Human Gene CCNL1 (ENST00000461804.5) Description and Page Index
  Description: Homo sapiens cyclin L1 (CCNL1), transcript variant 2, mRNA. (from RefSeq NM_001308185)
Gencode Transcript: ENST00000461804.5
Gencode Gene: ENSG00000163660.11
Transcript (Including UTRs)
   Position: hg38 chr3:157,146,508-157,160,760 Size: 14,253 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg38 chr3:157,146,553-157,160,094 Size: 13,542 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr3:157,146,508-157,160,760)mRNA (may differ from genome)Protein (428 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
Stanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Cyclin-L1; Short=Cyclin-L;
FUNCTION: Transcriptional regulator which participates in regulating the pre-mRNA splicing process. Seems to be involved in the regulation of RNA polymerase II (pol II). Functions in association with cyclin-dependent kinases (CDKs) and has a role in the second step of splicing. May be a candidate proto-oncogene in head and neck squamous cell carcinomas (HNSCC). Inhibited by the CDK-specific inhibitor p21.
SUBUNIT: Interacts with POLR2A via its hyperphosphorylated C- terminal domain (CTD) (By similarity). Interacts with CDK11A, CDK11B, CDK12, CDK13 and SFRS2.
SUBCELLULAR LOCATION: Nucleus speckle (By similarity). Note=More specifically found in nuclear intrachromatin granules clusters (IGC), also called nuclear speckles, which are storage compartments for nuclear proteins involved in mRNA processing (By similarity).
TISSUE SPECIFICITY: Ubiquitous with higher level in thymus. Overexpression in primary tumors of head and neck squamous cell carcinomas (HNSCC).
DOMAIN: Contains a RS region (arginine-serine dipeptide repeat) within the C-terminal domain which is the hallmark of the SR family of splicing factors. This region probably plays a role in protein-protein interactions.
MISCELLANEOUS: CCNL1 is amplified in several HNSCC. May play a critical role in the formation of loco-regional metastases and an unfavorable clinical outcome of HNSCC.
SIMILARITY: Belongs to the cyclin family. Cyclin L subfamily.
SEQUENCE CAUTION: Sequence=AAF64257.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact; Sequence=AAQ89026.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact;

-  MalaCards Disease Associations
  MalaCards Gene Search: CCNL1
Diseases sorted by gene-association score: squamous cell carcinoma, head and neck (3)

-  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: 67.63 RPKM in Adipose - Visceral (Omentum)
Total median expression: 1629.36 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 -273.60666-0.411 Picture PostScript Text
3' UTR -1.7045-0.038 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
IPR013763 - Cyclin-like
IPR015429 - Cyclin_C/H/T/L
IPR017060 - Cyclin_L
IPR015431 - Cyclin_L_met/fun
IPR006671 - Cyclin_N

Pfam Domains:
PF00134 - Cyclin, N-terminal domain

ModBase Predicted Comparative 3D Structure on Q9UK58
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     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity

Biological Process:
GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006396 RNA processing
GO:0045737 positive regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:1901409 positive regulation of phosphorylation of RNA polymerase II C-terminal domain

Cellular Component:
GO:0000307 cyclin-dependent protein kinase holoenzyme complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016607 nuclear speck

-  Descriptions from all associated GenBank mRNAs
  AK122738 - Homo sapiens cDNA FLJ16257 fis, clone HLUNG2017307, highly similar to Homo sapiens cyclin L ania-6a mRNA.
BC038394 - Homo sapiens cyclin L1, mRNA (cDNA clone IMAGE:4342552), complete cds.
BC067812 - Homo sapiens cyclin L1, mRNA (cDNA clone MGC:87292 IMAGE:5298716), complete cds.
BC007081 - Homo sapiens cyclin L1, mRNA (cDNA clone MGC:14615 IMAGE:4066376), complete cds.
AK022974 - Homo sapiens cDNA FLJ12912 fis, clone NT2RP2004476, highly similar to Cyclin-L1.
AF180920 - Homo sapiens cyclin L ania-6a mRNA, complete cds.
AF367476 - Homo sapiens cyclin L beta mRNA, complete cds; alternatively spliced.
KJ894378 - Synthetic construct Homo sapiens clone ccsbBroadEn_03772 CCNL1 gene, encodes complete protein.
AY034790 - Homo sapiens cyclin L gamma mRNA, complete cds, alternatively spliced.
AK125606 - Homo sapiens cDNA FLJ43618 fis, clone SPLEN2018683.
AY358663 - Homo sapiens clone DNA57710 CCNL1 (UNQ530) mRNA, complete cds.
BX647554 - Homo sapiens mRNA; cDNA DKFZp686J2297 (from clone DKFZp686J2297).
BX641146 - Homo sapiens mRNA; cDNA DKFZp686K21243 (from clone DKFZp686K21243).
AF208843 - Homo sapiens BM-001 mRNA, complete cds.
AK098021 - Homo sapiens cDNA FLJ40702 fis, clone THYMU2025939, highly similar to Mus musculus cyclin ania-6a mRNA.
AF367477 - Homo sapiens cyclin L gamma mRNA, complete cds; alternatively spliced.
JF432881 - Synthetic construct Homo sapiens clone IMAGE:100074204 cyclin L1 (CCNL1) gene, encodes complete protein.
KJ906263 - Synthetic construct Homo sapiens clone ccsbBroadEn_15933 CCNL1 gene, encodes complete protein.
JD021066 - Sequence 2090 from Patent EP1572962.
JD034721 - Sequence 15745 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_mcmPathway - CDK Regulation of DNA Replication

-  Other Names for This Gene
  Alternate Gene Symbols: B3KMY3, BM-001, CCNL1_HUMAN, NM_001308185, Q6NVY9, Q6UWS7, Q8NI48, Q96QT0, Q9NZF3, Q9UK58, uc003fbd.1, uc003fbd.2, UNQ530/PRO1073
UCSC ID: uc003fbd.2
RefSeq Accession: NM_001308185
Protein: Q9UK58 (aka CCNL1_HUMAN)
CCDS: CCDS77847.1

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