Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q3SXY8 (AR13B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 84. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:ARL13B
Synonyms:ARL2L1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length428 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.10 Ref.11

Subunit structure

Monomer By similarity. Interacts with PIFO. Interacts with IFT complex B components IFT46 and IFT74. Ref.7 Ref.9

Subcellular location

Cell projectioncilium membrane; Lipid-anchor. Note: Associates to the cilium membrane via palmitoylation. Localizes to proximal ciliary membranes, to an inversin-like subciliary membrane compartment, excluding the transition zone. Ref.6 Ref.12

Post-translational modification

Sumoylation is required for PKD2 entry into cilium. Ref.8

Involvement in disease

Joubert syndrome 8 (JBTS8) [MIM:612291]: A 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.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.13

Miscellaneous

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

Sequence similarities

Belongs to the small GTPase superfamily. Arf family.

Caution

Was initially thought to form a homodimer (Ref.6). However, 3D structure of C.reinhardtii ortholog showed that it is probably not the case.

Ontologies

Keywords
   Cellular componentCell membrane
Cell projection
Cilium
Membrane
   Coding sequence diversityAlternative splicing
Polymorphism
   DiseaseCiliopathy
Disease mutation
Joubert syndrome
   DomainCoiled coil
   LigandGTP-binding
Nucleotide-binding
   PTMIsopeptide bond
Lipoprotein
Palmitate
Ubl conjugation
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcilium assembly

Inferred from sequence or structural similarity. Source: UniProtKB

determination of left/right symmetry

Inferred from electronic annotation. Source: Ensembl

dorsal/ventral pattern formation

Inferred from electronic annotation. Source: Ensembl

formation of radial glial scaffolds

Inferred from sequence or structural similarity. Source: UniProtKB

interneuron migration from the subpallium to the cortex

Inferred from sequence or structural similarity. Source: UniProtKB

neural tube patterning

Inferred from sequence or structural similarity. Source: UniProtKB

nonmotile primary cilium assembly

Inferred from sequence or structural similarity. Source: UniProtKB

small GTPase mediated signal transduction

Inferred from electronic annotation. Source: InterPro

smoothened signaling pathway

Inferred from sequence or structural similarity. Source: UniProtKB

   Cellular_componentciliary membrane

Inferred from sequence or structural similarity. Source: UniProtKB

cilium

Inferred from sequence or structural similarity. Source: UniProtKB

intracellular

Inferred from electronic annotation. Source: InterPro

primary cilium

Inferred from sequence or structural similarity. Source: UniProtKB

   Molecular_functionGTP binding

Inferred from electronic annotation. Source: UniProtKB-KW

protein binding

Inferred from physical interaction Ref.7. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q3SXY8-1)

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.
Isoform 2 (identifier: Q3SXY8-2)

The sequence of this isoform differs from the canonical sequence as follows:
     21-127: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: Q3SXY8-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-103: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 428428ADP-ribosylation factor-like protein 13B
PRO_0000251137

Regions

Nucleotide binding28 – 358GTP By similarity
Nucleotide binding71 – 755GTP By similarity
Nucleotide binding130 – 1334GTP By similarity
Coiled coil192 – 24554 Potential
Compositional bias369 – 41951Pro-rich

Amino acid modifications

Lipidation81S-palmitoyl cysteine By similarity
Lipidation91S-palmitoyl cysteine By similarity
Cross-link329Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Probable

Natural variations

Alternative sequence1 – 103103Missing in isoform 3.
VSP_045421
Alternative sequence21 – 127107Missing in isoform 2.
VSP_020733
Natural variant791R → Q in JBTS8; reduces binding to GTP. Ref.13
VAR_054371
Natural variant2001R → C in JBTS8. Ref.13
VAR_054372
Natural variant3481T → S.
Corresponds to variant rs33944211 [ dbSNP | Ensembl ].
VAR_048319
Natural variant3901R → L in a nephronophthisis (NPHP) patient. Ref.14
VAR_069190

Experimental info

Mutagenesis351T → N: Does not affect localization to cilia. Ref.6
Mutagenesis1301N → I: Does not affect localization to cilia. Ref.6
Mutagenesis2311K → R: No effect. Abolishes sumoylation; when associated with R-270; R-275; R-276; R-279 and R-329. Ref.8
Mutagenesis2701K → R: No effect. Abolishes sumoylation; when associated with R-231; R-275; R-276; R-279 and R-329. Ref.8
Mutagenesis2751K → R: No effect. Abolishes sumoylation; when associated with R-231; R-270; R-276; R-279 and R-329. Ref.8
Mutagenesis2761K → R: No effect. Abolishes sumoylation; when associated with R-231; R-270; R-275; R-279 and R-329. Ref.8
Mutagenesis2791K → R: No effect. Abolishes sumoylation; when associated with R-231; R-270; R-275; R-276 and R-329. Ref.8
Mutagenesis3291K → R: Abolishes sumoylation. Abolishes sumoylation; when associated with R-231; R-270; R-275; R-276 and R-279. Ref.8
Sequence conflict2751K → KK in CAD28544. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified October 11, 2005. Version 1.
Checksum: 002B38A38D1F7BDD

FASTA42848,643
        10         20         30         40         50         60 
MFSLMASCCG WFKRWREPVR KVTLLMVGLD NAGKTATAKG IQGEYPEDVA PTVGFSKINL 

        70         80         90        100        110        120 
RQGKFEVTIF DLGGGIRIRG IWKNYYAESY GVIFVVDSSD EERMEETKEA MSEMLRHPRI 

       130        140        150        160        170        180 
SGKPILVLAN KQDKEGALGE ADVIECLSLE KLVNEHKCLC QIEPCSAISG YGKKIDKSIK 

       190        200        210        220        230        240 
KGLYWLLHVI ARDFDALNER IQKETTEQRA LEEQEKQERA ERVRKLREER KQNEQEQAEL 

       250        260        270        280        290        300 
DGTSGLAELD PEPTNPFQPI ASVIIENEGK LEREKKNQKM EKDSDGCHLK HKMEHEQIET 

       310        320        330        340        350        360 
QGQVNHNGQK NNEFGLVENY KEALTQQLKN EDETDRPSLE SANGKKKTKK LRMKRNHRVE 

       370        380        390        400        410        420 
PLNIDDCAPE SPTPPPPPPP VGWGTPKVTR LPKLEPLGET HHNDFYRKPL PPLAVPQRPN 


SDAHDVIS 

« Hide

Isoform 2 [UniParc].

Checksum: D4D82D271E9E7F1E
Show »

FASTA32136,795
Isoform 3 [UniParc].

Checksum: 21F4DA7BFC23125C
Show »

FASTA32537,087

References

« Hide 'large scale' references
[1]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
Tissue: Amygdala.
[2]"The DNA sequence, annotation and analysis of human chromosome 3."
Muzny D.M., Scherer S.E., Kaul R., Wang J., Yu J., Sudbrak R., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J. expand/collapse author list , Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R., Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Morgan M.B., Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Wei S., Wheeler D.A., Wright M.W., Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z., Clendenning J., Clerc-Blankenburg K.P., Chen R., Chen Z., Davis C., Delgado O., Dinh H.H., Dong W., Draper H., Ernst S., Fu G., Gonzalez-Garay M.L., Garcia D.K., Gillett W., Gu J., Hao B., Haugen E., Havlak P., He X., Hennig S., Hu S., Huang W., Jackson L.R., Jacob L.S., Kelly S.H., Kube M., Levy R., Li Z., Liu B., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Palmeiri A., Pasternak S., Perez L.M., Phelps K.A., Plopper F.J., Qiang B., Raymond C., Rodriguez R., Saenphimmachak C., Santibanez J., Shen H., Shen Y., Subramanian S., Tabor P.E., Verduzco D., Waldron L., Wang J., Wang J., Wang Q., Williams G.A., Wong G.K.-S., Yao Z., Zhang J., Zhang X., Zhao G., Zhou J., Zhou Y., Nelson D., Lehrach H., Reinhardt R., Naylor S.L., Yang H., Olson M., Weinstock G., Gibbs R.A.
Nature 440:1194-1198(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
Tissue: Brain.
[5]"Mutations in a member of the Ras superfamily of small GTP-binding proteins causes Bardet-Biedl syndrome."
Fan Y., Esmail M.A., Ansley S.J., Blacque O.E., Boroevich K., Ross A.J., Moore S.J., Badano J.L., May-Simera H., Compton D.S., Green J.S., Lewis R.A., van Haelst M.M., Parfrey P.S., Baillie D.L., Beales P.L., Katsanis N., Davidson W.S., Leroux M.R.
Nat. Genet. 36:989-993(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION.
[6]"Domain architecture of the atypical Arf-family GTPase Arl13b involved in cilia formation."
Hori Y., Kobayashi T., Kikko Y., Kontani K., Katada T.
Biochem. Biophys. Res. Commun. 373:119-124(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, GTP-BINDING, MUTAGENESIS OF THR-35 AND ASN-130.
[7]"Pitchfork regulates primary cilia disassembly and left-right asymmetry."
Kinzel D., Boldt K., Davis E.E., Burtscher I., Trumbach D., Diplas B., Attie-Bitach T., Wurst W., Katsanis N., Ueffing M., Lickert H.
Dev. Cell 19:66-77(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH PIFO.
[8]"SUMOylation of the small GTPase ARL-13 promotes ciliary targeting of sensory receptors."
Li Y., Zhang Q., Wei Q., Zhang Y., Ling K., Hu J.
J. Cell Biol. 199:589-598(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: SUMOYLATION AT LYS-329, MUTAGENESIS OF LYS-231; LYS-270; LYS-275; LYS-276; LYS-279 AND LYS-329.
[9]"Active transport and diffusion barriers restrict Joubert syndrome-associated ARL13B/ARL-13 to an inv-like ciliary membrane subdomain."
Cevik S., Sanders A.A., Van Wijk E., Boldt K., Clarke L., van Reeuwijk J., Hori Y., Horn N., Hetterschijt L., Wdowicz A., Mullins A., Kida K., Kaplan O.I., van Beersum S.E., Man Wu K., Letteboer S.J., Mans D.A., Katada T. expand/collapse author list , Kontani K., Ueffing M., Roepman R., Kremer H., Blacque O.E.
PLoS Genet. 9:E1003977-E1003977(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH IFT46 AND IFT74.
[10]"ARL13B, PDE6D, and CEP164 form a functional network for INPP5E ciliary targeting."
Humbert M.C., Weihbrecht K., Searby C.C., Li Y., Pope R.M., Sheffield V.C., Seo S.
Proc. Natl. Acad. Sci. U.S.A. 109:19691-19696(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[11]"Arl13b regulates endocytic recycling traffic."
Barral D.C., Garg S., Casalou C., Watts G.F., Sandoval J.L., Ramalho J.S., Hsu V.W., Brenner M.B.
Proc. Natl. Acad. Sci. U.S.A. 109:21354-21359(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: POSSIBLE FUNCTION.
[12]"Asymmetric inheritance of centrosome-associated primary cilium membrane directs ciliogenesis after cell division."
Paridaen J.T., Wilsch-Brauninger M., Huttner W.B.
Cell 155:333-344(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[13]"Mutations in the cilia gene ARL13B lead to the classical form of Joubert syndrome."
The international Joubert syndrome related disorders (JSRD) study group
Cantagrel V., Silhavy J.L., Bielas S.L., Swistun D., Marsh S.E., Bertrand J.Y., Audollent S., Attie-Bitach T., Holden K.R., Dobyns W.B., Traver D., Al-Gazali L., Ali B.R., Lindner T.H., Caspary T., Otto E.A., Hildebrandt F., Glass I.A. expand/collapse author list , Logan C.V., Johnson C.A., Bennett C., Brancati F., Valente E.M., Woods C.G., Gleeson J.G.
Am. J. Hum. Genet. 83:170-179(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS JBTS8 GLN-79 AND CYS-200, CHARACTERIZATION OF VARIANT JBTS8 GLN-79.
[14]"Mutation analysis of 18 nephronophthisis associated ciliopathy disease genes using a DNA pooling and next generation sequencing strategy."
Otto E.A., Ramaswami G., Janssen S., Chaki M., Allen S.J., Zhou W., Airik R., Hurd T.W., Ghosh A.K., Wolf M.T., Hoppe B., Neuhaus T.J., Bockenhauer D., Milford D.V., Soliman N.A., Antignac C., Saunier S., Johnson C.A., Hildebrandt F.
J. Med. Genet. 48:105-116(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT LEU-390.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS2924.1. [Q3SXY8-2]
CCDS2925.1. [Q3SXY8-1]
CCDS54615.1. [Q3SXY8-3]
RefSeqNP_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]
UniGeneHs.533086.

3D structure databases

ProteinModelPortalQ3SXY8.
SMRQ3SXY8. Positions 20-219.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid128353. 2 interactions.
STRING9606.ENSP00000377769.

PTM databases

PhosphoSiteQ3SXY8.

Polymorphism databases

DMDM115503786.

Proteomic databases

MaxQBQ3SXY8.
PaxDbQ3SXY8.
PRIDEQ3SXY8.

Protocols and materials databases

DNASU200894.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000303097; ENSP00000306225; ENSG00000169379. [Q3SXY8-2]
ENST00000394222; ENSP00000377769; ENSG00000169379. [Q3SXY8-1]
ENST00000471138; ENSP00000420780; ENSG00000169379. [Q3SXY8-1]
ENST00000535334; ENSP00000445145; ENSG00000169379. [Q3SXY8-3]
GeneID200894.
KEGGhsa:200894.
UCSCuc003drc.3. human. [Q3SXY8-1]
uc003drd.3. human. [Q3SXY8-2]

Organism-specific databases

CTD200894.
GeneCardsGC03P093698.
GeneReviewsARL13B.
HGNCHGNC:25419. ARL13B.
HPAHPA048926.
MIM608922. gene.
612291. phenotype.
neXtProtNX_Q3SXY8.
Orphanet475. Joubert syndrome.
PharmGKBPA134975272.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1100.
HOGENOMHOG000034031.
HOVERGENHBG060221.
InParanoidQ3SXY8.
KOK07962.
OMAINLRQGK.
PhylomeDBQ3SXY8.
TreeFamTF105476.

Gene expression databases

ArrayExpressQ3SXY8.
BgeeQ3SXY8.
CleanExHS_ARL13B.
GenevestigatorQ3SXY8.

Family and domain databases

Gene3D3.40.50.300. 1 hit.
InterProIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR024156. Small_GTPase_ARF.
IPR006689. Small_GTPase_ARF/SAR.
[Graphical view]
PfamPF00025. Arf. 1 hit.
[Graphical view]
PRINTSPR00328. SAR1GTPBP.
SUPFAMSSF52540. SSF52540. 1 hit.
TIGRFAMsTIGR00231. small_GTP. 1 hit.
PROSITEPS51417. ARF. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSARL13B. human.
GeneWikiARL13B.
GenomeRNAi200894.
NextBio89994.
PROQ3SXY8.
SOURCESearch...

Entry information

Entry nameAR13B_HUMAN
AccessionPrimary (citable) accession number: Q3SXY8
Secondary accession number(s): D3DN29 expand/collapse secondary AC list , G3V1S8, Q504W8, Q8TCL5
Entry history
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: October 11, 2005
Last modified: July 9, 2014
This is version 84 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 3

Human chromosome 3: entries, gene names and cross-references to MIM