Human Gene KIF3A (uc003kxo.3)
  Description: Homo sapiens kinesin family member 3A (KIF3A), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:132,028,323-132,073,265 Size: 44,943 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr5:132,032,326-132,073,111 Size: 40,786 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:132,028,323-132,073,265)mRNA (may differ from genome)Protein (699 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: KIF3A_HUMAN
DESCRIPTION: RecName: Full=Kinesin-like protein KIF3A; AltName: Full=Microtubule plus end-directed kinesin motor 3A;
FUNCTION: Microtubule-based anterograde translocator for membranous organelles. Plus end-directed microtubule sliding activity in vitro. Plays a role in primary cilia formation (By similarity).
SUBUNIT: Heterodimer of KIF3A and KIF3B. Interacts with PIFO. Interacts with CLN3.
INTERACTION: Q9NRI5:DISC1; NbExp=3; IntAct=EBI-1104844, EBI-529989;
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton (Probable). Cell projection, cilium (By similarity).
SIMILARITY: Belongs to the kinesin-like protein family. Kinesin II subfamily.
SIMILARITY: Contains 1 kinesin-motor domain.
SEQUENCE CAUTION: Sequence=AAC04475.1; Type=Erroneous gene model prediction; Sequence=BAD93017.1; 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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): KIF3A
CDC HuGE Published Literature: KIF3A
Positive Disease Associations: Albumins , Dermatitis, Atopic
Related Studies:
  1. Albumins
    , , . [PubMed 0]
  2. Dermatitis, Atopic
    Lavinia Paternoster et al. Nature genetics 2012, Meta-analysis of genome-wide association studies identifies three new risk loci for atopic dermatitis., Nature genetics. [PubMed 22197932]

-  MalaCards Disease Associations
  MalaCards Gene Search: KIF3A
Diseases sorted by gene-association score: retinitis pigmentosa (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 18.02 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 244.88 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 -77.00154-0.500 Picture PostScript Text
3' UTR -1333.334003-0.333 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
IPR019821 - Kinesin_motor_CS
IPR001752 - Kinesin_motor_dom

Pfam Domains:
PF00225 - Kinesin motor domain
PF16796 - Microtubule binding

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q9Y496
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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 BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003777 microtubule motor activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008017 microtubule binding
GO:0008574 ATP-dependent microtubule motor activity, plus-end-directed
GO:0017137 Rab GTPase binding
GO:0030507 spectrin binding

Biological Process:
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER
GO:0006996 organelle organization
GO:0007018 microtubule-based movement
GO:0010457 centriole-centriole cohesion
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0022008 neurogenesis
GO:0030030 cell projection organization
GO:0034454 microtubule anchoring at centrosome
GO:0035735 intraciliary transport involved in cilium assembly
GO:0060271 cilium assembly
GO:0072383 plus-end-directed vesicle transport along microtubule

Cellular Component:
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005814 centriole
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0005929 cilium
GO:0015630 microtubule cytoskeleton
GO:0016939 kinesin II complex
GO:0042995 cell projection
GO:0070062 extracellular exosome
GO:0097542 ciliary tip
GO:0005876 spindle microtubule


-  Descriptions from all associated GenBank mRNAs
  JD330923 - Sequence 311947 from Patent EP1572962.
JD242681 - Sequence 223705 from Patent EP1572962.
JD511967 - Sequence 492991 from Patent EP1572962.
JD220922 - Sequence 201946 from Patent EP1572962.
BC045542 - Homo sapiens kinesin family member 3A, mRNA (cDNA clone MGC:57178 IMAGE:5298675), complete cds.
AB209780 - Homo sapiens mRNA for Kinesin-like protein KIF3A variant protein.
AK295089 - Homo sapiens cDNA FLJ60533 complete cds, highly similar to Kinesin-like protein KIF3A.
AF041853 - Homo sapiens kinesin family member protein KIF3A mRNA, complete cds.
AM177178 - Homo sapiens mRNA for kinesin-like protein KIF3Abeta (KIF3A gene).
AK313359 - Homo sapiens cDNA, FLJ93885.
KJ904667 - Synthetic construct Homo sapiens clone ccsbBroadEn_14061 KIF3A gene, encodes complete protein.
AB463090 - Synthetic construct DNA, clone: pF1KB5220, Homo sapiens KIF3A gene for kinesin family member 3A, without stop codon, in Flexi system.
BC020890 - Homo sapiens kinesin family member 3A, mRNA (cDNA clone IMAGE:4693968), partial cds.
BC039592 - Homo sapiens, clone IMAGE:5403936, mRNA, partial cds.
BC032599 - Homo sapiens kinesin family member 3A, mRNA (cDNA clone IMAGE:5533541), partial cds.
CU692264 - Synthetic construct Homo sapiens gateway clone IMAGE:100020952 5' read KIF3A mRNA.

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

Protein Q9Y496 (Reactome details) participates in the following event(s):

R-HSA-984708 Kinesin-2 is a heterotrimer
R-HSA-5632667 SMO dimer binds ARRB and KIF3A
R-HSA-2316347 RAB4A:GTP binds KIF3 and activates KIF3
R-HSA-984733 Kinesin-3 is a dimer
R-HSA-983266 Kinesins bind microtubules
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-6811426 Retrograde COPI vesicles bind kinesin and microtubules
R-HSA-6811423 Retrograde vesicle is tethered at the ER by the NRZ complex and t-SNAREs
R-HSA-5624949 Assembly of the anterograde IFT train
R-HSA-983189 Kinesins
R-HSA-5635838 Activation of SMO
R-HSA-1445148 Translocation of GLUT4 to the plasma membrane
R-HSA-983231 Factors involved in megakaryocyte development and platelet production
R-HSA-5632684 Hedgehog 'on' state
R-HSA-199991 Membrane Trafficking
R-HSA-109582 Hemostasis
R-HSA-5358351 Signaling by Hedgehog
R-HSA-5620924 Intraflagellar transport
R-HSA-2132295 MHC class II antigen presentation
R-HSA-6811434 COPI-dependent Golgi-to-ER retrograde traffic
R-HSA-5653656 Vesicle-mediated transport
R-HSA-162582 Signal Transduction
R-HSA-5617833 Cilium Assembly
R-HSA-1280218 Adaptive Immune System
R-HSA-8856688 Golgi-to-ER retrograde transport
R-HSA-1852241 Organelle biogenesis and maintenance
R-HSA-168256 Immune System
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic

-  Other Names for This Gene
  Alternate Gene Symbols: A8MSW9, KIF3, KIF3A_HUMAN, NM_007054, NP_008985, Q59EN1, Q86XE9, Q9Y496, Q9Y6V4
UCSC ID: uc003kxo.3
RefSeq Accession: NM_007054
Protein: Q9Y496 (aka KIF3A_HUMAN or KF3A_HUMAN)
CCDS: CCDS34235.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_007054.5
exon count: 17CDS single in 3' UTR: no RNA size: 6257
ORF size: 2100CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4351.00frame shift in genome: no % Coverage: 100.00
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.