Slc18b1 (solute carrier family 18 member B1) - Rat Genome Database

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Gene: Slc18b1 (solute carrier family 18 member B1) Rattus norvegicus
Analyze
Symbol: Slc18b1
Name: solute carrier family 18 member B1
RGD ID: 1306962
Description: Predicted to enable monoamine:proton antiporter activity and polyamine:proton antiporter activity. Predicted to be involved in serotonin uptake; spermidine transport; and spermine transport. Located in synaptic vesicle membrane. Orthologous to human SLC18B1 (solute carrier family 18 member B1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC309570; MFS-type transporter SLC18B1; RGD1306962; similar to dJ55C23.6 gene product; solute carrier family 18, subfamily B, member 1; vesicular polyamine transporter; VPAT
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
GRCr8123,447,462 - 23,490,043 (-)NCBIGRCr8
mRatBN7.2121,628,235 - 21,670,807 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl121,628,237 - 21,670,684 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx121,407,457 - 21,449,845 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0127,407,521 - 27,449,909 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0121,604,805 - 21,647,175 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0122,705,980 - 22,748,571 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,705,916 - 22,748,422 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0124,178,238 - 24,220,850 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4122,201,424 - 22,255,955 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1122,205,186 - 22,268,291 (-)NCBI
Celera120,372,342 - 20,414,026 (-)NCBICelera
Cytogenetic Map1p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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. Identification of a mammalian vesicular polyamine transporter. Hiasa M, etal., Sci Rep. 2014 Oct 30;4:6836. doi: 10.1038/srep06836.
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:28082679  


Genomics

Comparative Map Data
Slc18b1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8123,447,462 - 23,490,043 (-)NCBIGRCr8
mRatBN7.2121,628,235 - 21,670,807 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl121,628,237 - 21,670,684 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx121,407,457 - 21,449,845 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0127,407,521 - 27,449,909 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0121,604,805 - 21,647,175 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0122,705,980 - 22,748,571 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,705,916 - 22,748,422 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0124,178,238 - 24,220,850 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4122,201,424 - 22,255,955 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1122,205,186 - 22,268,291 (-)NCBI
Celera120,372,342 - 20,414,026 (-)NCBICelera
Cytogenetic Map1p12NCBI
SLC18B1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386132,769,370 - 132,798,637 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6132,769,370 - 132,813,339 (-)EnsemblGRCh38hg38GRCh38
GRCh376133,090,509 - 133,119,776 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366133,132,200 - 133,161,440 (-)NCBINCBI36Build 36hg18NCBI36
Build 346133,132,201 - 133,161,384NCBI
Celera6133,837,336 - 133,866,574 (-)NCBICelera
Cytogenetic Map6q23.2NCBI
HuRef6130,665,507 - 130,694,782 (-)NCBIHuRef
CHM1_16133,354,206 - 133,383,446 (-)NCBICHM1_1
T2T-CHM13v2.06133,964,359 - 133,993,657 (-)NCBIT2T-CHM13v2.0
Slc18b1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391023,672,876 - 23,703,867 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1023,672,884 - 23,703,866 (+)EnsemblGRCm39 Ensembl
GRCm381023,796,859 - 23,827,969 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1023,796,986 - 23,827,968 (+)EnsemblGRCm38mm10GRCm38
MGSCv371023,516,792 - 23,547,774 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361023,486,402 - 23,517,384 (+)NCBIMGSCv36mm8
Celera1024,728,038 - 24,759,177 (+)NCBICelera
Cytogenetic Map10A4NCBI
cM Map1011.12NCBI
Slc18b1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543613,286,520 - 13,316,174 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543613,286,811 - 13,316,037 (-)NCBIChiLan1.0ChiLan1.0
SLC18B1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25152,753,456 - 152,783,132 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16150,660,511 - 150,690,216 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06130,547,192 - 130,576,466 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16134,654,796 - 134,683,049 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6134,654,489 - 134,683,182 (-)Ensemblpanpan1.1panPan2
SLC18B1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1125,797,992 - 25,821,943 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl125,798,306 - 25,836,146 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha126,808,278 - 26,832,025 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0125,948,952 - 25,972,866 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl125,948,956 - 25,972,872 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1125,828,739 - 25,852,699 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0125,719,413 - 25,743,371 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0126,021,294 - 26,045,267 (-)NCBIUU_Cfam_GSD_1.0
Slc18b1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946121,007,460 - 121,040,072 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936560786,676 - 819,319 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936560790,063 - 819,275 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC18B1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl130,923,765 - 30,954,260 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1130,923,716 - 30,956,898 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2134,453,119 - 34,474,663 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC18B1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11340,721,153 - 40,750,423 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1340,721,186 - 40,750,526 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604012,908,323 - 12,937,609 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc18b1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247536,915,376 - 6,934,015 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247536,916,124 - 6,933,953 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc18b1
501 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:45
Count of miRNA genes:42
Interacting mature miRNAs:44
Transcripts:ENSRNOT00000021944
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
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)150910843284926Rat
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124744506Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)150910843284926Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)11148131282174945Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1439328949393289Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1132356093Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11620621049268520Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)11543162149361612Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128736750Rat
5684999Bss102Bone structure and strength QTL 1025.57e-07tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)11543162149361612Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)11148148232355910Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)1985600154856001Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1132356093Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1592587724697545Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12078482865784828Rat
1558642Prcr2Prostate cancer resistance QTL 24.3prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)12076315844095856Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1224439043433040Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)150910843284926Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11099206555992065Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)11933357156983283Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1132356093Rat

Markers in Region
RH134563  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2121,628,359 - 21,628,563 (+)MAPPERmRatBN7.2
Rnor_6.0122,706,105 - 22,706,308NCBIRnor6.0
Rnor_5.0124,178,363 - 24,178,566UniSTSRnor5.0
RGSC_v3.4122,201,552 - 22,201,755UniSTSRGSC3.4
Celera120,372,467 - 20,372,670UniSTS
RH 3.4 Map1213.7UniSTS
Cytogenetic Map1p12UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000021944   ⟹   ENSRNOP00000021944
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl121,628,237 - 21,670,684 (-)Ensembl
Rnor_6.0 Ensembl122,705,916 - 22,748,422 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000118149   ⟹   ENSRNOP00000092228
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl121,628,255 - 21,670,684 (-)Ensembl
RefSeq Acc Id: NM_001400828   ⟹   NP_001387757
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8123,447,462 - 23,489,918 (-)NCBI
mRatBN7.2121,628,235 - 21,670,694 (-)NCBI
RefSeq Acc Id: XR_010053972
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8123,448,842 - 23,490,043 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001387757 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D4A9K4 (Get FASTA)   NCBI Sequence Viewer  
  EDL87744 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000021944.7
  ENSRNOP00000092228.1
Ensembl Acc Id: ENSRNOP00000021944   ⟸   ENSRNOT00000021944
Ensembl Acc Id: ENSRNOP00000092228   ⟸   ENSRNOT00000118149
RefSeq Acc Id: NP_001387757   ⟸   NM_001400828
- UniProtKB: D4A9K4 (UniProtKB/Swiss-Prot)
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A9K4-F1-model_v2 AlphaFold D4A9K4 1-455 view protein structure

Transcriptome

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

Promoters
RGD ID:13689551
Promoter ID:EPDNEW_R57
Type:initiation region
Name:Slc18b1_1
Description:solute carrier family 18 member B1
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_6.0122,748,401 - 22,748,461EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306962 AgrOrtholog
BioCyc Gene G2FUF-62075 BioCyc
Ensembl Genes ENSRNOG00000016371 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021944.8 UniProtKB/Swiss-Prot
  ENSRNOT00000118149.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1250.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Major_facilitator_SF UniProtKB/TrEMBL
  MFS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MFS_dom UniProtKB/Swiss-Prot
  MFS_trans_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MFS_Vesicular_Transporter UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 309570 ENTREZGENE
PANTHER MFS-TYPE TRANSPORTER SLC18B1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR23506 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam MFS_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc18b1 PhenoGen
PROSITE MFS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016371 RatGTEx
Superfamily-SCOP MFS general substrate transporter UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6GK33_RAT UniProtKB/TrEMBL
  D4A9K4 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-25 Slc18b1  solute carrier family 18 member B1  Slc18b1  solute carrier family 18, subfamily B, member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-10 Slc18b1  solute carrier family 18, subfamily B, member 1  RGD1306962  similar to dJ55C23.6 gene product  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1306962  similar to dJ55C23.6 gene product   RGD1306962_predicted  similar to dJ55C23.6 gene product (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1306962_predicted  similar to dJ55C23.6 gene product (predicted)  LOC309570_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC309570_predicted  similar to dJ55C23.6 gene product (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL