Human Gene CLIP4 (ENST00000401605.5) from GENCODE V44
  Description: Homo sapiens CAP-Gly domain containing linker protein family member 4 (CLIP4), transcript variant 3, mRNA. (from RefSeq NM_001287528)
Gencode Transcript: ENST00000401605.5
Gencode Gene: ENSG00000115295.21
Transcript (Including UTRs)
   Position: hg38 chr2:29,097,705-29,174,713 Size: 77,009 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg38 chr2:29,121,389-29,174,449 Size: 53,061 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:29,097,705-29,174,713)mRNA (may differ from genome)Protein (599 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMGIneXtProtPubMed
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CLIP4_HUMAN
DESCRIPTION: RecName: Full=CAP-Gly domain-containing linker protein 4; AltName: Full=Restin-like protein 2;
SIMILARITY: Contains 3 ANK repeats.
SIMILARITY: Contains 3 CAP-Gly domains.
SEQUENCE CAUTION: Sequence=BAB14974.1; Type=Erroneous initiation;

-  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


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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.39 RPKM in Muscle - Skeletal
Total median expression: 469.82 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 -77.90258-0.302 Picture PostScript Text
3' UTR -50.90264-0.193 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
IPR002110 - Ankyrin_rpt
IPR020683 - Ankyrin_rpt-contain_dom
IPR000938 - CAP-Gly_domain

Pfam Domains:
PF12796 - Ankyrin repeats (3 copies)
PF01302 - CAP-Gly domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2Z0W - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8N3C7
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Cellular Component:
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AF433661 - Homo sapiens unknown mRNA.
AK302325 - Homo sapiens cDNA FLJ55798 complete cds, highly similar to Restin-like protein 2.
AK291595 - Homo sapiens cDNA FLJ75496 complete cds, highly similar to Homo sapiens restin-like 2 (RSNL2), mRNA.
AK057267 - Homo sapiens cDNA FLJ32705 fis, clone TESTI2000600, weakly similar to RESTIN.
BC013862 - Homo sapiens CAP-GLY domain containing linker protein family, member 4, mRNA (cDNA clone IMAGE:3923805).
AL834443 - Homo sapiens mRNA; cDNA DKFZp761O0610 (from clone DKFZp761O0610).
AB209042 - Homo sapiens premature mRNA for hypothetical protein FLJ32705 variant.
BC126167 - Homo sapiens CAP-GLY domain containing linker protein family, member 4, mRNA (cDNA clone MGC:161445 IMAGE:8991883), complete cds.
BC136331 - Homo sapiens CAP-GLY domain containing linker protein family, member 4, mRNA (cDNA clone MGC:167941 IMAGE:9020318), complete cds.
HQ258339 - Synthetic construct Homo sapiens clone IMAGE:100072648 CAP-GLY domain containing linker protein family, member 4 (CLIP4) (CLIP4) gene, encodes complete protein.
KJ899560 - Synthetic construct Homo sapiens clone ccsbBroadEn_08954 CLIP4 gene, encodes complete protein.
AK304384 - Homo sapiens cDNA FLJ55608 complete cds, highly similar to Restin-like protein 2.
BC107760 - Homo sapiens CAP-GLY domain containing linker protein family, member 4, mRNA (cDNA clone IMAGE:4616730), with apparent retained intron.
JD167208 - Sequence 148232 from Patent EP1572962.
BC015310 - Homo sapiens CAP-GLY domain containing linker protein family, member 4, mRNA (cDNA clone IMAGE:4431888), partial cds.
JD558223 - Sequence 539247 from Patent EP1572962.
JD333700 - Sequence 314724 from Patent EP1572962.
AK225074 - Homo sapiens mRNA for restin-like 2 variant, clone: CAS01594.
AK024722 - Homo sapiens cDNA: FLJ21069 fis, clone CAS01594.
CU677253 - Synthetic construct Homo sapiens gateway clone IMAGE:100019661 5' read CLIP4 mRNA.
KJ906319 - Synthetic construct Homo sapiens clone ccsbBroadEn_15989 CLIP4 gene, encodes complete protein.
JD548769 - Sequence 529793 from Patent EP1572962.
JD110362 - Sequence 91386 from Patent EP1572962.
JD102543 - Sequence 83567 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A0AV10, B2RMQ3, B7Z7N8, CLIP4_HUMAN, ENST00000401605.1, ENST00000401605.2, ENST00000401605.3, ENST00000401605.4, NM_001287528, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0, RSNL2, uc002rmu.1, uc002rmu.2, uc002rmu.3, uc002rmu.4, uc002rmu.5
UCSC ID: ENST00000401605.5
RefSeq Accession: NM_001287528
Protein: Q8N3C7 (aka CLIP4_HUMAN)
CCDS: CCDS74502.1

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