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Protein

ADP-ribosylation factor-like protein 13B

Gene

arl13b

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Cilium-specific protein required to control the microtubule-based, ciliary axoneme structure. May act by maintaining the association between IFT subcomplexes A and B. Binds GTP but is not able to hydrolyze it; the GTPase activity remains unclear. Required to pattern the neural tube. Involved in cerebral cortex development: required for the initial formation of a polarized radial glial scaffold, the first step in the construction of the cerebral cortex, by regulating ciliary signaling. Regulates the migration and placement of postmitotic interneurons in the developing cerebral cortex Required during embryogenesis for cilia formation in multiple organs such as the pronephric duct.3 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi28 – 358GTPBy similarity
Nucleotide bindingi71 – 755GTPBy similarity
Nucleotide bindingi130 – 1334GTPBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Ligandi

GTP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-DRE-5624958. ARL13B-mediated ciliary trafficking of INPP5E.

Names & Taxonomyi

Protein namesi
Recommended name:
ADP-ribosylation factor-like protein 13B
Alternative name(s):
ADP-ribosylation factor-like protein 2-like 1
Short name:
ARL2-like protein 1
Protein scorpion
Gene namesi
Name:arl13b
Synonyms:arl2l1
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Chromosome 1

Organism-specific databases

ZFINiZDB-GENE-021217-3. arl13b.

Subcellular locationi

  • Cell projectioncilium membrane 1 Publication; Lipid-anchor 1 Publication

  • Note: Associates to the cilium membrane via palmitoylation. Localizes to proximal ciliary membranes, to an inversin-like subciliary membrane compartment, excluding the transition zone.

GO - Cellular componenti

  • ciliary membrane Source: UniProtKB
  • cilium Source: ZFIN
  • intracellular Source: InterPro
  • primary cilium Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cell projection, Cilium, Membrane

Pathology & Biotechi

Disruption phenotypei

Embryos have a ventrally curved tail, ciliary defects and cystic kidneys.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi28 – 281G → V: Abolishes ability to rescue a arl13b mutant when transfected, without affecting localization to cilium. 1 Publication
Mutagenesisi35 – 351T → N: Abolishes ability to rescue a arl13b mutant when transfected, without affecting localization to cilium. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 407407ADP-ribosylation factor-like protein 13BPRO_0000251139Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Lipidationi8 – 81S-palmitoyl cysteineBy similarity
Lipidationi9 – 91S-palmitoyl cysteineBy similarity

Keywords - PTMi

Lipoprotein, Palmitate

Proteomic databases

PaxDbiQ8JHI3.

Expressioni

Tissue specificityi

Cilium-specific.1 Publication

Developmental stagei

Detected at the 4- to 32-cell stage, suggesting it is expressed maternally.1 Publication

Gene expression databases

BgeeiENSDARG00000012763.

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000092960.

Structurei

3D structure databases

ProteinModelPortaliQ8JHI3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili195 – 313119Sequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi207 – 318112Glu-richAdd
BLAST

Sequence similaritiesi

Belongs to the small GTPase superfamily. Arf family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG0074. Eukaryota.
KOG0076. Eukaryota.
ENOG410XRG9. LUCA.
GeneTreeiENSGT00550000074639.
HOGENOMiHOG000034031.
HOVERGENiHBG060221.
InParanoidiQ8JHI3.
KOiK07962.
OrthoDBiEOG091G0BQV.
PhylomeDBiQ8JHI3.
TreeFamiTF105476.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR024156. Small_GTPase_ARF.
IPR006689. Small_GTPase_ARF/SAR.
[Graphical view]
PfamiPF00025. Arf. 1 hit.
[Graphical view]
PRINTSiPR00328. SAR1GTPBP.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiPS51417. ARF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8JHI3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFNLMANCCN WLKRWREPAR KVTLVMVGLD NAGKTATVRG IQGESPLDVA
60 70 80 90 100
PTVGFSKVDL KQGKFEVTIF DLGGGKRIRG IWKNYYSESY GVVFVVDSSD
110 120 130 140 150
VQRIQETRDT MAEVLRHPRI AGKPVLVLAN KQDQDGAMAE ADIIETLSLE
160 170 180 190 200
KLVNENKCLC QIEPCSAVLG YGKKVDKSIK NGLNWLLNNI AKDYEAISER
210 220 230 240 250
VQKDTAEQKA QEEQDKKERA ERVRRIREER DRQEREEAER EGRTLKEEEL
260 270 280 290 300
DDVNMFNPFQ PINNVLTENQ DRLNREKEMQ RQRENGQQGS VQEQIALQDE
310 320 330 340 350
EEEEEDEESE RQTPESTESG AVDQTKKKTR KLRLKRKHRV DPLRMEEAAP
360 370 380 390 400
KSPTPPPLPV GWATPKVSRL PKLEPLGDTR HSDFYGKPLP PVAIRQRPNS

DTHDVIS
Length:407
Mass (Da):46,566
Last modified:October 1, 2002 - v1
Checksum:iDE491E88F57FAEC9
GO

Sequence cautioni

The sequence AAH92689 differs from that shown.Contaminating sequence. Potential poly-A sequence.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti43 – 431G → E in AAH92689 (Ref. 2) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF506213 mRNA. Translation: AAM34657.1.
BC092689 mRNA. Translation: AAH92689.1. Sequence problems.
RefSeqiNP_775379.1. NM_173272.1.
UniGeneiDr.94425.

Genome annotation databases

EnsembliENSDART00000102184; ENSDARP00000092960; ENSDARG00000012763.
GeneIDi286784.
KEGGidre:286784.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF506213 mRNA. Translation: AAM34657.1.
BC092689 mRNA. Translation: AAH92689.1. Sequence problems.
RefSeqiNP_775379.1. NM_173272.1.
UniGeneiDr.94425.

3D structure databases

ProteinModelPortaliQ8JHI3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000092960.

Proteomic databases

PaxDbiQ8JHI3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000102184; ENSDARP00000092960; ENSDARG00000012763.
GeneIDi286784.
KEGGidre:286784.

Organism-specific databases

CTDi200894.
ZFINiZDB-GENE-021217-3. arl13b.

Phylogenomic databases

eggNOGiKOG0074. Eukaryota.
KOG0076. Eukaryota.
ENOG410XRG9. LUCA.
GeneTreeiENSGT00550000074639.
HOGENOMiHOG000034031.
HOVERGENiHBG060221.
InParanoidiQ8JHI3.
KOiK07962.
OrthoDBiEOG091G0BQV.
PhylomeDBiQ8JHI3.
TreeFamiTF105476.

Enzyme and pathway databases

ReactomeiR-DRE-5624958. ARL13B-mediated ciliary trafficking of INPP5E.

Miscellaneous databases

PROiQ8JHI3.

Gene expression databases

BgeeiENSDARG00000012763.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR024156. Small_GTPase_ARF.
IPR006689. Small_GTPase_ARF/SAR.
[Graphical view]
PfamiPF00025. Arf. 1 hit.
[Graphical view]
PRINTSiPR00328. SAR1GTPBP.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiPS51417. ARF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiAR13B_DANRE
AccessioniPrimary (citable) accession number: Q8JHI3
Secondary accession number(s): Q561Z5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: October 1, 2002
Last modified: September 7, 2016
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.