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    ARL13B ARF like GTPase 13B [ Homo sapiens (human) ]

    Gene ID: 200894, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ARL13Bprovided by HGNC
    Official Full Name
    ARF 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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (93980155..94055678)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (96678283..96754130)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. 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
    2. 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
    3. 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
    4. Novel compound heterozygous variants in ARL13B lead to Joubert syndrome. Lin Z, et al. J Cell Physiol, 2024 Apr. PMID 38219074
    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 (68) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel compound heterozygous variants in ARL13B lead to Joubert syndrome.
      Title: Novel compound heterozygous variants in ARL13B lead to Joubert syndrome.
    2. 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.
    3. 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.
    4. 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.
    5. ARL3 activation requires the co-GEF BART and effector-mediated turnover.
      Title: ARL3 activation requires the co-GEF BART and effector-mediated turnover.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. Joubert syndrome protein ARL13B controls axoneme polyglutamylation.
      Title: Axoneme polyglutamylation regulated by Joubert syndrome protein ARL13B controls ciliary targeting of signaling molecules.
    Submit: New GeneRIF Correction See all GeneRIFs (29)

    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)

    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 GTPase 13B
    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, B4DLH1
      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_2024_08

    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, A0A7P0Z4M2
      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

      UniProtKB/TrEMBL
      A0A7P0T9C1

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

      UniProtKB/TrEMBL
      A0A7P0T892, A0A7P0T9C1

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

      UniProtKB/TrEMBL
      A0A7P0T9C1

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

      UniProtKB/TrEMBL
      A0A7P0Z4M2

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

      UniProtKB/TrEMBL
      A0A7P0T9C1

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

      UniProtKB/TrEMBL
      A0A7P0T933, A0A7P0Z4M2
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3SXY8.1 GenPept UniProtKB/Swiss-Prot:Q3SXY8

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