Arl13b (ADP-ribosylation factor like GTPase 13B) - Rat Genome Database

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Gene: Arl13b (ADP-ribosylation factor like GTPase 13B) Rattus norvegicus
Analyze
Symbol: Arl13b
Name: ADP-ribosylation factor like GTPase 13B
RGD ID: 1584979
Description: Predicted to enable GTP binding activity and GTPase activity. Predicted to be involved in several processes, including nervous system development; non-motile cilium assembly; and receptor localization to non-motile cilium. Predicted to act upstream of or within dorsal/ventral pattern formation; heart looping; and left/right axis specification. Predicted to be located in axoneme. Predicted to be active in ciliary membrane; motile cilium; and non-motile cilium. Human ortholog(s) of this gene implicated in Joubert syndrome 8. Orthologous to human ARL13B (ADP ribosylation factor like GTPase 13B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ADP-ribosylation factor-like 13B; ADP-ribosylation factor-like protein 13B; LOC304037; similar to ADP-ribosylation factor-like 2-like 1
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
GRCr81113,597,538 - 13,663,681 (-)NCBIGRCr8
mRatBN7.211150,100 - 217,103 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl11150,955 - 217,197 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx118,747,109 - 8,813,116 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0111,540,368 - 1,606,375 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.011645,150 - 711,155 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.071,122,567 - 1,188,209 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl71,122,567 - 1,188,209 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.071,111,829 - 1,181,765 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera13160,428 - 223,413 (-)NCBICelera
Cytogenetic Map11p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
axoneme  (ISO)
ciliary membrane  (IBA,ISO)
cilium  (ISO)
motile cilium  (IBA,ISO)
non-motile cilium  (IBA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Mutations in the cilia gene ARL13B lead to the classical form of Joubert syndrome. Cantagrel V, etal., Am J Hum Genet. 2008 Aug;83(2):170-9. doi: 10.1016/j.ajhg.2008.06.023.
2. The graded response to Sonic Hedgehog depends on cilia architecture. Caspary T, etal., Dev Cell. 2007 May;12(5):767-78.
3. 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.
4. A truncating mutation of Alms1 reduces the number of hypothalamic neuronal cilia in obese mice. Heydet D, etal., Dev Neurobiol. 2013 Jan;73(1):1-13. doi: 10.1002/dneu.22031. Epub 2012 Jul 20.
5. Deletion of ADP Ribosylation Factor-Like GTPase 13B Leads to Kidney Cysts. Li Y, etal., J Am Soc Nephrol. 2016 May 6. pii: ASN.2015091004.
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Comprehensive gene review and curation RGD comprehensive gene curation
11. Lithium chloride modulates chondrocyte primary cilia and inhibits Hedgehog signaling. Thompson CL, etal., FASEB J. 2016 Feb;30(2):716-26. doi: 10.1096/fj.15-274944. Epub 2015 Oct 23.
Additional References at PubMed
PMID:15755804   PMID:20159594   PMID:21209331   PMID:21976698   PMID:22179047   PMID:22554696   PMID:22689656   PMID:23014696   PMID:23153492   PMID:23351563   PMID:23817546   PMID:24336288  
PMID:24421332   PMID:26582389   PMID:27623382   PMID:29487109  


Genomics

Comparative Map Data
Arl13b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81113,597,538 - 13,663,681 (-)NCBIGRCr8
mRatBN7.211150,100 - 217,103 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl11150,955 - 217,197 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx118,747,109 - 8,813,116 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0111,540,368 - 1,606,375 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.011645,150 - 711,155 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.071,122,567 - 1,188,209 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl71,122,567 - 1,188,209 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.071,111,829 - 1,181,765 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera13160,428 - 223,413 (-)NCBICelera
Cytogenetic Map11p12NCBI
ARL13B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38393,980,155 - 94,055,678 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl393,980,139 - 94,055,678 (+)EnsemblGRCh38hg38GRCh38
GRCh37393,698,999 - 93,774,522 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36395,181,672 - 95,256,813 (+)NCBINCBI36Build 36hg18NCBI36
Build 34395,181,671 - 95,256,811NCBI
Celera392,082,477 - 92,158,408 (+)NCBICelera
Cytogenetic Map3q11.1-q11.2NCBI
HuRef391,061,683 - 91,137,139 (+)NCBIHuRef
CHM1_1393,662,067 - 93,737,527 (+)NCBICHM1_1
T2T-CHM13v2.0396,678,283 - 96,754,130 (+)NCBIT2T-CHM13v2.0
Arl13b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391662,613,671 - 62,667,418 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1662,614,048 - 62,667,403 (-)EnsemblGRCm39 Ensembl
GRCm381662,793,308 - 62,847,055 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1662,793,685 - 62,847,040 (-)EnsemblGRCm38mm10GRCm38
MGSCv371662,793,515 - 62,846,866 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361662,735,945 - 62,789,253 (-)NCBIMGSCv36mm8
Celera1663,102,388 - 63,155,607 (-)NCBICelera
Cytogenetic Map16C1.3NCBI
cM Map1636.43NCBI
Arl13b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554073,402,908 - 3,460,105 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554073,402,214 - 3,477,839 (-)NCBIChiLan1.0ChiLan1.0
ARL13B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2291,890,580 - 91,972,922 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1391,895,366 - 91,974,311 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0391,044,332 - 91,121,686 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1397,725,136 - 97,799,932 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl397,725,136 - 97,799,932 (+)Ensemblpanpan1.1panPan2
ARL13B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1331,698,360 - 1,762,846 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl331,698,363 - 1,761,641 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha331,878,107 - 1,942,635 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0331,798,026 - 1,862,534 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl331,798,051 - 1,862,531 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1331,707,188 - 1,771,378 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0331,742,070 - 1,806,566 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0331,967,145 - 2,031,460 (+)NCBIUU_Cfam_GSD_1.0
Arl13b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602155,334,820 - 155,399,714 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936666116,264 - 177,989 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936666115,964 - 179,639 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ARL13B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13165,828,059 - 165,910,961 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113165,829,772 - 165,910,959 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
ARL13B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12286,648,924 - 86,722,006 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2286,651,076 - 86,721,948 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604179,960,967 - 80,033,874 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Arl13b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247896,710,681 - 6,783,667 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247896,710,858 - 6,783,097 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Arl13b
83 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:240
Count of miRNA genes:165
Interacting mature miRNAs:201
Transcripts:ENSRNOT00000074108
Prediction methods:Miranda, 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
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)11121836709Rat
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11135331169Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat

Markers in Region
RH144230  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.211172,117 - 172,238 (+)MAPPERmRatBN7.2
Rnor_6.071,144,265 - 1,144,385NCBIRnor6.0
Rnor_5.071,133,252 - 1,133,372UniSTSRnor5.0
Celera13181,559 - 181,679UniSTS
Cytogenetic Map11q21UniSTS


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 22 14 6 9 6 73 22 39 11
Low 3 21 43 35 10 35 8 10 1 13 2 8
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000074108   ⟹   ENSRNOP00000067810
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl11150,955 - 216,967 (-)Ensembl
Rnor_6.0 Ensembl71,122,567 - 1,188,209 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076063   ⟹   ENSRNOP00000068236
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl11150,955 - 217,197 (-)Ensembl
Rnor_6.0 Ensembl71,122,577 - 1,188,165 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099706   ⟹   ENSRNOP00000084231
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl11152,144 - 216,967 (-)Ensembl
RefSeq Acc Id: NM_001107101   ⟹   NP_001100571
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81113,597,538 - 13,663,546 (-)NCBI
mRatBN7.211150,955 - 216,967 (-)NCBI
Rnor_6.071,122,567 - 1,188,209 (-)NCBI
Rnor_5.071,111,829 - 1,181,765 (-)NCBI
Celera13160,428 - 223,413 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240716   ⟹   XP_006240778
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81113,597,546 - 13,663,681 (-)NCBI
mRatBN7.211154,522 - 217,103 (-)NCBI
Rnor_6.071,126,631 - 1,161,902 (-)NCBI
Rnor_5.071,111,829 - 1,181,765 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088391   ⟹   XP_038944319
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81113,597,546 - 13,663,530 (-)NCBI
mRatBN7.211154,522 - 216,948 (-)NCBI
RefSeq Acc Id: XM_039088392   ⟹   XP_038944320
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81113,597,546 - 13,663,530 (-)NCBI
mRatBN7.211150,963 - 216,947 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001100571   ⟸   NM_001107101
- UniProtKB: M0RDU9 (UniProtKB/TrEMBL),   A6KSZ8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240778   ⟸   XM_006240716
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000068236   ⟸   ENSRNOT00000076063
RefSeq Acc Id: ENSRNOP00000067810   ⟸   ENSRNOT00000074108
RefSeq Acc Id: XP_038944320   ⟸   XM_039088392
- Peptide Label: isoform X3
- UniProtKB: A0A8I5ZXD0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038944319   ⟸   XM_039088391
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000084231   ⟸   ENSRNOT00000099706

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RDU9-F1-model_v2 AlphaFold M0RDU9 1-427 view protein structure

Transcriptome

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

Promoters
RGD ID:13694916
Promoter ID:EPDNEW_R5438
Type:multiple initiation site
Name:Arl13b_1
Description:ADP-ribosylation factor like GTPase 13B
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_6.071,188,162 - 1,188,222EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1584979 AgrOrtholog
BioCyc Gene G2FUF-22338 BioCyc
Ensembl Genes ENSRNOG00000047194 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074108 ENTREZGENE
  ENSRNOT00000074108.4 UniProtKB/TrEMBL
  ENSRNOT00000076063.2 UniProtKB/TrEMBL
  ENSRNOT00000099706.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro P-loop_NTPase UniProtKB/TrEMBL
  Small_GTP-bd_dom UniProtKB/TrEMBL
  Small_GTPase_ARF/SAR UniProtKB/TrEMBL
KEGG Report rno:304037 UniProtKB/TrEMBL
NCBI Gene 304037 ENTREZGENE
PANTHER ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 13B UniProtKB/TrEMBL
  ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 13B UniProtKB/TrEMBL
Pfam Arf UniProtKB/TrEMBL
PhenoGen Arl13b PhenoGen
PRINTS SAR1GTPBP UniProtKB/TrEMBL
PROSITE ARF UniProtKB/TrEMBL
RatGTEx ENSRNOG00000047194 RatGTEx
SMART ARF UniProtKB/TrEMBL
  SAR UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A0A096MJR8_RAT UniProtKB/TrEMBL
  A0A8I5ZXD0 ENTREZGENE, UniProtKB/TrEMBL
  A6KSZ8 ENTREZGENE, UniProtKB/TrEMBL
  M0RDU9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Arl13b  ADP-ribosylation factor like GTPase 13B  Arl13b  ADP-ribosylation factor-like 13B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Arl13b  ADP-ribosylation factor-like 13B  LOC304037  similar to ADP-ribosylation factor-like 2-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC304037  similar to ADP-ribosylation factor-like 2-like 1      Symbol and Name status set to provisional 70820 PROVISIONAL