arl13b ADP-ribosylation factor-like 13b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: arl13bprovided by ZNC
Official Full Name: ADP-ribosylation factor-like 13bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-021217-3
See related: Ensembl:ENSDARG00000012763 AllianceGenome:ZFIN:ZDB-GENE-021217-3
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: arl2l1; fc23g07; chunp6872; wu:fc23g07; zgc:123149
Summary: Predicted to enable GTP binding activity and GTPase activity. Acts upstream of or within cilium assembly and photoreceptor cell outer segment organization. Located in cilium. Is expressed in Kupffer's vesicle; nervous system; otic vesicle; and renal system. Used to study Joubert syndrome 8. Human ortholog(s) of this gene implicated in Joubert syndrome 8. Orthologous to human ARL13B (ADP ribosylation factor like GTPase 13B). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 1

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	1	NC_007112.7 (33668236..33694795)
105	previous assembly	GRCz10 (GCF_000002035.5)	1	NC_007112.6 (32935690..32962227)

Chromosome 1 - NC_007112.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Joubert Syndrome Gene arl13b is Critical for Early Cerebellar Development in Zebrafish.
Title: The Joubert Syndrome Gene arl13b is Critical for Early Cerebellar Development in Zebrafish.
Between 2 and 5 days post fertilization (dpf), arl13b is expressed in neural tissues while expression of arl13a is downregulated by 2 dpf and restricted to craniofacial structures. These results indicate that arl13a and arl13b have evolved different roles and that arl13a does not function in the zebrafish retina.
Title: Developmental expression of the zebrafish Arf-like small GTPase paralogs arl13a and arl13b.
loss of Arl13b leads to slow photoreceptor degeneration, but can be exacerbated by the loss of vangl2. Importantly, the data show that Arl13b can genetically and physically interact with Vangl2 and this association is important for normal photoreceptor structure.
Title: Arl13b Interacts With Vangl2 to Regulate Cilia and Photoreceptor Outer Segment Length in Zebrafish.
Arl13b is an important effector of ciliary membrane biogenesis and ciliary length regulation.
Title: A function for the Joubert syndrome protein Arl13b in ciliary membrane extension and ciliary length regulation.
Cilia localization is essential for in vivo functions of the Joubert syndrome protein arl13b.
Title: Cilia localization is essential for in vivo functions of the Joubert syndrome protein Arl13b/Scorpion.

Submit: New GeneRIF Correction

General gene information

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Markers

fc23g07.x1 (e-PCR)
- UniSTS:187844

fk36f05.y1 (e-PCR)
- UniSTS:200912

Gene Ontology Provided by ZFIN

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 nucleotide binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cilium assembly	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in formation of radial glial scaffolds	ISS Inferred from Sequence or Structural Similarity more info
involved_in interneuron migration from the subpallium to the cortex	ISS Inferred from Sequence or Structural Similarity 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
acts_upstream_of_or_within photoreceptor cell outer segment organization	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within photoreceptor cell outer segment organization	IMP Inferred from Mutant Phenotype more info	PubMed
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 cell projection	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	IEA Inferred from Electronic Annotation more info
located_in cilium	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	IEA Inferred from Electronic Annotation 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
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ADP-ribosylation factor-like protein 13B

Names: ADP-ribosylation factor-like 2-like 1; ADP-ribosylation factor-like protein 2-like 1; ARL2-like protein 1; protein scorpion; scorpion; un-named hi459; unm hi459

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.

mRNA and Protein(s)

NM_173272.2 → NP_775379.1 ADP-ribosylation factor-like protein 13B

See identical proteins and their annotated locations for NP_775379.1

Status: VALIDATED

Source sequence(s)

CR762462

UniProtKB/Swiss-Prot

Q561Z5, Q8JHI3

Related

ENSDARP00000092960.3, ENSDART00000102184.4

Conserved Domains (2) summary

cd04161
Location:23 → 189

Arl2l1_Arl13_like; Arl2-like protein 1 (Arl2l1) and Arl13

smart00178
Location:12 → 186

SAR; Sar1p-like members of the Ras-family of small GTPases

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007112.7 Reference GRCz11 Primary Assembly

Range

33668236..33694795

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_068221828.1 → XP_068077929.1 ADP-ribosylation factor-like protein 13B isoform X3
XM_068221812.1 → XP_068077913.1 ADP-ribosylation factor-like protein 13B isoform X2
XM_068221876.1 → XP_068077977.1 ADP-ribosylation factor-like protein 13B isoform X5
XM_068221797.1 → XP_068077898.1 ADP-ribosylation factor-like protein 13B isoform X1
XM_068221848.1 → XP_068077949.1 ADP-ribosylation factor-like protein 13B isoform X4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001037425.1: Suppressed sequence

Description

NM_001037425.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.