264   ⟸   ENSRNOT00000099701
Protein Domains
BART

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4V8E4-F1-model_v2 AlphaFold Q4V8E4 1-343 view protein structure

Transcriptome

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

Promoters
RGD ID:13699532
Promoter ID:EPDNEW_R10056
Type:initiation region
Name:Cfap36_1
Description:cilia and flagella associated protein 36
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_6.014113,644,838 - 113,644,898EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311732 AgrOrtholog
BioCyc Gene G2FUF-14655 BioCyc
Ensembl Genes ENSRNOG00000003901 Ensembl, ENTREZGENE
  ENSRNOG00055003590 UniProtKB/Swiss-Prot
  ENSRNOG00060008170 UniProtKB/Swiss-Prot
  ENSRNOG00065001393 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000005306 ENTREZGENE
  ENSRNOT00000118027 ENTREZGENE
  ENSRNOT00055005604 UniProtKB/Swiss-Prot
  ENSRNOT00060013528 UniProtKB/Swiss-Prot
  ENSRNOT00065001842 UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.1520.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7455112 IMAGE-MGC_LOAD
InterPro BART_dom UniProtKB/Swiss-Prot
  BART_sf UniProtKB/Swiss-Prot
  CFAP36 UniProtKB/Swiss-Prot
KEGG Report rno:289859 UniProtKB/Swiss-Prot
MGC_CLONE MGC:114472 IMAGE-MGC_LOAD
NCBI Gene 289859 ENTREZGENE
PANTHER CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 36 UniProtKB/Swiss-Prot
  PTHR21532 UniProtKB/Swiss-Prot
Pfam ARL2_Bind_BART UniProtKB/Swiss-Prot
PhenoGen Cfap36 PhenoGen
RatGTEx ENSRNOG00000003901 RatGTEx
  ENSRNOG00055003590 RatGTEx
  ENSRNOG00060008170 RatGTEx
  ENSRNOG00065001393 RatGTEx
UniProt A0A8I5ZR96_RAT UniProtKB/TrEMBL
  A0A8I6ATJ2 ENTREZGENE, UniProtKB/TrEMBL
  A0ACJ1L2T0 ENTREZGENE, UniProtKB/TrEMBL
  CFA36_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-09-16 Cfap36  cilia and flagella associated protein 36  Ccdc104  coiled-coil domain containing 104  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-27 Ccdc104  coiled-coil domain containing 104  RGD1311732  similar to hypothetical protein MGC15407  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1311732  similar to hypothetical protein MGC15407  RGD1311732_predicted  similar to hypothetical protein MGC15407 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1311732_predicted  similar to hypothetical protein MGC15407 (predicted)  LOC289859_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC289859_predicted  similar to hypothetical protein MGC15407 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL