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Protein

ADP-ribosylation factor-like protein 13B

Gene

ARL13B

Organism
Homo sapiens (Human)
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. May regulate endocytic recycling traffic; however, additional evidences are required to confirm these data.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi28 – 35GTPBy similarity8
Nucleotide bindingi71 – 75GTPBy similarity5
Nucleotide bindingi130 – 133GTPBy similarity4

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

GTP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-HSA-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
Gene namesi
Name:ARL13B
Synonyms:ARL2L1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:25419. ARL13B.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cell projection, Cilium, Membrane

Pathology & Biotechi

Involvement in diseasei

Joubert syndrome 8 (JBTS8)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy and renal disease.
See also OMIM:612291
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05437179R → Q in JBTS8; reduces binding to GTP. 1 PublicationCorresponds to variant rs121912606dbSNPEnsembl.1
Natural variantiVAR_054372200R → C in JBTS8. 1 PublicationCorresponds to variant rs121912608dbSNPEnsembl.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi35T → N: Does not affect localization to cilia. 1 Publication1
Mutagenesisi130N → I: Does not affect localization to cilia. 1 Publication1
Mutagenesisi231K → R: No effect. Abolishes sumoylation; when associated with R-270; R-275; R-276; R-279 and R-329. 1 Publication1
Mutagenesisi270K → R: No effect. Abolishes sumoylation; when associated with R-231; R-275; R-276; R-279 and R-329. 1 Publication1
Mutagenesisi275K → R: No effect. Abolishes sumoylation; when associated with R-231; R-270; R-276; R-279 and R-329. 1 Publication1
Mutagenesisi276K → R: No effect. Abolishes sumoylation; when associated with R-231; R-270; R-275; R-279 and R-329. 1 Publication1
Mutagenesisi279K → R: No effect. Abolishes sumoylation; when associated with R-231; R-270; R-275; R-276 and R-329. 1 Publication1
Mutagenesisi329K → R: Abolishes sumoylation. Abolishes sumoylation; when associated with R-231; R-270; R-275; R-276 and R-279. 1 Publication1

Keywords - Diseasei

Ciliopathy, Disease mutation, Joubert syndrome

Organism-specific databases

DisGeNETi200894.
MalaCardsiARL13B.
MIMi612291. phenotype.
OpenTargetsiENSG00000169379.
Orphaneti475. Joubert syndrome.
PharmGKBiPA134975272.

Polymorphism and mutation databases

BioMutaiARL13B.
DMDMi115503786.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002511371 – 428ADP-ribosylation factor-like protein 13BAdd BLAST428

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi8S-palmitoyl cysteineBy similarity1
Lipidationi9S-palmitoyl cysteineBy similarity1
Cross-linki329Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)Curated

Post-translational modificationi

Sumoylation is required for PKD2 entry into cilium.1 Publication

Keywords - PTMi

Isopeptide bond, Lipoprotein, Palmitate, Ubl conjugation

Proteomic databases

EPDiQ3SXY8.
MaxQBiQ3SXY8.
PaxDbiQ3SXY8.
PeptideAtlasiQ3SXY8.
PRIDEiQ3SXY8.

PTM databases

iPTMnetiQ3SXY8.
PhosphoSitePlusiQ3SXY8.
SwissPalmiQ3SXY8.

Expressioni

Gene expression databases

BgeeiENSG00000169379.
CleanExiHS_ARL13B.
ExpressionAtlasiQ3SXY8. baseline and differential.
GenevisibleiQ3SXY8. HS.

Organism-specific databases

HPAiHPA048926.

Interactioni

Subunit structurei

Monomer (By similarity). Interacts with PIFO. Interacts with IFT complex B components IFT46 and IFT74.By similarity2 Publications

Protein-protein interaction databases

BioGridi128353. 21 interactors.
IntActiQ3SXY8. 1 interactor.
STRINGi9606.ENSP00000377769.

Structurei

3D structure databases

ProteinModelPortaliQ3SXY8.
SMRiQ3SXY8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili192 – 245Sequence analysisAdd BLAST54

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi369 – 419Pro-richAdd BLAST51

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.
InParanoidiQ3SXY8.
KOiK07962.
OMAiINLRQGK.
OrthoDBiEOG091G0BQV.
PhylomeDBiQ3SXY8.
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]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q3SXY8-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MFSLMASCCG WFKRWREPVR KVTLLMVGLD NAGKTATAKG IQGEYPEDVA
60 70 80 90 100
PTVGFSKINL RQGKFEVTIF DLGGGIRIRG IWKNYYAESY GVIFVVDSSD
110 120 130 140 150
EERMEETKEA MSEMLRHPRI SGKPILVLAN KQDKEGALGE ADVIECLSLE
160 170 180 190 200
KLVNEHKCLC QIEPCSAISG YGKKIDKSIK KGLYWLLHVI ARDFDALNER
210 220 230 240 250
IQKETTEQRA LEEQEKQERA ERVRKLREER KQNEQEQAEL DGTSGLAELD
260 270 280 290 300
PEPTNPFQPI ASVIIENEGK LEREKKNQKM EKDSDGCHLK HKMEHEQIET
310 320 330 340 350
QGQVNHNGQK NNEFGLVENY KEALTQQLKN EDETDRPSLE SANGKKKTKK
360 370 380 390 400
LRMKRNHRVE PLNIDDCAPE SPTPPPPPPP VGWGTPKVTR LPKLEPLGET
410 420
HHNDFYRKPL PPLAVPQRPN SDAHDVIS
Length:428
Mass (Da):48,643
Last modified:October 11, 2005 - v1
Checksum:i002B38A38D1F7BDD
GO
Isoform 2 (identifier: Q3SXY8-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     21-127: Missing.

Note: No experimental confirmation available.
Show »
Length:321
Mass (Da):36,795
Checksum:iD4D82D271E9E7F1E
GO
Isoform 3 (identifier: Q3SXY8-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-103: Missing.

Note: No experimental confirmation available.
Show »
Length:325
Mass (Da):37,087
Checksum:i21F4DA7BFC23125C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti275K → KK in CAD28544 (PubMed:17974005).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05437179R → Q in JBTS8; reduces binding to GTP. 1 PublicationCorresponds to variant rs121912606dbSNPEnsembl.1
Natural variantiVAR_054372200R → C in JBTS8. 1 PublicationCorresponds to variant rs121912608dbSNPEnsembl.1
Natural variantiVAR_048319348T → S.Corresponds to variant rs33944211dbSNPEnsembl.1
Natural variantiVAR_069190390R → L in a nephronophthisis (NPHP) patient. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0454211 – 103Missing in isoform 3. 1 PublicationAdd BLAST103
Alternative sequenceiVSP_02073321 – 127Missing in isoform 2. 1 PublicationAdd BLAST107

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL713789 mRNA. Translation: CAD28544.2.
AC117474 Genomic DNA. No translation available.
AC130896 Genomic DNA. No translation available.
CH471052 Genomic DNA. Translation: EAW79897.1.
CH471052 Genomic DNA. Translation: EAW79901.1.
CH471052 Genomic DNA. Translation: EAW79898.1.
BC094725 mRNA. Translation: AAH94725.1.
BC104035 mRNA. Translation: AAI04036.1.
BC104036 mRNA. Translation: AAI04037.1.
CCDSiCCDS2924.1. [Q3SXY8-2]
CCDS2925.1. [Q3SXY8-1]
CCDS54615.1. [Q3SXY8-3]
RefSeqiNP_001167621.1. NM_001174150.1. [Q3SXY8-1]
NP_001167622.1. NM_001174151.1. [Q3SXY8-3]
NP_659433.2. NM_144996.3. [Q3SXY8-2]
NP_878899.1. NM_182896.2. [Q3SXY8-1]
XP_016861342.1. XM_017005853.1. [Q3SXY8-3]
UniGeneiHs.533086.

Genome annotation databases

EnsembliENST00000303097; ENSP00000306225; ENSG00000169379. [Q3SXY8-2]
ENST00000394222; ENSP00000377769; ENSG00000169379. [Q3SXY8-1]
ENST00000471138; ENSP00000420780; ENSG00000169379. [Q3SXY8-1]
ENST00000535334; ENSP00000445145; ENSG00000169379. [Q3SXY8-3]
GeneIDi200894.
KEGGihsa:200894.
UCSCiuc003drc.4. human. [Q3SXY8-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL713789 mRNA. Translation: CAD28544.2.
AC117474 Genomic DNA. No translation available.
AC130896 Genomic DNA. No translation available.
CH471052 Genomic DNA. Translation: EAW79897.1.
CH471052 Genomic DNA. Translation: EAW79901.1.
CH471052 Genomic DNA. Translation: EAW79898.1.
BC094725 mRNA. Translation: AAH94725.1.
BC104035 mRNA. Translation: AAI04036.1.
BC104036 mRNA. Translation: AAI04037.1.
CCDSiCCDS2924.1. [Q3SXY8-2]
CCDS2925.1. [Q3SXY8-1]
CCDS54615.1. [Q3SXY8-3]
RefSeqiNP_001167621.1. NM_001174150.1. [Q3SXY8-1]
NP_001167622.1. NM_001174151.1. [Q3SXY8-3]
NP_659433.2. NM_144996.3. [Q3SXY8-2]
NP_878899.1. NM_182896.2. [Q3SXY8-1]
XP_016861342.1. XM_017005853.1. [Q3SXY8-3]
UniGeneiHs.533086.

3D structure databases

ProteinModelPortaliQ3SXY8.
SMRiQ3SXY8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi128353. 21 interactors.
IntActiQ3SXY8. 1 interactor.
STRINGi9606.ENSP00000377769.

PTM databases

iPTMnetiQ3SXY8.
PhosphoSitePlusiQ3SXY8.
SwissPalmiQ3SXY8.

Polymorphism and mutation databases

BioMutaiARL13B.
DMDMi115503786.

Proteomic databases

EPDiQ3SXY8.
MaxQBiQ3SXY8.
PaxDbiQ3SXY8.
PeptideAtlasiQ3SXY8.
PRIDEiQ3SXY8.

Protocols and materials databases

DNASUi200894.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000303097; ENSP00000306225; ENSG00000169379. [Q3SXY8-2]
ENST00000394222; ENSP00000377769; ENSG00000169379. [Q3SXY8-1]
ENST00000471138; ENSP00000420780; ENSG00000169379. [Q3SXY8-1]
ENST00000535334; ENSP00000445145; ENSG00000169379. [Q3SXY8-3]
GeneIDi200894.
KEGGihsa:200894.
UCSCiuc003drc.4. human. [Q3SXY8-1]

Organism-specific databases

CTDi200894.
DisGeNETi200894.
GeneCardsiARL13B.
GeneReviewsiARL13B.
HGNCiHGNC:25419. ARL13B.
HPAiHPA048926.
MalaCardsiARL13B.
MIMi608922. gene.
612291. phenotype.
neXtProtiNX_Q3SXY8.
OpenTargetsiENSG00000169379.
Orphaneti475. Joubert syndrome.
PharmGKBiPA134975272.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0074. Eukaryota.
KOG0076. Eukaryota.
ENOG410XRG9. LUCA.
GeneTreeiENSGT00550000074639.
HOGENOMiHOG000034031.
HOVERGENiHBG060221.
InParanoidiQ3SXY8.
KOiK07962.
OMAiINLRQGK.
OrthoDBiEOG091G0BQV.
PhylomeDBiQ3SXY8.
TreeFamiTF105476.

Enzyme and pathway databases

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

Miscellaneous databases

ChiTaRSiARL13B. human.
GeneWikiiARL13B.
GenomeRNAii200894.
PROiQ3SXY8.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000169379.
CleanExiHS_ARL13B.
ExpressionAtlasiQ3SXY8. baseline and differential.
GenevisibleiQ3SXY8. HS.

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_HUMAN
AccessioniPrimary (citable) accession number: Q3SXY8
Secondary accession number(s): D3DN29
, G3V1S8, Q504W8, Q8TCL5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: October 11, 2005
Last modified: November 30, 2016
This is version 107 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Miscellaneous

Used as a ciliary marker because of its specific localization to microtubule doublets of the ciliary axoneme.

Caution

Was initially thought to form a homodimer (PubMed:18554500). However, 3D structure of C.reinhardtii ortholog showed that it is probably not the case.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. 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.