Human Gene CDC5L (ENST00000371477.4_4) from GENCODE V47lift37
  Description: cell division cycle 5 like (from RefSeq NM_001253.4)
Gencode Transcript: ENST00000371477.4_4
Gencode Gene: ENSG00000096401.8_7
Transcript (Including UTRs)
   Position: hg19 chr6:44,355,443-44,418,162 Size: 62,720 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr6:44,355,561-44,414,448 Size: 58,888 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:44,355,443-44,418,162)mRNA (may differ from genome)Protein (802 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CDC5L_HUMAN
DESCRIPTION: RecName: Full=Cell division cycle 5-like protein; Short=Cdc5-like protein; AltName: Full=Pombe cdc5-related protein;
FUNCTION: DNA-binding protein involved in cell cycle control. May act as a transcription activator. Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing.
SUBUNIT: Homodimer. Interacts with DAPK3 (By similarity). Binds DNA. Binds to adeno-pre-mRNA in an ATP-stimulated manner. Belongs to the spliceosome complex. Part of a spliceosomal 'core' complex consisting of CDC5L, PLRG1, SPF27, CCAP1, CCAP3 and CCAP6. Interacts with PLRG1, Lodestar/TTF2, and NIPP1/PPP1R8. Identified in the spliceosome C complex. Component of the PRP19-CDC5L splicing complex composed of a core complex comprising a homotetramer of PRPF19, CDC5L, PLRG1 and BCAS2, and at least three less stably associated proteins CTNNBL1, CWC15 and HSPA8. Interacts (via its C-terminus) directly in the complex with PRPF19 and BCAS2. Interacts (via its C-terminus) directly with PRGL1 (via its WD40 repeat domain); the interaction is required for mRNA splicing but not for spliceosome assembly. Also interacts with CTNNBL1.
SUBCELLULAR LOCATION: Nucleus. Nucleus speckle. Cytoplasm. Note=May shuttle between cytoplasm and nucleus.
TISSUE SPECIFICITY: Ubiquitously expressed in both fetal and adult tissues.
PTM: Phosphorylated on serine and threonine residues. Phosphorylation on Thr-411 and Thr-438 is required for CDC5L- mediated mRNA splicing. Has no effect on subcellular location nor on homodimerization. Phosphorylated in vitro by CDK2. Phosphorylation enhances interaction with PPP1R8.
DISEASE: Note=A chromosomal aberration involving CDC5L is found in multicystic renal dysplasia. Translocation t(6;19)(p21;q13.1) with USF2.
SIMILARITY: Belongs to the CEF1 family.
SIMILARITY: Contains 2 HTH myb-type DNA-binding domains.
SEQUENCE CAUTION: Sequence=BAA24862.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/cdc5l/";

-  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: CDC5L
Diseases sorted by gene-association score: cystoisosporiasis (17), renal dysplasia (14), poikiloderma with neutropenia (10), vaginal discharge (5)

-  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: 10.80 RPKM in Testis
Total median expression: 352.82 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 -42.90118-0.364 Picture PostScript Text
3' UTR -1008.803714-0.272 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
IPR021786 - DUF3351
IPR009057 - Homeodomain-like
IPR017930 - Myb_dom
IPR001005 - SANT/Myb

Pfam Domains:
PF00249 - Myb-like DNA-binding domain
PF11831 - pre-mRNA splicing factor component
PF13921 - Myb-like DNA-binding domain

SCOP Domains:
46689 - Homeodomain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2DIM - NMR MuPIT 2DIN - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q99459
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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 orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001135 transcription factor activity, RNA polymerase II transcription factor recruiting
GO:0001222 transcription corepressor binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008157 protein phosphatase 1 binding
GO:0019901 protein kinase binding
GO:0043522 leucine zipper domain binding
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding
GO:0071987 WD40-repeat domain binding

Biological Process:
GO:0000278 mitotic cell cycle
GO:0000398 mRNA splicing, via spliceosome
GO:0006281 DNA repair
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0006397 mRNA processing
GO:0006974 cellular response to DNA damage stimulus
GO:0007049 cell cycle
GO:0008380 RNA splicing
GO:0030154 cell differentiation
GO:0044344 cellular response to fibroblast growth factor stimulus
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0071352 cellular response to interleukin-2
GO:0072422 signal transduction involved in DNA damage checkpoint
GO:1904568 cellular response to wortmannin
GO:1990090 cellular response to nerve growth factor stimulus
GO:1990646 cellular response to prolactin

Cellular Component:
GO:0000974 Prp19 complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005737 cytoplasm
GO:0016020 membrane
GO:0016607 nuclear speck
GO:0032993 protein-DNA complex
GO:0048471 perinuclear region of cytoplasm
GO:0071007 U2-type catalytic step 2 spliceosome
GO:0071013 catalytic step 2 spliceosome
GO:0005662 DNA replication factor A complex


-  Descriptions from all associated GenBank mRNAs
  AK128737 - Homo sapiens cDNA FLJ16777 fis, clone BRHIP2029567, highly similar to Cell division cycle 5-like protein.
AK299738 - Homo sapiens cDNA FLJ51295 complete cds, highly similar to Cell division cycle 5-like protein.
LF208899 - JP 2014500723-A/16402: Polycomb-Associated Non-Coding RNAs.
LF208898 - JP 2014500723-A/16401: Polycomb-Associated Non-Coding RNAs.
BC001568 - Homo sapiens CDC5 cell division cycle 5-like (S. pombe), mRNA (cDNA clone MGC:5485 IMAGE:3452352), complete cds.
AB007892 - Homo sapiens KIAA0432 mRNA.
JD180627 - Sequence 161651 from Patent EP1572962.
JD332860 - Sequence 313884 from Patent EP1572962.
CU674768 - Synthetic construct Homo sapiens gateway clone IMAGE:100020410 5' read CDC5L mRNA.
AB590067 - Synthetic construct DNA, clone: pFN21AA0432, Homo sapiens CDC5L gene for CDC5 cell division cycle 5-like, without stop codon, in Flexi system.
DQ891623 - Synthetic construct clone IMAGE:100004253; FLH178725.01X; RZPDo839G05128D CDC5 cell division cycle 5-like (S. pombe) (CDC5L) gene, encodes complete protein.
DQ894814 - Synthetic construct Homo sapiens clone IMAGE:100009274; FLH178721.01L; RZPDo839G05127D CDC5 cell division cycle 5-like (S. pombe) (CDC5L) gene, encodes complete protein.
KJ896575 - Synthetic construct Homo sapiens clone ccsbBroadEn_05969 CDC5L gene, encodes complete protein.
U86753 - Human Cdc5-related protein (PCDC5RP) mRNA, complete cds.
LF323883 - JP 2014500723-A/131386: Polycomb-Associated Non-Coding RNAs.
LF323884 - JP 2014500723-A/131387: Polycomb-Associated Non-Coding RNAs.
D85423 - Homo sapiens mRNA for Cdc5, partial cds.
LF323885 - JP 2014500723-A/131388: Polycomb-Associated Non-Coding RNAs.
LF323886 - JP 2014500723-A/131389: Polycomb-Associated Non-Coding RNAs.
LF323882 - JP 2014500723-A/131385: Polycomb-Associated Non-Coding RNAs.
LF323887 - JP 2014500723-A/131390: Polycomb-Associated Non-Coding RNAs.
LF323881 - JP 2014500723-A/131384: Polycomb-Associated Non-Coding RNAs.
LF323888 - JP 2014500723-A/131391: Polycomb-Associated Non-Coding RNAs.
LF323880 - JP 2014500723-A/131383: Polycomb-Associated Non-Coding RNAs.
LF323889 - JP 2014500723-A/131392: Polycomb-Associated Non-Coding RNAs.
LF323879 - JP 2014500723-A/131382: Polycomb-Associated Non-Coding RNAs.
LF323890 - JP 2014500723-A/131393: Polycomb-Associated Non-Coding RNAs.
LF323878 - JP 2014500723-A/131381: Polycomb-Associated Non-Coding RNAs.
LF323891 - JP 2014500723-A/131394: Polycomb-Associated Non-Coding RNAs.
LF323877 - JP 2014500723-A/131380: Polycomb-Associated Non-Coding RNAs.
JD288238 - Sequence 269262 from Patent EP1572962.
JD113697 - Sequence 94721 from Patent EP1572962.
JD303885 - Sequence 284909 from Patent EP1572962.
JD077953 - Sequence 58977 from Patent EP1572962.
JD560555 - Sequence 541579 from Patent EP1572962.
JD560554 - Sequence 541578 from Patent EP1572962.
JD342452 - Sequence 323476 from Patent EP1572962.
JD342453 - Sequence 323477 from Patent EP1572962.
JD342454 - Sequence 323478 from Patent EP1572962.
DQ597608 - Homo sapiens piRNA piR-35674, complete sequence.
JD476699 - Sequence 457723 from Patent EP1572962.
JD414740 - Sequence 395764 from Patent EP1572962.
JD251844 - Sequence 232868 from Patent EP1572962.
MA559460 - JP 2018138019-A/131386: Polycomb-Associated Non-Coding RNAs.
MA559461 - JP 2018138019-A/131387: Polycomb-Associated Non-Coding RNAs.
MA559462 - JP 2018138019-A/131388: Polycomb-Associated Non-Coding RNAs.
MA559463 - JP 2018138019-A/131389: Polycomb-Associated Non-Coding RNAs.
MA559459 - JP 2018138019-A/131385: Polycomb-Associated Non-Coding RNAs.
MA559464 - JP 2018138019-A/131390: Polycomb-Associated Non-Coding RNAs.
MA559458 - JP 2018138019-A/131384: Polycomb-Associated Non-Coding RNAs.
MA559465 - JP 2018138019-A/131391: Polycomb-Associated Non-Coding RNAs.
MA559457 - JP 2018138019-A/131383: Polycomb-Associated Non-Coding RNAs.
MA559466 - JP 2018138019-A/131392: Polycomb-Associated Non-Coding RNAs.
MA559456 - JP 2018138019-A/131382: Polycomb-Associated Non-Coding RNAs.
MA559467 - JP 2018138019-A/131393: Polycomb-Associated Non-Coding RNAs.
MA559455 - JP 2018138019-A/131381: Polycomb-Associated Non-Coding RNAs.
MA559468 - JP 2018138019-A/131394: Polycomb-Associated Non-Coding RNAs.
MA559454 - JP 2018138019-A/131380: Polycomb-Associated Non-Coding RNAs.
MA444476 - JP 2018138019-A/16402: Polycomb-Associated Non-Coding RNAs.
MA444475 - JP 2018138019-A/16401: Polycomb-Associated Non-Coding RNAs.

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

Protein Q99459 (Reactome details) participates in the following event(s):

R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: CDC5L_HUMAN, ENST00000371477.1, ENST00000371477.2, ENST00000371477.3, KIAA0432, NM_001253, PCDC5RP, Q76N46, Q99459, Q99974, uc318jeg.1, uc318jeg.2
UCSC ID: ENST00000371477.4_4
RefSeq Accession: NM_001253.4
Protein: Q99459 (aka CDC5L_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.