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

Gene ID: 200894, updated on 15-Jun-2019

Summary

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
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

Genomic context

See ARL13B in Genome Data Viewer
Location:
3q11.1-q11.2
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (93980139..94055678)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (93698983..93774522)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene protein S 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 dihydrofolate reductase 2 Neighboring gene NOP2/Sun RNA methyltransferase 3 Neighboring gene RBBP4 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • ARL13B-mediated ciliary trafficking of INPP5E, organism-specific biosystem (from REACTOME)
    ARL13B-mediated ciliary trafficking of INPP5E, organism-specific biosystemARL13B is a ciliary-localized small GTPase with an atypical C-terminus containing a coiled coil domain and a proline rich domain (PRD) (Hori et al, 2008). Mutations in ARL13B are associated with the ...
  • Cargo trafficking to the periciliary membrane, organism-specific biosystem (from REACTOME)
    Cargo trafficking to the periciliary membrane, organism-specific biosystemProteomic studies suggest that the cilium is home to approximately a thousand proteins, and has a unique protein and lipid make up relative to the bulk cytoplasm and plasma membrane (Pazour et al, 20...
  • Cilium Assembly, organism-specific biosystem (from REACTOME)
    Cilium Assembly, organism-specific biosystemCilia are membrane covered organelles that extend from the surface of eukaryotic cells. Cilia may be motile, such as respiratory cilia) or non-motile (such as the primary cilium) and are distinguishe...
  • Organelle biogenesis and maintenance, organism-specific biosystem (from REACTOME)
    Organelle biogenesis and maintenance, organism-specific biosystemThis module describes the biogenesis of organelles. Organelles are subcellular structures of distinctive morphology and function. The organelles of human cells include: mitochondria, endoplasmic reti...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

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

Gene Ontology Provided by GOA

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

General protein information

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)

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
    5001..80540
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001174150.2NP_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
    Q3SXY8
    Related
    ENSP00000377769.3, ENST00000394222.7
    Conserved Domains (2) summary
    cd04161
    Location:23189
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    cl26557
    Location:198259
    RNase_E_G; Ribonuclease E/G family
  2. NM_001174151.1NP_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/Swiss-Prot
    Q3SXY8
    Related
    ENSP00000445145.1, ENST00000535334.5
    Conserved Domains (2) summary
    pfam04514
    Location:69230
    BTV_NS2; Bluetongue virus non-structural protein NS2
    cl21455
    Location:186
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
  3. NM_001321328.2NP_001308257.1  ADP-ribosylation factor-like protein 13B isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC130896, CR936753, CR936763
    Conserved Domains (3) summary
    cd04161
    Location:29174
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    pfam04514
    Location:157318
    BTV_NS2; Bluetongue virus non-structural protein NS2
    pfam13900
    Location:226
    GVQW; Putative domain of unknown function
  4. NM_144996.4NP_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/Swiss-Prot
    Q3SXY8
    Related
    ENSP00000306225.7, ENST00000303097.11
    Conserved Domains (2) summary
    pfam04514
    Location:65226
    BTV_NS2; Bluetongue virus non-structural protein NS2
    cl21455
    Location:2182
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
  5. NM_182896.3NP_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
    Q3SXY8
    Related
    ENSP00000420780.1, ENST00000471138.5
    Conserved Domains (2) summary
    cd04161
    Location:23189
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    cl26557
    Location:198259
    RNase_E_G; Ribonuclease E/G family

RNA

  1. NR_033427.1 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, AC117474, AK299284, BC094725
  2. NR_135621.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    BG705058, CR936753, CR936756, CR936763
    Related
    ENST00000460371.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    93980139..94055678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011512534.2XP_011510836.1  ADP-ribosylation factor-like protein 13B isoform X2

    See identical proteins and their annotated locations for XP_011510836.1

    Conserved Domains (3) summary
    cd04161
    Location:29174
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    pfam04514
    Location:157318
    BTV_NS2; Bluetongue virus non-structural protein NS2
    pfam13900
    Location:226
    GVQW; Putative domain of unknown function
  2. XM_006713532.3XP_006713595.1  ADP-ribosylation factor-like protein 13B isoform X2

    See identical proteins and their annotated locations for XP_006713595.1

    Conserved Domains (3) summary
    cd04161
    Location:29174
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    pfam04514
    Location:157318
    BTV_NS2; Bluetongue virus non-structural protein NS2
    pfam13900
    Location:226
    GVQW; Putative domain of unknown function
  3. XM_011512535.2XP_011510837.1  ADP-ribosylation factor-like protein 13B isoform X3

    Conserved Domains (2) summary
    cd04161
    Location:1164
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    pfam04514
    Location:147308
    BTV_NS2; Bluetongue virus non-structural protein NS2
  4. XM_017005853.1XP_016861342.1  ADP-ribosylation factor-like protein 13B isoform X4

    UniProtKB/Swiss-Prot
    Q3SXY8
    Conserved Domains (2) summary
    pfam04514
    Location:69230
    BTV_NS2; Bluetongue virus non-structural protein NS2
    cl21455
    Location:186
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
  5. XM_011512532.2XP_011510834.1  ADP-ribosylation factor-like protein 13B isoform X1

    See identical proteins and their annotated locations for XP_011510834.1

    Conserved Domains (2) summary
    cd04161
    Location:31177
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    pfam04514
    Location:160321
    BTV_NS2; Bluetongue virus non-structural protein NS2
  6. XM_011512533.2XP_011510835.1  ADP-ribosylation factor-like protein 13B isoform X1

    See identical proteins and their annotated locations for XP_011510835.1

    Conserved Domains (2) summary
    cd04161
    Location:31177
    Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13
    pfam04514
    Location:160321
    BTV_NS2; Bluetongue virus non-structural protein NS2
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