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ARL13B ADP ribosylation factor like GTPase 13B [ Homo sapiens (human) ]

Gene ID: 200894, updated on 7-Apr-2024

Summary

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Official Symbol
ARL13Bprovided by HGNC
Official Full Name
ADP ribosylation factor like GTPase 13Bprovided by HGNC
Primary source
HGNC:HGNC:25419
See related
Ensembl:ENSG00000169379 MIM:608922; AllianceGenome:HGNC:25419
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
JBTS8; ARL2L1
Summary
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]
Expression
Ubiquitous expression in thyroid (RPKM 5.4), lung (RPKM 4.2) and 25 other tissues See more
Orthologs
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Genomic context

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See ARL13B in Genome Data Viewer
Location:
3q11.1-q11.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (93980155..94055678)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (96678283..96754130)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (93698999..93774522)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene protein S Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 17 Neighboring gene Sharpr-MPRA regulatory region 12381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20123 Neighboring gene RNA, U6 small nuclear 511, pseudogene Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 7 Neighboring gene syntaxin 19 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20124 Neighboring gene dihydrofolate reductase 2 Neighboring gene NOP2/Sun RNA methyltransferase 3 Neighboring gene RBBP4 pseudogene 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Axoneme polyglutamylation regulated by Joubert syndrome protein ARL13B controls ciliary targeting of signaling molecules. He K, et al. Nat Commun, 2018 Aug 17. PMID 30120249, Free PMC Article
  2. A novel homozygous ARL13B variant in patients with Joubert syndrome impairs its guanine nucleotide-exchange factor activity. Rafiullah R, et al. Eur J Hum Genet, 2017 Dec. PMID 29255182, Free PMC Article
  3. Palmitoylation of the ciliary GTPase ARL13b is necessary for its stability and its role in cilia formation. Roy K, et al. J Biol Chem, 2017 Oct 27. PMID 28848045, Free PMC Article
  4. Arl13b Promotes Gastric Tumorigenesis by Regulating Smo Trafficking and Activation of the Hedgehog Signaling Pathway. Shao J, et al. Cancer Res, 2017 Aug 1. PMID 28611043, Free PMC Article
  5. Reduced primary cilia length and altered Arl13b expression are associated with deregulated chondrocyte Hedgehog signaling in alkaptonuria. Thorpe SD, et al. J Cell Physiol, 2017 Sep. PMID 28158906, Free PMC Article

See all (57) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Increasing Ciliary ARL13B Expression Drives Active and Inhibitor-Resistant Smoothened and GLI into Glioma Primary Cilia.
    Title: Increasing Ciliary ARL13B Expression Drives Active and Inhibitor-Resistant Smoothened and GLI into Glioma Primary Cilia.
  2. Rab8 and TNPO1 are ciliary transport adaptors for GTPase Arl13b by interacting with its RVEP motif containing ciliary targeting sequence.
    Title: Rab8 and TNPO1 are ciliary transport adaptors for GTPase Arl13b by interacting with its RVEP motif containing ciliary targeting sequence.
  3. TMEM67 is required for the gating function of the transition zone that controls entry of membrane-associated proteins ARL13B and INPP5E into primary cilia.
    Title: TMEM67 is required for the gating function of the transition zone that controls entry of membrane-associated proteins ARL13B and INPP5E into primary cilia.
  4. ARL3 activation requires the co-GEF BART and effector-mediated turnover.
    Title: ARL3 activation requires the co-GEF BART and effector-mediated turnover.
  5. Interaction of INPP5E with ARL13B is essential for its ciliary membrane retention but dispensable for its ciliary entry.
    Title: Interaction of INPP5E with ARL13B is essential for its ciliary membrane retention but dispensable for its ciliary entry.
  6. RAB family small GTP binding protein RAB 23 (Rab23) and ADP-ribosylation factor-like 13B (Arl13b) have been implicated in ciliopathy-associated human diseases and could regulate hedgehog proteins (Hh) signalling cascade in multifaceted manners [Review].
    Title: Small GTPases in hedgehog signalling: emerging insights into the disease mechanisms of Rab23-mediated and Arl13b-mediated ciliopathies.
  7. Authors propose a so far unknown function of ARL13B in anchoring ciliary membrane proteins to the axoneme through the direct interaction of its G-domain with tubulin.
    Title: The Joubert syndrome protein ARL13B binds tubulin to maintain uniform distribution of proteins along the ciliary membrane.
  8. Formation of primary cilia is downregulated in TULP3-knockout (KO) RPE1 cells. ARL13B and INPP5E fail to localize to primary cilia in TULP3-KO cells.
    Title: TULP3 is required for localization of membrane-associated proteins ARL13B and INPP5E to primary cilia.
  9. Joubert syndrome protein ARL13B controls axoneme polyglutamylation.
    Title: Axoneme polyglutamylation regulated by Joubert syndrome protein ARL13B controls ciliary targeting of signaling molecules.
  10. A novel homozygous loss of function mutation in ARL13B was identified in patients with Joubert syndrome
    Title: A novel homozygous ARL13B variant in patients with Joubert syndrome impairs its guanine nucleotide-exchange factor activity.
Submit: New GeneRIF Correction See all GeneRIFs (28)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Joubert syndrome 8
MedGen: C2676771 OMIM: 612291 GeneReviews: Joubert Syndrome
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC120611, MGC120612, DKFZp761H079, DKFZp686E2075, DKFZp686L2472, DKFZp686M2074

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTP binding IEA
Inferred from Electronic Annotation
more info
  
enables GTPase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cilium assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in dorsal/ventral pattern formation IEA
Inferred from Electronic Annotation
more info
  
involved_in formation of radial glial scaffolds ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in heart looping IEA
Inferred from Electronic Annotation
more info
  
involved_in interneuron migration from the subpallium to the cortex ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in left/right axis specification IEA
Inferred from Electronic Annotation
more info
  
involved_in neural tube patterning ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in non-motile cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in non-motile cilium assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in receptor localization to non-motile cilium IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in smoothened signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in axoneme IEA
Inferred from Electronic Annotation
more info
  
is_active_in ciliary membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in ciliary membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cilium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cilium ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cilium TAS
Traceable Author Statement
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in motile cilium IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in non-motile cilium IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
ADP-ribosylation factor-like protein 13B
Names
ADP-ribosylation factor-like 13B
ADP-ribosylation factor-like 2-like 1
ARL2-like protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_017076.1 RefSeqGene

    Range
    5017..80540
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001174150.2 → NP_001167621.1  ADP-ribosylation factor-like protein 13B isoform 1

    See identical proteins and their annotated locations for NP_001167621.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 3' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AA775026, BC062993, BC104036
    Consensus CDS
    CCDS2925.1
    UniProtKB/Swiss-Prot
    D3DN29, G3V1S8, Q3SXY8, Q504W8, Q8TCL5
    UniProtKB/TrEMBL
    B4DLH1
    Related
    ENSP00000377769.3, ENST00000394222.8
    Conserved Domains (2) summary
    cd04161
    Location:23 → 189
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    cl26557
    Location:198 → 259
    RNase_E_G; Ribonuclease E/G family

  2. NM_001174151.2 → NP_001167622.1  ADP-ribosylation factor-like protein 13B isoform 3

    See identical proteins and their annotated locations for NP_001167622.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 3' UTR, lacks an in-frame exon in the 5' coding region and uses a downstream start codon, compared to variant 1. The encoded isoform 3 has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AA775026, AC117474, AL713789
    Consensus CDS
    CCDS54615.1
    UniProtKB/TrEMBL
    A0A7P0Z4M2
    Related
    ENSP00000445145.1, ENST00000535334.5
    Conserved Domains (2) summary
    pfam04514
    Location:69 → 230
    BTV_NS2; Bluetongue virus non-structural protein NS2
    cl21455
    Location:1 → 86
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  3. NM_001321328.2 → NP_001308257.1  ADP-ribosylation factor-like protein 13B isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC130896, CR936753, CR936763
    UniProtKB/TrEMBL
    A0A7P0T9C1
    Conserved Domains (3) summary
    cd04161
    Location:29 → 174
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    pfam04514
    Location:157 → 318
    BTV_NS2; Bluetongue virus non-structural protein NS2
    pfam13900
    Location:2 → 26
    GVQW; Putative domain of unknown function

  4. NM_001410782.1 → NP_001397711.1  ADP-ribosylation factor-like protein 13B isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC117474, AC130896
    Consensus CDS
    CCDS93326.1
    UniProtKB/TrEMBL
    A0A7P0Z473
    Related
    ENSP00000505396.1, ENST00000679587.1

  5. NM_144996.4 → NP_659433.2  ADP-ribosylation factor-like protein 13B isoform 2

    See identical proteins and their annotated locations for NP_659433.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and lacks two in-frame exons in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AA775026, BC094725
    Consensus CDS
    CCDS2924.1
    UniProtKB/TrEMBL
    A0A7P0Z4M2
    Related
    ENSP00000306225.7, ENST00000303097.11
    Conserved Domains (2) summary
    pfam04514
    Location:65 → 226
    BTV_NS2; Bluetongue virus non-structural protein NS2
    cl21455
    Location:21 → 82
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  6. NM_182896.3 → NP_878899.1  ADP-ribosylation factor-like protein 13B isoform 1

    See identical proteins and their annotated locations for NP_878899.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AA775026, AC130896, BC031093, BC094725
    Consensus CDS
    CCDS2925.1
    UniProtKB/Swiss-Prot
    D3DN29, G3V1S8, Q3SXY8, Q504W8, Q8TCL5
    UniProtKB/TrEMBL
    B4DLH1
    Related
    ENSP00000420780.1, ENST00000471138.5
    Conserved Domains (2) summary
    cd04161
    Location:23 → 189
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    cl26557
    Location:198 → 259
    RNase_E_G; Ribonuclease E/G family

RNA

  1. NR_033427.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 3' UTR and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA775026, AK299284, BC094725
    Related
    ENST00000460371.5

  2. NR_135621.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC130896, CR936753, CR936756, CR936763
    Related
    ENST00000680994.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    93980155..94055678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011512533.3 → XP_011510835.1  ADP-ribosylation factor-like protein 13B isoform X1

    See identical proteins and their annotated locations for XP_011510835.1

    UniProtKB/TrEMBL
    A0A7P0T9C1
    Conserved Domains (2) summary
    cd04161
    Location:31 → 177
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    pfam04514
    Location:160 → 321
    BTV_NS2; Bluetongue virus non-structural protein NS2

  2. XM_011512535.3 → XP_011510837.1  ADP-ribosylation factor-like protein 13B isoform X3

    UniProtKB/TrEMBL
    A0A7P0T892, A0A7P0T9C1
    Related
    ENSP00000505036.1, ENST00000681655.1
    Conserved Domains (2) summary
    cd04161
    Location:1 → 164
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    pfam04514
    Location:147 → 308
    BTV_NS2; Bluetongue virus non-structural protein NS2

  3. XM_006713532.4 → XP_006713595.1  ADP-ribosylation factor-like protein 13B isoform X2

    See identical proteins and their annotated locations for XP_006713595.1

    UniProtKB/TrEMBL
    A0A7P0T9C1
    Conserved Domains (3) summary
    cd04161
    Location:29 → 174
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    pfam04514
    Location:157 → 318
    BTV_NS2; Bluetongue virus non-structural protein NS2
    pfam13900
    Location:2 → 26
    GVQW; Putative domain of unknown function

  4. XM_017005853.2 → XP_016861342.1  ADP-ribosylation factor-like protein 13B isoform X4

    UniProtKB/TrEMBL
    A0A7P0Z4M2
    Conserved Domains (2) summary
    pfam04514
    Location:69 → 230
    BTV_NS2; Bluetongue virus non-structural protein NS2
    cl21455
    Location:1 → 86
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  5. XM_011512532.3 → XP_011510834.1  ADP-ribosylation factor-like protein 13B isoform X1

    See identical proteins and their annotated locations for XP_011510834.1

    UniProtKB/TrEMBL
    A0A7P0T9C1
    Conserved Domains (2) summary
    cd04161
    Location:31 → 177
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    pfam04514
    Location:160 → 321
    BTV_NS2; Bluetongue virus non-structural protein NS2

  6. XM_047447661.1 → XP_047303617.1  ADP-ribosylation factor-like protein 13B isoform X5

    UniProtKB/TrEMBL
    A0A7P0T933
    Related
    ENSP00000505366.1, ENST00000486562.2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    96678283..96754130
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345621.1 → XP_054201596.1  ADP-ribosylation factor-like protein 13B isoform X1

  2. XM_054345624.1 → XP_054201599.1  ADP-ribosylation factor-like protein 13B isoform X3

    UniProtKB/TrEMBL
    A0A7P0T892

  3. XM_054345623.1 → XP_054201598.1  ADP-ribosylation factor-like protein 13B isoform X2

  4. XM_054345625.1 → XP_054201600.1  ADP-ribosylation factor-like protein 13B isoform X4

  5. XM_054345622.1 → XP_054201597.1  ADP-ribosylation factor-like protein 13B isoform X1

  6. XM_054345626.1 → XP_054201601.1  ADP-ribosylation factor-like protein 13B isoform X5

    UniProtKB/TrEMBL
    A0A7P0T933
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q3SXY8.1 GenPept UniProtKB/Swiss-Prot:Q3SXY8

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