Human Gene ARL13B (ENST00000303097.11) from GENCODE V44
  Description: Homo sapiens ADP ribosylation factor like GTPase 13B (ARL13B), transcript variant 2, mRNA. (from RefSeq NM_144996)
RefSeq Summary (NM_001174151): This gene encodes a member of the ADP-ribosylation factor-like family. The encoded protein is a small GTPase that contains both N-terminal and C-terminal guanine nucleotide-binding motifs. This protein is localized in the cilia and plays a role in cilia formation and in maintenance of cilia. Mutations in this gene are the cause of Joubert syndrome 8. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010].
Gencode Transcript: ENST00000303097.11
Gencode Gene: ENSG00000169379.17
Transcript (Including UTRs)
   Position: hg38 chr3:93,980,142-94,055,279 Size: 75,138 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg38 chr3:93,980,424-94,053,263 Size: 72,840 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:93,980,142-94,055,279)mRNA (may differ from genome)Protein (321 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGImyGene2neXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: AR13B_HUMAN
DESCRIPTION: RecName: Full=ADP-ribosylation factor-like protein 13B; AltName: Full=ADP-ribosylation factor-like protein 2-like 1; Short=ARL2-like protein 1;
SUBUNIT: Interacts with PIFO.
DISEASE: Defects in ARL13B are the cause of Joubert syndrome type 8 (JBTS8) [MIM:612291]. JBTS is an autosomal recessive disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermis hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy and renal disease.
SIMILARITY: Belongs to the small GTPase superfamily. Arf family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/ARL13B";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: ARL13B
Diseases sorted by gene-association score: joubert syndrome 8* (1240), arl13b-related joubert syndrome* (500), joubert syndrome 1* (87), alkaptonuria (13), ciliopathy (6), adamantinous craniopharyngioma (5), meckel syndrome 1 (5), orofaciodigital syndrome vi (4), senior-loken syndrome-1 (3), nephronophthisis (2), asphyxiating thoracic dystrophy (1), bardet-biedl syndrome (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.99 RPKM in Nerve - Tibial
Total median expression: 118.31 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -131.00282-0.465 Picture PostScript Text
3' UTR -377.102016-0.187 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR005225 - Small_GTP-bd_dom
IPR024156 - Small_GTPase_ARF
IPR006689 - Small_GTPase_ARF/SAR

Pfam Domains:
PF00025 - ADP-ribosylation factor family

ModBase Predicted Comparative 3D Structure on Q3SXY8
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005515 protein binding
GO:0005525 GTP binding

Biological Process:
GO:0001947 heart looping
GO:0007224 smoothened signaling pathway
GO:0007368 determination of left/right symmetry
GO:0009953 dorsal/ventral pattern formation
GO:0010226 response to lithium ion
GO:0021532 neural tube patterning
GO:0021830 interneuron migration from the subpallium to the cortex
GO:0021943 formation of radial glial scaffolds
GO:0060271 cilium assembly
GO:0070986 left/right axis specification
GO:1905515 non-motile cilium assembly

Cellular Component:
GO:0005622 intracellular
GO:0005886 plasma membrane
GO:0005929 cilium
GO:0005930 axoneme
GO:0016020 membrane
GO:0031514 motile cilium
GO:0042995 cell projection
GO:0060170 ciliary membrane


-  Descriptions from all associated GenBank mRNAs
  BC073842 - Homo sapiens cDNA clone IMAGE:5179066, partial cds.
CR936753 - Homo sapiens mRNA; cDNA DKFZp686L2472 (from clone DKFZp686L2472).
BC094725 - Homo sapiens ADP-ribosylation factor-like 13B, mRNA (cDNA clone MGC:104548 IMAGE:4818884), complete cds.
BC104033 - Homo sapiens cDNA clone IMAGE:40026396, containing frame-shift errors.
BC104034 - Homo sapiens cDNA clone IMAGE:40026397, containing frame-shift errors.
BC104035 - Homo sapiens ADP-ribosylation factor-like 13B, mRNA (cDNA clone MGC:120611 IMAGE:40026398), complete cds.
BC104036 - Homo sapiens ADP-ribosylation factor-like 13B, mRNA (cDNA clone MGC:120612 IMAGE:40026399), complete cds.
AK299284 - Homo sapiens cDNA FLJ60832 complete cds, highly similar to Homo sapiens ADP-ribosylation factor-like 2-like 1 (ARL2L1), transcript variant 1, mRNA.
BC031093 - Homo sapiens cDNA clone IMAGE:5296373, containing frame-shift errors.
AK296994 - Homo sapiens cDNA FLJ55982 complete cds, highly similar to Homo sapiens ADP-ribosylation factor-like 2-like 1 (ARL2L1), transcript variant 1, mRNA.
BC062993 - Homo sapiens cDNA clone IMAGE:5497454, containing frame-shift errors.
BC015439 - Homo sapiens ADP-ribosylation factor-like 13B, mRNA (cDNA clone IMAGE:4421648).
CR936763 - Homo sapiens mRNA; cDNA DKFZp686M2074 (from clone DKFZp686M2074).
AL713789 - Homo sapiens mRNA; cDNA DKFZp761H079 (from clone DKFZp761H079).
CR936756 - Homo sapiens mRNA; cDNA DKFZp686E2075 (from clone DKFZp686E2075).
JD326549 - Sequence 307573 from Patent EP1572962.
EU832840 - Synthetic construct Homo sapiens clone HAIB:100067869; DKFZo008H0433 ADP-ribosylation factor-like 13B protein (ARL13B) gene, encodes complete protein.
GQ129241 - Synthetic construct Homo sapiens clone HAIB:100068531; DKFZo004H0434 ADP-ribosylation factor-like 13B protein (ARL13B) gene, partial cds.
KJ895801 - Synthetic construct Homo sapiens clone ccsbBroadEn_05195 ARL13B gene, encodes complete protein.
KR711493 - Synthetic construct Homo sapiens clone CCSBHm_00024378 ARL13B (ARL13B) mRNA, encodes complete protein.
EU832148 - Synthetic construct Homo sapiens clone HAIB:100067177; DKFZo008F0225 ADP-ribosylation factor-like 13B protein (ARL13B) gene, encodes complete protein.
EU832241 - Synthetic construct Homo sapiens clone HAIB:100067270; DKFZo004F0226 ADP-ribosylation factor-like 13B protein (ARL13B) gene, encodes complete protein.
JD173901 - Sequence 154925 from Patent EP1572962.
JD552629 - Sequence 533653 from Patent EP1572962.
JD370756 - Sequence 351780 from Patent EP1572962.
JD530205 - Sequence 511229 from Patent EP1572962.
JD154204 - Sequence 135228 from Patent EP1572962.
JD436800 - Sequence 417824 from Patent EP1572962.
JD309974 - Sequence 290998 from Patent EP1572962.
JD362319 - Sequence 343343 from Patent EP1572962.
JD553526 - Sequence 534550 from Patent EP1572962.
JD358726 - Sequence 339750 from Patent EP1572962.
JD287674 - Sequence 268698 from Patent EP1572962.
JD271660 - Sequence 252684 from Patent EP1572962.
JD325061 - Sequence 306085 from Patent EP1572962.
JD394351 - Sequence 375375 from Patent EP1572962.
JD562512 - Sequence 543536 from Patent EP1572962.
JD175355 - Sequence 156379 from Patent EP1572962.
JD083886 - Sequence 64910 from Patent EP1572962.
JD314630 - Sequence 295654 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q3SXY8 (Reactome details) participates in the following event(s):

R-HSA-5624953 ARL13B binds INPP5E
R-HSA-5638012 PDE6D dissociates from ARL13B:INPP5E
R-HSA-5624958 ARL13B-mediated ciliary trafficking of INPP5E
R-HSA-5620920 Cargo trafficking to the periciliary membrane
R-HSA-5617833 Cilium Assembly
R-HSA-1852241 Organelle biogenesis and maintenance

-  Other Names for This Gene
  Alternate Gene Symbols: AR13B_HUMAN, ARL2L1, D3DN29, ENST00000303097.1, ENST00000303097.10, ENST00000303097.2, ENST00000303097.3, ENST00000303097.4, ENST00000303097.5, ENST00000303097.6, ENST00000303097.7, ENST00000303097.8, ENST00000303097.9, NM_144996, Q3SXY8, Q504W8, uc003drd.1, uc003drd.2, uc003drd.3, uc003drd.4
UCSC ID: ENST00000303097.11
RefSeq Accession: NM_001174151
Protein: Q3SXY8 (aka AR13B_HUMAN)
CCDS: CCDS2924.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene ARL13B:
joubert (Joubert Syndrome)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.