Human Gene CLIP2 (uc003uam.3) Description and Page Index
  Description: Homo sapiens CAP-GLY domain containing linker protein 2 (CLIP2), transcript variant 1, mRNA.
RefSeq Summary (NM_003388): The protein encoded by this gene belongs to the family of cytoplasmic linker proteins, which have been proposed to mediate the interaction between specific membranous organelles and microtubules. This protein was found to associate with both microtubules and an organelle called the dendritic lamellar body. This gene is hemizygously deleted in Williams syndrome, a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.23. Alternative splicing of this gene generates 2 transcript variants. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr7:73,703,805-73,820,273 Size: 116,469 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr7:73,731,877-73,818,178 Size: 86,302 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:73,703,805-73,820,273)mRNA (may differ from genome)Protein (1046 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: CLIP2_HUMAN
DESCRIPTION: RecName: Full=CAP-Gly domain-containing linker protein 2; AltName: Full=Cytoplasmic linker protein 115; Short=CLIP-115; AltName: Full=Cytoplasmic linker protein 2; AltName: Full=Williams-Beuren syndrome chromosomal region 3 protein; AltName: Full=Williams-Beuren syndrome chromosomal region 4 protein;
FUNCTION: Seems to link microtubules to dendritic lamellar body (DLB), a membranous organelle predominantly present in bulbous dendritic appendages of neurons linked by dendrodendritic gap junctions. May operate in the control of brain-specific organelle translocations (By similarity).
SUBUNIT: Interacts with CLASP1 and CLASP2.
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Cytoplasm, cytoskeleton (By similarity). Note=Associated with the cytoskeleton (By similarity).
DISEASE: Note=CLIP2 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. Haploinsufficiency of CLIP2 may be the cause of certain cardiovascular and musculo-skeletal abnormalities observed in the disease.
SIMILARITY: Contains 2 CAP-Gly domains.
SEQUENCE CAUTION: Sequence=BAA22960.2; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CLIP2
CDC HuGE Published Literature: CLIP2
Positive Disease Associations: Leukocyte Count
Related Studies:
  1. Leukocyte Count
    , , . [PubMed 0]
  2. Leukocyte Count
    , , . [PubMed 0]
  3. Leukocyte Count
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CLIP2
Diseases sorted by gene-association score: williams-beuren syndrome* (27)
* = Manually curated disease association

-  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: 46.44 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 777.60 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 -184.80327-0.565 Picture PostScript Text
3' UTR -874.342095-0.417 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
IPR000938 - CAP-Gly_domain

Pfam Domains:
PF01302 - CAP-Gly domain

SCOP Domains:
74924 - Cap-Gly domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2CP2
- NMR MuPIT

2CP3
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9UDT6
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008017 microtubule binding
GO:0051010 microtubule plus-end binding

Cellular Component:
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0005875 microtubule associated complex
GO:0005881 cytoplasmic microtubule
GO:0035371 microtubule plus-end


-  Descriptions from all associated GenBank mRNAs
  AB006629 - Homo sapiens mRNA for KIAA0291 gene.
BC150332 - Homo sapiens CAP-GLY domain containing linker protein 2, mRNA (cDNA clone MGC:167827 IMAGE:8860506), complete cds.
HM005353 - Homo sapiens clone HTL-T-40 testicular tissue protein Li 40 mRNA, complete cds.
AB462969 - Synthetic construct DNA, clone: pF1KA0291, Homo sapiens CLIP2 gene for CAP-GLY domain containing linker protein 2, without stop codon, in Flexi system.
BC140369 - Synthetic construct Homo sapiens clone IMAGE:100014349, MGC:173213 CAP-GLY domain containing linker protein 2 (CLIP2) mRNA, encodes complete protein.
BC148702 - Synthetic construct Homo sapiens clone IMAGE:100015679, MGC:183149 CAP-GLY domain containing linker protein 2 (CLIP2) mRNA, encodes complete protein.
AY927469 - Homo sapiens mRNA sequence.
AY295764 - Homo sapiens cytoplasmic linker 2 (CYLN2) mRNA, partial cds.
JD478302 - Sequence 459326 from Patent EP1572962.
JD461754 - Sequence 442778 from Patent EP1572962.
JD134085 - Sequence 115109 from Patent EP1572962.
JD125412 - Sequence 106436 from Patent EP1572962.
JD395075 - Sequence 376099 from Patent EP1572962.
JD485811 - Sequence 466835 from Patent EP1572962.
JD125847 - Sequence 106871 from Patent EP1572962.
JD404572 - Sequence 385596 from Patent EP1572962.
JD496196 - Sequence 477220 from Patent EP1572962.
AK095186 - Homo sapiens cDNA FLJ37867 fis, clone BRSSN2016905.
DQ579088 - Homo sapiens piRNA piR-47200, complete sequence.
AY927468 - Homo sapiens mRNA sequence.
JD547458 - Sequence 528482 from Patent EP1572962.
JD506409 - Sequence 487433 from Patent EP1572962.
JD122270 - Sequence 103294 from Patent EP1572962.
JD475010 - Sequence 456034 from Patent EP1572962.
JD118151 - Sequence 99175 from Patent EP1572962.
JD164970 - Sequence 145994 from Patent EP1572962.
JD227150 - Sequence 208174 from Patent EP1572962.
JD120049 - Sequence 101073 from Patent EP1572962.
JD216898 - Sequence 197922 from Patent EP1572962.
JD100080 - Sequence 81104 from Patent EP1572962.
JD126772 - Sequence 107796 from Patent EP1572962.
JD131691 - Sequence 112715 from Patent EP1572962.
JD193939 - Sequence 174963 from Patent EP1572962.
JD336346 - Sequence 317370 from Patent EP1572962.
JD336347 - Sequence 317371 from Patent EP1572962.
JD488747 - Sequence 469771 from Patent EP1572962.
JD026585 - Sequence 7609 from Patent EP1572962.
JD550530 - Sequence 531554 from Patent EP1572962.
JD031110 - Sequence 12134 from Patent EP1572962.
JD294346 - Sequence 275370 from Patent EP1572962.
JD141591 - Sequence 122615 from Patent EP1572962.
JD443071 - Sequence 424095 from Patent EP1572962.
JD368800 - Sequence 349824 from Patent EP1572962.
JD065738 - Sequence 46762 from Patent EP1572962.
JD515622 - Sequence 496646 from Patent EP1572962.
JD557937 - Sequence 538961 from Patent EP1572962.
BC006259 - Homo sapiens cDNA clone IMAGE:3952627.
JD312371 - Sequence 293395 from Patent EP1572962.
JD098994 - Sequence 80018 from Patent EP1572962.
JD424947 - Sequence 405971 from Patent EP1572962.
JD059303 - Sequence 40327 from Patent EP1572962.
JD352161 - Sequence 333185 from Patent EP1572962.
JD310394 - Sequence 291418 from Patent EP1572962.
JD036596 - Sequence 17620 from Patent EP1572962.
JD560602 - Sequence 541626 from Patent EP1572962.
JD276317 - Sequence 257341 from Patent EP1572962.
JD157235 - Sequence 138259 from Patent EP1572962.
JD078627 - Sequence 59651 from Patent EP1572962.
JD298003 - Sequence 279027 from Patent EP1572962.
JD213498 - Sequence 194522 from Patent EP1572962.
JD463423 - Sequence 444447 from Patent EP1572962.
JD090117 - Sequence 71141 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CLIP2_HUMAN, CYLN2, KIAA0291, NM_003388, NP_003379, O14527, O43611, Q9UDT6, WBSCR3, WBSCR4, WSCR4
UCSC ID: uc003uam.3
RefSeq Accession: NM_003388
Protein: Q9UDT6 (aka CLIP2_HUMAN)
CCDS: CCDS5569.1, CCDS5570.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003388.4
exon count: 17CDS single in 3' UTR: no RNA size: 5563
ORF size: 3141CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 4039.50frame 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.