Tnfsf13b (TNF superfamily member 13b) - Rat Genome Database

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Gene: Tnfsf13b (TNF superfamily member 13b) Rattus norvegicus
Analyze
Symbol: Tnfsf13b
Name: TNF superfamily member 13b (Ensembl:tumor necrosis factor (ligand) superfamily, member 13b)
RGD ID: 1561519
Description: Predicted to enable receptor ligand activity. Predicted to be involved in B cell differentiation; positive regulation of B cell proliferation; and tumor necrosis factor-mediated signaling pathway. Predicted to act upstream of or within B cell homeostasis; positive regulation of germinal center formation; and positive regulation of lymphocyte activation. Predicted to be located in several cellular components, including focal adhesion; perinuclear region of cytoplasm; and plasma membrane. Predicted to be active in extracellular space. Orthologous to human TNFSF13B (TNF superfamily member 13b); PARTICIPATES IN cytokine mediated signaling pathway; rheumatoid arthritis pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: B-cell-activating factor; BAFF; LOC498666; RGD1561519; similar to NZB B-cell activating factor; Tnlg7a; tumor necrosis factor (ligand) superfamily, member 13b; tumor necrosis factor ligand 7a; tumor necrosis factor ligand superfamily member 13B; tumor necrosis factor superfamily member 13b
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
mRatBN7.21679,462,406 - 79,492,888 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1679,462,402 - 79,492,693 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1684,742,790 - 84,772,905 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01688,195,437 - 88,225,559 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01683,437,519 - 83,467,617 (-)NCBIRnor_WKY
Rnor_6.01685,275,690 - 85,306,419 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1685,275,678 - 85,306,366 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01684,714,936 - 84,745,392 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41684,837,266 - 84,856,103 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1677,261,395 - 77,279,849 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
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
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. Circulating BAFF and CXCL10 levels predict response to pegylated interferon in patients with HBeAg-positive chronic hepatitis B. Khlaiphuengsin A, etal., Asian Pac J Allergy Immunol. 2019 Jan 13. doi: 10.12932/AP-050718-0365.
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14557413   PMID:15240667   PMID:15368291   PMID:15485634   PMID:17499850   PMID:19828625   PMID:22124120   PMID:22391142   PMID:25598291   PMID:26417991   PMID:26646413   PMID:26688104  
PMID:27196292  


Genomics

Comparative Map Data
Tnfsf13b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21679,462,406 - 79,492,888 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1679,462,402 - 79,492,693 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1684,742,790 - 84,772,905 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01688,195,437 - 88,225,559 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01683,437,519 - 83,467,617 (-)NCBIRnor_WKY
Rnor_6.01685,275,690 - 85,306,419 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1685,275,678 - 85,306,366 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01684,714,936 - 84,745,392 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41684,837,266 - 84,856,103 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1677,261,395 - 77,279,849 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
TNFSF13B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3813108,269,629 - 108,308,484 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl13108,251,240 - 108,308,484 (+)EnsemblGRCh38hg38GRCh38
GRCh3713108,921,977 - 108,960,832 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3613107,719,978 - 107,757,366 (+)NCBINCBI36Build 36hg18NCBI36
Build 3413107,719,977 - 107,757,366NCBI
Celera1389,766,721 - 89,804,112 (+)NCBICelera
Cytogenetic Map13q33.3NCBI
HuRef1389,512,942 - 89,552,797 (+)NCBIHuRef
CHM1_113108,891,226 - 108,925,602 (+)NCBICHM1_1
T2T-CHM13v2.013107,496,022 - 107,535,489 (+)NCBIT2T-CHM13v2.0
Tnfsf13b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39810,056,229 - 10,086,000 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl810,056,467 - 10,089,072 (+)EnsemblGRCm39 Ensembl
GRCm38810,006,229 - 10,036,000 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl810,006,467 - 10,039,072 (+)EnsemblGRCm38mm10GRCm38
MGSCv37810,006,633 - 10,036,000 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36810,006,605 - 10,035,972 (+)NCBIMGSCv36mm8
Celera810,182,059 - 10,211,354 (+)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map84.55NCBI
Tnfsf13b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554043,536,868 - 3,569,750 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554043,536,041 - 3,573,242 (-)NCBIChiLan1.0ChiLan1.0
TNFSF13B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.113108,536,617 - 108,575,739 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13108,536,617 - 108,574,296 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01389,399,044 - 89,438,837 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
TNFSF13B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12257,036,307 - 57,069,053 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2257,036,292 - 57,068,320 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2256,808,400 - 56,840,043 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02257,557,150 - 57,589,282 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2257,557,147 - 57,589,110 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12257,158,662 - 57,190,034 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02257,146,582 - 57,177,958 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02257,184,020 - 57,215,438 (+)NCBIUU_Cfam_GSD_1.0
Tnfsf13b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945192,116,853 - 192,164,060 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049364723,789,111 - 3,834,163 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNFSF13B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1175,599,598 - 75,633,041 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11175,599,296 - 75,633,044 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21183,014,191 - 83,048,071 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TNFSF13B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1386,637,988 - 86,675,774 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl386,638,302 - 86,675,772 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604643,297,800 - 43,335,384 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tnfsf13b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247933,629,425 - 3,664,258 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tnfsf13b
191 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:10
Count of miRNA genes:10
Interacting mature miRNAs:10
Transcripts:ENSRNOT00000067511
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat

Markers in Region
RH131199  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21679,462,463 - 79,462,646 (+)MAPPERmRatBN7.2
Rnor_6.01685,275,736 - 85,275,918NCBIRnor6.0
Rnor_5.01684,714,982 - 84,715,164UniSTSRnor5.0
RGSC_v3.41684,825,181 - 84,825,363UniSTSRGSC3.4
Celera1677,249,701 - 77,249,883UniSTS
RH 3.4 Map16769.4UniSTS
Cytogenetic Map16q12.5UniSTS


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 1 2 1 1 5
Low 2 12 49 35 18 35 2 2 5 14 20 6 2
Below cutoff 25 4 4 4 6 9 65 21 19 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067511   ⟹   ENSRNOP00000062950
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1679,462,402 - 79,492,693 (-)Ensembl
Rnor_6.0 Ensembl1685,287,828 - 85,305,782 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076737   ⟹   ENSRNOP00000068118
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1679,462,402 - 79,492,387 (-)Ensembl
Rnor_6.0 Ensembl1685,275,678 - 85,305,839 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089650   ⟹   ENSRNOP00000073755
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1679,462,402 - 79,492,693 (-)Ensembl
Rnor_6.0 Ensembl1685,275,689 - 85,306,366 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105292   ⟹   ENSRNOP00000084627
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1679,462,514 - 79,492,693 (-)Ensembl
RefSeq Acc Id: NM_001109112   ⟹   NP_001102582
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21679,474,242 - 79,492,693 (-)NCBI
Rnor_6.01685,287,516 - 85,306,088 (-)NCBI
Rnor_5.01684,714,936 - 84,745,392 (-)NCBI
RGSC_v3.41684,837,266 - 84,856,103 (-)RGD
Celera1677,261,395 - 77,279,849 (-)RGD
Sequence:
RefSeq Acc Id: XM_006253480   ⟹   XP_006253542
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21679,462,406 - 79,492,772 (-)NCBI
Rnor_6.01685,275,690 - 85,306,419 (-)NCBI
Rnor_5.01684,714,936 - 84,745,392 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253481   ⟹   XP_006253543
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21679,462,406 - 79,492,888 (-)NCBI
Rnor_6.01685,275,690 - 85,306,419 (-)NCBI
Rnor_5.01684,714,936 - 84,745,392 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253482   ⟹   XP_006253544
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21679,462,406 - 79,492,886 (-)NCBI
Rnor_6.01685,275,690 - 85,306,418 (-)NCBI
Rnor_5.01684,714,936 - 84,745,392 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253483   ⟹   XP_006253545
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21679,462,406 - 79,492,759 (-)NCBI
Rnor_6.01685,275,690 - 85,306,417 (-)NCBI
Rnor_5.01684,714,936 - 84,745,392 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001102582   ⟸   NM_001109112
- Sequence:
RefSeq Acc Id: XP_006253543   ⟸   XM_006253481
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006253542   ⟸   XM_006253480
- Peptide Label: isoform X1
- UniProtKB: A0A096MJG3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253544   ⟸   XM_006253482
- Peptide Label: isoform X3
- UniProtKB: A0A0U5JXV5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253545   ⟸   XM_006253483
- Peptide Label: isoform X4
- UniProtKB: A0A0G2K6C2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000062950   ⟸   ENSRNOT00000067511
RefSeq Acc Id: ENSRNOP00000073755   ⟸   ENSRNOT00000089650
RefSeq Acc Id: ENSRNOP00000068118   ⟸   ENSRNOT00000076737
RefSeq Acc Id: ENSRNOP00000084627   ⟸   ENSRNOT00000105292
Protein Domains
TNF_2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A096MJG3-F1-model_v2 AlphaFold A0A096MJG3 1-325 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:1561519 AgrOrtholog
BioCyc Gene G2FUF-10616 BioCyc
Ensembl Genes ENSRNOG00000014464 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000062950 ENTREZGENE
  ENSRNOP00000062950.2 UniProtKB/TrEMBL
  ENSRNOP00000068118 ENTREZGENE
  ENSRNOP00000068118.2 UniProtKB/TrEMBL
  ENSRNOP00000073755 ENTREZGENE
  ENSRNOP00000073755.1 UniProtKB/TrEMBL
  ENSRNOP00000084627 ENTREZGENE
  ENSRNOP00000084627.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067511 ENTREZGENE
  ENSRNOT00000067511.3 UniProtKB/TrEMBL
  ENSRNOT00000076737 ENTREZGENE
  ENSRNOT00000076737.3 UniProtKB/TrEMBL
  ENSRNOT00000089650 ENTREZGENE
  ENSRNOT00000089650.2 UniProtKB/TrEMBL
  ENSRNOT00000105292 ENTREZGENE
  ENSRNOT00000105292.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.40 UniProtKB/TrEMBL
InterPro TNF_dom UniProtKB/TrEMBL
  Tumour_necrosis_fac-like_dom UniProtKB/TrEMBL
KEGG Report rno:498666 UniProtKB/TrEMBL
NCBI Gene 498666 ENTREZGENE
Pfam TNF UniProtKB/TrEMBL
PhenoGen Tnfsf13b PhenoGen
PROSITE TNF_2 UniProtKB/TrEMBL
Superfamily-SCOP SSF49842 UniProtKB/TrEMBL
UniProt A0A096MJG3 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K6C2 ENTREZGENE, UniProtKB/TrEMBL
  A0A0U5JXV5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZFD8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-21 Tnfsf13b  TNF superfamily member 13b  Tnfsf13b  tumor necrosis factor superfamily member 13b  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-25 Tnfsf13b  tumor necrosis factor superfamily member 13b  Tnfsf13b  tumor necrosis factor (ligand) superfamily, member 13b  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 Tnfsf13b  tumor necrosis factor (ligand) superfamily, member 13b  RGD1561519_predicted  similar to NZB B-cell activating factor (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561519_predicted  similar to NZB B-cell activating factor (predicted)  LOC498666  similar to NZB B-cell activating factor  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498666  similar to NZB B-cell activating factor      Symbol and Name status set to provisional 70820 PROVISIONAL