Human Gene WDR35 (uc002rdi.3)
  Description: Homo sapiens WD repeat domain 35 (WDR35), transcript variant 1, mRNA.
RefSeq Summary (NM_001006657): This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. Two patients with Sensenbrenner syndrome / cranioectodermal dysplasia (CED) were identified with mutations in this gene, consistent with a possible ciliary function.[provided by RefSeq, Sep 2010].
Transcript (Including UTRs)
   Position: hg19 chr2:20,110,029-20,189,884 Size: 79,856 Total Exon Count: 28 Strand: -
Coding Region
   Position: hg19 chr2:20,113,319-20,189,776 Size: 76,458 Coding Exon Count: 28 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:20,110,029-20,189,884)mRNA (may differ from genome)Protein (1181 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: WDR35_HUMAN
DESCRIPTION: RecName: Full=WD repeat-containing protein 35; AltName: Full=Intraflagellar transport protein 121 homolog;
FUNCTION: May promote CASP3 activation and TNF-stimulated apoptosis. Required for ciliogenesis.
SUBUNIT: Interacts with IFT43.
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton, centrosome (By similarity). Cytoplasm, cytoskeleton, cilium axoneme (By similarity). Cytoplasm, cytoskeleton, cilium basal body (By similarity).
INDUCTION: By TNF.
DISEASE: Defects in WDR35 are the cause of cranioectodermal dysplasia type 2 (CED2) [MIM:613610]. A disorder characterized by craniofacial, skeletal and ectodermal abnormalities. Clinical features include short stature, dolichocephaly, craniosynostosis, narrow thorax with pectus excavatum, short limbs, brachydactyly, joint laxity, narrow palpebral fissures, telecanthus with hypertelorism, low-set simple ears, everted lower lip, and short neck. Teeth abnormalities included widely spaced, hypoplastic and fused teeth.
DISEASE: Defects in WDR35 are the cause of short rib-polydactyly syndrome type 5 (SRPS5) [MIM:614091]. A lethal skeletal dysplasia characterized by markedly short ribs, short limbs, polydactyly, narrow thorax, and multiple anomalies of major organs, including heart, intestines, genitalia, kidney, liver, and pancreas. Additional SRPS5 hallmarks are acromesomelic hypomineralization, campomelia, polysyndactyly, laterality defects, and cystic kidneys. Note=WDR35 mutations cause short rib-polydactyly syndrome through impaired cilia formation. Primary fibroblasts from SRPS5 patients lacking WDR35 fail to produce cilia (PubMed:21473986).
SIMILARITY: Contains 5 WD repeats.
SEQUENCE CAUTION: Sequence=BAA92574.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: WDR35
Diseases sorted by gene-association score: short-rib thoracic dysplasia 7 with or without polydactyly* (1330), cranioectodermal dysplasia 2* (1329), cranioectodermal dysplasia 1* (332), short-rib thoracic dysplasia 3 with or without polydactyly* (138), ellis-van creveld syndrome (18), polydactyly (10), asphyxiating thoracic dystrophy (7), hemophagocytic lymphohistiocytosis, familial, 2 (7), hemophagocytic lymphohistiocytosis, familial, 1 (6), ciliopathy (3), cleft lip/palate (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.79 RPKM in Testis
Total median expression: 165.61 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -43.10108-0.399 Picture PostScript Text
3' UTR -879.273290-0.267 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR017986 - WD40_repeat_dom
IPR017233 - WD_repeat_p35

Pfam Domains:
PF12894 - Anaphase-promoting complex subunit 4 WD40 domain

SCOP Domains:
48452 - TPR-like
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Prolyl oligopeptidase, N-terminal domain
69322 - Tricorn protease domain 2
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - Dipeptidyl peptidase IV/CD26, N-terminal domain

ModBase Predicted Comparative 3D Structure on Q9P2L0
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0035091 phosphatidylinositol binding

Biological Process:
GO:0009636 response to toxic substance
GO:0010629 negative regulation of gene expression
GO:0030030 cell projection organization
GO:0032496 response to lipopolysaccharide
GO:0035721 intraciliary retrograde transport
GO:0035735 intraciliary transport involved in cilium assembly
GO:0043065 positive regulation of apoptotic process
GO:0043280 positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0045019 negative regulation of nitric oxide biosynthetic process
GO:0060271 cilium assembly
GO:0061512 protein localization to cilium
GO:0071333 cellular response to glucose stimulus
GO:0071356 cellular response to tumor necrosis factor
GO:0090200 positive regulation of release of cytochrome c from mitochondria
GO:0097421 liver regeneration
GO:1901555 response to paclitaxel
GO:1905705 cellular response to paclitaxel
GO:1990830 cellular response to leukemia inhibitory factor

Cellular Component:
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005856 cytoskeleton
GO:0005929 cilium
GO:0005930 axoneme
GO:0030991 intraciliary transport particle A
GO:0036064 ciliary basal body
GO:0042995 cell projection
GO:0097542 ciliary tip


-  Descriptions from all associated GenBank mRNAs
  AB037757 - Homo sapiens KIAA1336 mRNA for KIAA1336 protein.
BC036659 - Homo sapiens WD repeat domain 35, mRNA (cDNA clone MGC:33196 IMAGE:5266940), complete cds.
AK122917 - Homo sapiens cDNA FLJ16596 fis, clone TESTI4005635, highly similar to WD repeat protein 35.
AK315094 - Homo sapiens cDNA, FLJ96052.
AB385451 - Synthetic construct DNA, clone: pF1KA1336, Homo sapiens WDR35 gene for WD repeat protein 35, complete cds, without stop codon, in Flexi system.
BC033951 - Homo sapiens WD repeat domain 35, mRNA (cDNA clone IMAGE:5286529).
AK022866 - Homo sapiens cDNA FLJ12804 fis, clone NT2RP2002219.
JD303406 - Sequence 284430 from Patent EP1572962.
JD500848 - Sequence 481872 from Patent EP1572962.
JD073535 - Sequence 54559 from Patent EP1572962.
JD193207 - Sequence 174231 from Patent EP1572962.
AK091205 - Homo sapiens cDNA FLJ33886 fis, clone CTONG2007399, highly similar to WD repeat protein 35.
AX746847 - Sequence 372 from Patent EP1308459.
JD501446 - Sequence 482470 from Patent EP1572962.
JD226218 - Sequence 207242 from Patent EP1572962.
JD148512 - Sequence 129536 from Patent EP1572962.
AL832903 - Homo sapiens mRNA; cDNA DKFZp762F1313 (from clone DKFZp762F1313).

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9P2L0 (Reactome details) participates in the following event(s):

R-HSA-5617829 Assembly of IFT A complex
R-HSA-5624949 Assembly of the anterograde IFT train
R-HSA-5625424 The retrograde IFT train dissociates
R-HSA-5624952 Assembly of the retrograde IFT train
R-HSA-5625421 The anterograde IFT train dissociates
R-HSA-5610726 The IFT-A complex recruits TULP3
R-HSA-5610725 TULP3 is required for GPR161 localization in the cilium
R-HSA-5620924 Intraflagellar transport
R-HSA-5617833 Cilium Assembly
R-HSA-5610787 Hedgehog 'off' state
R-HSA-1852241 Organelle biogenesis and maintenance
R-HSA-5358351 Signaling by Hedgehog
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B3KVI5, IFT121, KIAA1336, NM_001006657, NP_001006658, Q4ZG01, Q8NE11, Q9P2L0, WDR35_HUMAN
UCSC ID: uc002rdi.3
RefSeq Accession: NM_001006657
Protein: Q9P2L0 (aka WDR35_HUMAN or WD35_HUMAN)
CCDS: CCDS1695.1, CCDS33152.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene WDR35:
ce-dysp (Cranioectodermal Dysplasia)
evc (Ellis-van Creveld Syndrome)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001006657.1
exon count: 28CDS single in 3' UTR: no RNA size: 6957
ORF size: 3546CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 7292.00frame shift in genome: no % Coverage: 99.81
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.