Human Gene CROCC (ENST00000375541.10_4) from GENCODE V47lift37
  Description: ciliary rootlet coiled-coil, rootletin (from RefSeq NM_014675.5)
Gencode Transcript: ENST00000375541.10_4
Gencode Gene: ENSG00000058453.17_15
Transcript (Including UTRs)
   Position: hg19 chr1:17,248,426-17,299,459 Size: 51,034 Total Exon Count: 37 Strand: +
Coding Region
   Position: hg19 chr1:17,248,514-17,298,941 Size: 50,428 Coding Exon Count: 37 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:17,248,426-17,299,459)mRNA (may differ from genome)Protein (2017 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CROCC_HUMAN
DESCRIPTION: RecName: Full=Rootletin; AltName: Full=Ciliary rootlet coiled-coil protein;
FUNCTION: Major structural component of the ciliary rootlet, a cytoskeletal-like structure in ciliated cells which originates from the basal body at the proximal end of a cilium and extends proximally toward the cell nucleus. Contributes to centrosome cohesion before mitosis.
SUBUNIT: Homopolymer. Interacts with KLC3, NEK2 and the N-terminus of CEP250.
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton, centrosome, centriole. Note=In ciliated cells, associated with ciliary rootlets. In non-ciliated cells, localized between, around and at the proximal ends of the centrioles. Dissociates from the centrioles at the onset of mitosis and reassociates with them at anaphase.
PTM: Phosphorylated by NEK2 which may regulate its association with centrosomes. Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the rootletin family.

-  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

+  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: 23.06 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 344.92 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 -38.9088-0.442 Picture PostScript Text
3' UTR -200.70518-0.387 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
IPR026733 - Rootletin

Pfam Domains:
PF15035 - Ciliary rootlet component, centrosome cohesion

SCOP Domains:
90257 - Myosin rod fragments
57997 - Tropomyosin

ModBase Predicted Comparative 3D Structure on Q5TZA2
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0005198 structural molecule activity
GO:0005515 protein binding
GO:0019894 kinesin binding

Biological Process:
GO:0007049 cell cycle
GO:0007098 centrosome cycle
GO:0008104 protein localization
GO:0010457 centriole-centriole cohesion
GO:0010669 epithelial structure maintenance
GO:0030030 cell projection organization
GO:0032053 ciliary basal body organization
GO:0033365 protein localization to organelle
GO:0045494 photoreceptor cell maintenance
GO:0045724 positive regulation of cilium assembly
GO:0051656 establishment of organelle localization
GO:1903566 positive regulation of protein localization to cilium

Cellular Component:
GO:0001917 photoreceptor inner segment
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005814 centriole
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005929 cilium
GO:0015629 actin cytoskeleton
GO:0035253 ciliary rootlet
GO:0042995 cell projection
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK026910 - Homo sapiens cDNA: FLJ23257 fis, clone COL05579.
AL834169 - Homo sapiens mRNA; cDNA DKFZp762M2112 (from clone DKFZp762M2112).
AB007914 - Homo sapiens mRNA for KIAA0445 protein, partial cds.
BC126911 - Homo sapiens ciliary rootlet coiled-coil, rootletin, mRNA (cDNA clone IMAGE:40073934), partial cds.
BC126912 - Homo sapiens ciliary rootlet coiled-coil, rootletin, mRNA (cDNA clone IMAGE:40073937), partial cds.
JD186864 - Sequence 167888 from Patent EP1572962.
JD540332 - Sequence 521356 from Patent EP1572962.
JD438528 - Sequence 419552 from Patent EP1572962.
JD200015 - Sequence 181039 from Patent EP1572962.
JD264810 - Sequence 245834 from Patent EP1572962.
JD420420 - Sequence 401444 from Patent EP1572962.
BC127868 - Homo sapiens cDNA clone IMAGE:40133403, partial cds.
JD540412 - Sequence 521436 from Patent EP1572962.
JD458109 - Sequence 439133 from Patent EP1572962.
JD210444 - Sequence 191468 from Patent EP1572962.
JD416044 - Sequence 397068 from Patent EP1572962.
JD096923 - Sequence 77947 from Patent EP1572962.
DQ139275 - Homo sapiens Tax1-binding protein 2 mRNA, complete cds, alternatively spliced.
JD460894 - Sequence 441918 from Patent EP1572962.
JD437130 - Sequence 418154 from Patent EP1572962.
JD373157 - Sequence 354181 from Patent EP1572962.
JD044449 - Sequence 25473 from Patent EP1572962.
DQ583199 - Homo sapiens piRNA piR-50311, complete sequence.
JD071042 - Sequence 52066 from Patent EP1572962.
AF527734 - Homo sapiens medulloblastoma antigen MU-MB-2.42 mRNA, partial cds.
JD054943 - Sequence 35967 from Patent EP1572962.
JD426443 - Sequence 407467 from Patent EP1572962.
JD200839 - Sequence 181863 from Patent EP1572962.
MH807442 - Homo sapiens Tax1-binding protein 2 isoform 2 (TAX1BP2) mRNA, complete cds.

-  Other Names for This Gene
  Alternate Gene Symbols: CROCC , CROCC_HUMAN, ENST00000375541.1, ENST00000375541.2, ENST00000375541.3, ENST00000375541.4, ENST00000375541.5, ENST00000375541.6, ENST00000375541.7, ENST00000375541.8, ENST00000375541.9, KIAA0445 , NM_014675, Q2VHY3, Q5TZA2, Q66GT7, Q7Z2L4, Q7Z5D7, uc318mik.1, uc318mik.2
UCSC ID: ENST00000375541.10_4
RefSeq Accession: NM_014675.5
Protein: Q5TZA2 (aka CROCC_HUMAN)

-  Gene Model Information
  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.