Cxcr6 (C-X-C motif chemokine receptor 6) - Rat Genome Database

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Gene: Cxcr6 (C-X-C motif chemokine receptor 6) Rattus norvegicus
Analyze
Symbol: Cxcr6
Name: C-X-C motif chemokine receptor 6
RGD ID: 1642118
Description: Predicted to enable chemokine binding activity and chemokine receptor activity. Predicted to be involved in several processes, including calcium-mediated signaling; cell chemotaxis; and positive regulation of cytosolic calcium ion concentration. Predicted to act upstream of or within chemokine-mediated signaling pathway. Predicted to be active in external side of plasma membrane. Orthologous to human CXCR6 (C-X-C motif chemokine receptor 6); PARTICIPATES IN chemokine mediated signaling pathway; cytokine mediated signaling pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C-X-C chemokine receptor type 6; chemokine (C-X-C motif) receptor 6; chemokine receptor CXCR6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88132,311,834 - 132,317,001 (+)NCBIGRCr8
mRatBN7.28123,434,417 - 123,439,568 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,416,325 - 123,439,526 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8129,029,512 - 129,031,301 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08127,228,489 - 127,230,278 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08125,057,730 - 125,059,519 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08132,869,712 - 132,870,766 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,869,712 - 132,870,767 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08132,020,812 - 132,021,866 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48128,569,564 - 128,570,619 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera8122,545,994 - 122,547,048 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

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. Dysregulated expression of MIG/CXCL9, IP-10/CXCL10 and CXCL16 and their receptors in systemic sclerosis. Rabquer BJ, etal., Arthritis Res Ther. 2011 Feb 8;13(1):R18.
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
Additional References at PubMed
PMID:11017100   PMID:17437534  


Genomics

Comparative Map Data
Cxcr6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88132,311,834 - 132,317,001 (+)NCBIGRCr8
mRatBN7.28123,434,417 - 123,439,568 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,416,325 - 123,439,526 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8129,029,512 - 129,031,301 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08127,228,489 - 127,230,278 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08125,057,730 - 125,059,519 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08132,869,712 - 132,870,766 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,869,712 - 132,870,767 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08132,020,812 - 132,021,866 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48128,569,564 - 128,570,619 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera8122,545,994 - 122,547,048 (+)NCBICelera
Cytogenetic Map8q32NCBI
CXCR6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38345,940,915 - 45,948,351 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl345,940,933 - 45,948,351 (+)EnsemblGRCh38hg38GRCh38
GRCh37345,982,407 - 45,989,843 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36345,959,977 - 45,964,849 (+)NCBINCBI36Build 36hg18NCBI36
Build 34345,959,976 - 45,964,849NCBI
Celera345,922,592 - 45,927,464 (+)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef346,029,014 - 46,033,886 (+)NCBIHuRef
CHM1_1345,934,937 - 45,939,809 (+)NCBICHM1_1
T2T-CHM13v2.0345,956,798 - 45,964,234 (+)NCBIT2T-CHM13v2.0
Cxcr6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399123,635,542 - 123,640,819 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9123,635,540 - 123,640,825 (+)EnsemblGRCm39 Ensembl
GRCm389123,806,477 - 123,811,754 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,806,475 - 123,811,760 (+)EnsemblGRCm38mm10GRCm38
MGSCv379123,715,595 - 123,720,872 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369123,655,183 - 123,660,452 (+)NCBIMGSCv36mm8
Celera9124,254,890 - 124,260,158 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map974.57NCBI
Cxcr6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542026,058,170 - 26,059,216 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542026,056,464 - 26,061,992 (-)NCBIChiLan1.0ChiLan1.0
CXCR6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2245,908,856 - 45,913,375 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1345,910,606 - 45,918,049 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0345,848,722 - 45,856,145 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1346,955,051 - 46,962,490 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl346,960,610 - 46,961,638 (+)Ensemblpanpan1.1panPan2
CXCR6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12042,565,251 - 42,569,647 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2042,565,251 - 42,566,276 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2042,480,213 - 42,484,961 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02043,047,331 - 43,052,077 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2043,047,336 - 43,052,021 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12042,288,235 - 42,292,978 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02042,695,451 - 42,700,197 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02042,970,759 - 42,975,506 (-)NCBIUU_Cfam_GSD_1.0
Cxcr6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118200,483,742 - 200,489,756 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493659637,067 - 38,092 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493659631,641 - 44,561 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CXCR6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1329,095,900 - 29,100,667 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11329,095,900 - 29,100,666 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21332,192,310 - 32,197,076 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CXCR6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1227,413,871 - 7,419,229 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl227,414,334 - 7,419,213 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041159,746,814 - 159,751,690 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cxcr6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473074,960,324 - 74,961,337 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cxcr6
19 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:69
Count of miRNA genes:60
Interacting mature miRNAs:63
Transcripts:ENSRNOT00000008294
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
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat

Markers in Region
BQ205885  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28123,439,115 - 123,439,281 (+)MAPPERmRatBN7.2
Rnor_6.08132,871,049 - 132,871,214NCBIRnor6.0
Rnor_5.08132,022,149 - 132,022,314UniSTSRnor5.0
RGSC_v3.48128,570,901 - 128,571,066UniSTSRGSC3.4
Celera8122,547,331 - 122,547,496UniSTS
RH 3.4 Map81333.2UniSTS
Cytogenetic Map8q32UniSTS


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 8 15 1 5
Low 3 14 17 9 4 9 8 8 8 15 11 6 8
Below cutoff 9 14 14 14 3 4 14 16

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001102587 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080642 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide DQ132631 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862603 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862605 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862606 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862607 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862609 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862610 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862611 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862612 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862613 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MN862622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000008294   ⟹   ENSRNOP00000008294
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,434,414 - 123,439,526 (+)Ensembl
Rnor_6.0 Ensembl8132,869,712 - 132,870,767 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000111911   ⟹   ENSRNOP00000079305
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,416,325 - 123,439,383 (+)Ensembl
RefSeq Acc Id: NM_001102587   ⟹   NP_001096057
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88132,315,206 - 132,316,995 (+)NCBI
mRatBN7.28123,437,779 - 123,439,568 (+)NCBI
Rnor_6.08132,869,712 - 132,870,766 (+)NCBI
Rnor_5.08132,020,812 - 132,021,866 (+)NCBI
RGSC_v3.48128,569,564 - 128,570,619 (+)RGD
Celera8122,545,994 - 122,547,048 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039080642   ⟹   XP_038936570
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88132,311,834 - 132,317,001 (+)NCBI
mRatBN7.28123,434,417 - 123,439,568 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001096057   ⟸   NM_001102587
- UniProtKB: A7ISD5 (UniProtKB/TrEMBL),   A0A6M4C4C7 (UniProtKB/TrEMBL),   A0A6M4C4D9 (UniProtKB/TrEMBL),   A0A6M4C4J1 (UniProtKB/TrEMBL),   A0A6M4C4K1 (UniProtKB/TrEMBL),   A0A6M4C534 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008294   ⟸   ENSRNOT00000008294
RefSeq Acc Id: XP_038936570   ⟸   XM_039080642
- Peptide Label: isoform X1
- UniProtKB: F7F415 (UniProtKB/TrEMBL),   A6I4C7 (UniProtKB/TrEMBL),   A0A6M4C4C7 (UniProtKB/TrEMBL),   A0A6M4C4D9 (UniProtKB/TrEMBL),   A0A6M4C4J1 (UniProtKB/TrEMBL),   A0A6M4C4K1 (UniProtKB/TrEMBL),   A0A6M4C534 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000079305   ⟸   ENSRNOT00000111911
Protein Domains
G-protein coupled receptors family 1 profile

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A7ISD5-F1-model_v2 AlphaFold A7ISD5 1-351 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:1642118 AgrOrtholog
BioCyc Gene G2FUF-28604 BioCyc
Ensembl Genes ENSRNOG00000006319 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008294.3 UniProtKB/TrEMBL
  ENSRNOT00000111911.1 UniProtKB/TrEMBL
Gene3D-CATH Rhodopsin 7-helix transmembrane proteins UniProtKB/TrEMBL
InterPro 7TM_GPCR_Rhodpsn UniProtKB/TrEMBL
  Chmkine_rcpt UniProtKB/TrEMBL
  CXC_6_rcpt UniProtKB/TrEMBL
  GPCR_Rhodpsn_supfam UniProtKB/TrEMBL
KEGG Report rno:100124593 UniProtKB/TrEMBL
NCBI Gene 100124593 ENTREZGENE
PANTHER CELL ADHESION MOLECULE UniProtKB/TrEMBL
  PTHR10489:SF705 UniProtKB/TrEMBL
Pfam 7tm_1 UniProtKB/TrEMBL
PhenoGen Cxcr6 PhenoGen
PRINTS CCCHEMOKINER UniProtKB/TrEMBL
  CXCCHMKINER6 UniProtKB/TrEMBL
  GPCRRHODOPSN UniProtKB/TrEMBL
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/TrEMBL
  G_PROTEIN_RECEP_F1_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006319 RatGTEx
Superfamily-SCOP Family A G protein-coupled receptor-like UniProtKB/TrEMBL
UniProt A0A6M4C4C7 ENTREZGENE, UniProtKB/TrEMBL
  A0A6M4C4D9 ENTREZGENE, UniProtKB/TrEMBL
  A0A6M4C4F5_RAT UniProtKB/TrEMBL
  A0A6M4C4G2_RAT UniProtKB/TrEMBL
  A0A6M4C4J1 ENTREZGENE, UniProtKB/TrEMBL
  A0A6M4C4K1 ENTREZGENE, UniProtKB/TrEMBL
  A0A6M4C4N8_RAT UniProtKB/TrEMBL
  A0A6M4C4Q0_RAT UniProtKB/TrEMBL
  A0A6M4C4Q9_RAT UniProtKB/TrEMBL
  A0A6M4C4U0_RAT UniProtKB/TrEMBL
  A0A6M4C527_RAT UniProtKB/TrEMBL
  A0A6M4C531_RAT UniProtKB/TrEMBL
  A0A6M4C534 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZMR2_RAT UniProtKB/TrEMBL
  A6I4C7 ENTREZGENE, UniProtKB/TrEMBL
  A7ISD5 ENTREZGENE, UniProtKB/TrEMBL
  F7F415 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-22 Cxcr6  C-X-C motif chemokine receptor 6  Cxcr6  chemokine (C-X-C motif) receptor 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-16 Cxcr6  chemokine (C-X-C motif) receptor 6  Cxcr6  chemokine receptor CXCR6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-08-31 Cxcr6  chemokine receptor CXCR6      Symbol and Name status set to provisional 70820 PROVISIONAL