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

Summary

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

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Novel compound heterozygous variants in ARL13B lead to Joubert syndrome.
Title: Novel compound heterozygous variants in ARL13B lead to Joubert syndrome.
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.
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.
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.
ARL3 activation requires the co-GEF BART and effector-mediated turnover.
Title: ARL3 activation requires the co-GEF BART and effector-mediated turnover.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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

NG_017076.1 RefSeqGene

Range

5017..80540

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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

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
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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

93980155..94055678

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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

NC_060927.1 Alternate T2T-CHM13v2.0

Range

96678283..96754130

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054345621.1 → XP_054201596.1 ADP-ribosylation factor-like protein 13B isoform X1
XM_054345624.1 → XP_054201599.1 ADP-ribosylation factor-like protein 13B isoform X3

UniProtKB/TrEMBL

A0A7P0T892
XM_054345623.1 → XP_054201598.1 ADP-ribosylation factor-like protein 13B isoform X2
XM_054345625.1 → XP_054201600.1 ADP-ribosylation factor-like protein 13B isoform X4
XM_054345622.1 → XP_054201597.1 ADP-ribosylation factor-like protein 13B isoform X1
XM_054345626.1 → XP_054201601.1 ADP-ribosylation factor-like protein 13B isoform X5

UniProtKB/TrEMBL

A0A7P0T933