Human Gene COIL (ENST00000240316.5_7) from GENCODE V47lift37
  Description: coilin (from RefSeq NM_004645.3)
Gencode Transcript: ENST00000240316.5_7
Gencode Gene: ENSG00000121058.5_10
Transcript (Including UTRs)
   Position: hg19 chr17:55,015,560-55,038,411 Size: 22,852 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr17:55,016,432-55,038,380 Size: 21,949 Coding Exon Count: 7 

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Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:55,015,560-55,038,411)mRNA (may differ from genome)Protein (576 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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-  Comments and Description Text from UniProtKB
  ID: COIL_HUMAN
DESCRIPTION: RecName: Full=Coilin; AltName: Full=p80;
FUNCTION: Is a component of the nuclear coiled bodies (CBS) which are involved in the function or assembly/disassembly of nucleoplasmic snRNPs. During mitosis, CBS disassemble, coinciding with a mitotic-specific phosphorylation of p80 coilin.
SUBUNIT: Interacts with ANKS1B.
INTERACTION: Self; NbExp=3; IntAct=EBI-945751, EBI-945751; P54253:ATXN1; NbExp=3; IntAct=EBI-945751, EBI-930964; P54253-1:ATXN1; NbExp=6; IntAct=EBI-945751, EBI-930975; Q8NHQ1:CEP70; NbExp=3; IntAct=EBI-945751, EBI-739624; Q8TBB1:LNX1; NbExp=2; IntAct=EBI-945751, EBI-739832; Q9NRD5:PICK1; NbExp=3; IntAct=EBI-945751, EBI-79165; P61289:PSME3; NbExp=3; IntAct=EBI-945751, EBI-355546; Q9Y3D8:TAF9; NbExp=5; IntAct=EBI-945751, EBI-2896123; Q99986:VRK1; NbExp=9; IntAct=EBI-945751, EBI-1769146;
SUBCELLULAR LOCATION: Nucleus. Note=Nuclear coiled body located in the interchromatin space between the nucleolus and the nucleus.
TISSUE SPECIFICITY: Found in all the cell types examined.
DOMAIN: The atypical Tudor domain at the C-terminus contains two large unstructured loops, and doesn't bind methylated residues.
PTM: Symmetrical dimethylation of arginine residues within the RG repeat region modulates affinity for SMN, and thus, localization of SMN complexes to the nuclear coiled bodies.
SIMILARITY: Belongs to the coilin family.
SIMILARITY: Contains 1 Tudor domain.

-  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: COIL
Diseases sorted by gene-association score: spinal muscular atrophy (5), ischemic neuropathy (2), spherocytosis, type 1 (2)

-  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: 55.40 RPKM in Testis
Total median expression: 319.89 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 -5.2031-0.168 Picture PostScript Text
3' UTR -202.50872-0.232 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
IPR024822 - Coilin

Pfam Domains:
PF15862 - Coilin N-terminus

ModBase Predicted Comparative 3D Structure on P38432
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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    
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 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008022 protein C-terminus binding
GO:0042802 identical protein binding

Cellular Component:
GO:0001650 fibrillar center
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0015030 Cajal body
GO:0016020 membrane
GO:0016604 nuclear body


-  Descriptions from all associated GenBank mRNAs
  M58411 - H.sapiens p80-coilin mRNA, 3' end.
U06632 - Homo sapiens p80-coilin mRNA, complete cds.
BC010385 - Homo sapiens coilin, mRNA (cDNA clone MGC:13569 IMAGE:4275993), complete cds.
JD434208 - Sequence 415232 from Patent EP1572962.
JD162205 - Sequence 143229 from Patent EP1572962.
JD538405 - Sequence 519429 from Patent EP1572962.
JD183098 - Sequence 164122 from Patent EP1572962.
JD348617 - Sequence 329641 from Patent EP1572962.
JD315397 - Sequence 296421 from Patent EP1572962.
JD286217 - Sequence 267241 from Patent EP1572962.
JD110884 - Sequence 91908 from Patent EP1572962.
KJ897811 - Synthetic construct Homo sapiens clone ccsbBroadEn_07205 COIL gene, encodes complete protein.
AK313616 - Homo sapiens cDNA, FLJ94186, Homo sapiens coilin (COIL), mRNA.
DQ892927 - Synthetic construct clone IMAGE:100005557; FLH190920.01X; RZPDo839F0576D coilin (COIL) gene, encodes complete protein.
DQ896176 - Synthetic construct Homo sapiens clone IMAGE:100010636; FLH190916.01L; RZPDo839F0566D coilin (COIL) gene, encodes complete protein.
JD030694 - Sequence 11718 from Patent EP1572962.
JD026636 - Sequence 7660 from Patent EP1572962.
JD381762 - Sequence 362786 from Patent EP1572962.
CU679689 - Synthetic construct Homo sapiens gateway clone IMAGE:100019901 5' read COIL mRNA.
DQ593445 - Homo sapiens piRNA piR-33557, complete sequence.
DQ597040 - Homo sapiens piRNA piR-35106, complete sequence.
JD176775 - Sequence 157799 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2R931, CLN80, COIL_HUMAN, ENST00000240316.1, ENST00000240316.2, ENST00000240316.3, ENST00000240316.4, NM_004645, P38432, uc317ehe.1, uc317ehe.2
UCSC ID: ENST00000240316.5_7
RefSeq Accession: NM_004645.3
Protein: P38432 (aka COIL_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.