CCNL2 cyclin L2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CCNL2provided by HGNC
Official Full Name: cyclin L2provided by HGNC
Primary source: HGNC:HGNC:20570
See related: Ensembl:ENSG00000221978 MIM:613482; AllianceGenome:HGNC:20570
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CCNM; CCNS; PCEE; SB138; ANIA-6B; HLA-ISO; HCLA-ISO
Summary: The protein encoded by this gene belongs to the cyclin family. Through its interaction with several proteins, such as RNA polymerase II, splicing factors, and cyclin-dependent kinases, this protein functions as a regulator of the pre-mRNA splicing process, as well as in inducing apoptosis by modulating the expression of apoptotic and antiapoptotic proteins. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]
Expression: Ubiquitous expression in skin (RPKM 45.3), endometrium (RPKM 44.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p36.33

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (1385711..1399335, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (817645..832544, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (1321091..1334715, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Exosome miR-23a-3p from Osteoblast Alleviates Spinal Cord Ischemia/Reperfusion Injury by Down-Regulating KLF3-Activated CCNL2 Transcription.
Title: Exosome miR-23a-3p from Osteoblast Alleviates Spinal Cord Ischemia/Reperfusion Injury by Down-Regulating KLF3-Activated CCNL2 Transcription.
CLK1/SRSF5 pathway induces aberrant exon skipping of METTL14 and Cyclin L2 and promotes growth and metastasis of pancreatic cancer.
Title: CLK1/SRSF5 pathway induces aberrant exon skipping of METTL14 and Cyclin L2 and promotes growth and metastasis of pancreatic cancer.
The Dual-Specificity Kinase DYRK1A Modulates the Levels of Cyclin L2 To Control HIV Replication in Macrophages.
Title: The Dual-Specificity Kinase DYRK1A Modulates the Levels of Cyclin L2 To Control HIV Replication in Macrophages.
Therefore, cyclin L2-mediated control of SAMHD1 levels in macrophages supports HIV-1 replication.
Title: Cyclin L2 is a critical HIV dependency factor in macrophages that controls SAMHD1 abundance.
CDK10/cyclin M is a protein kinase that controls ETS2 degradation and is deficient in STAR syndrome.
Title: CDK10/cyclin M is a protein kinase that controls ETS2 degradation and is deficient in STAR syndrome.
CDK11(p110) interacts physically and functionally with cyclin Lalpha and -beta isoforms and SR proteins to regulate splicing.
Title: Characterization of cyclin L1 and L2 interactions with CDK11 and splicing factors: influence of cyclin L isoforms on splice site selection.
Data show that a green fluorescent protein (GFP) fusion protein of cyclin L1, in contrast to cyclin L2, was not mobile within the nucleus of living COS7 cells.
Title: Characterization of cyclin L1 as an immobile component of the splicing factor compartment.
characterize cyclin L2 as a highly mobile component of nuclear speckles and suggest that DYRK1A may regulate splicing by phosphorylation of cyclin L2
Title: Characterization of cyclin L2, a novel cyclin with an arginine/serine-rich domain: phosphorylation by DYRK1A and colocalization with splicing factors.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G31515 (e-PCR)
- UniSTS:58369

CCNL2_1347 (e-PCR)
- UniSTS:277062

CCNL2_v423 (e-PCR)
- UniSTS:277062

SHGC-74125 (e-PCR)
- UniSTS:840

SHGC-74123 (e-PCR)
- UniSTS:16820

SHGC-74124 (e-PCR)
- UniSTS:49662

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cyclin-dependent protein serine/threonine kinase regulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in regulation of RNA splicing	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of RNA splicing	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of apoptotic process	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of cell cycle	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of centrosome cycle	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of cyclin-dependent protein kinase holoenzyme complex	IPI Inferred from Physical Interaction more info	PubMed
part_of cyclin-dependent protein kinase holoenzyme complex	ISS Inferred from Sequence or Structural Similarity more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: cyclin-L2

Names: cyclin M; cyclin S; paneth cell-enhanced expression protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029782.1 RefSeqGene

Range

5004..18628

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001039577.5 → NP_001034666.1 cyclin-L2 isoform B

See identical proteins and their annotated locations for NP_001034666.1

Status: REVIEWED

Description

Transcript Variant: This variant (2, also known as L2betaA3 or T3) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (B), also known as L2betaA, contains the cyclin box in the N-terminus and lacks the arginine/serine-rich domain (RS domain) in the C-terminus, compared to isoform A.

Source sequence(s)

BC016333, DA360436, HY002650

Consensus CDS

CCDS30558.1

UniProtKB/Swiss-Prot

Q96S94

Related

ENSP00000386158.4, ENST00000408918.8

Conserved Domains (1) summary

cd00043
Location:77 → 150

CYCLIN; Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB ...
NM_001320153.3 → NP_001307082.1 cyclin-L2 isoform C

Status: REVIEWED

Source sequence(s)

AK000685, AK056120, AK074112, AL391244, CR628411, HY002650

UniProtKB/TrEMBL

B3KQ08

Conserved Domains (1) summary

cl40454
Location:1 → 95

CYCLIN_SF; Cyclin box fold superfamily
NM_001320155.3 → NP_001307084.1 cyclin-L2 isoform C

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains an alternate exon compared to variant 1. The resulting isoform (C) is shorter at the N-terminus compared to isoform A. Variants 3, 4, 6, and 7 encode the same isoform (C).

Source sequence(s)

AK000685, AK074112, AY116620, CR628411, HY002650

UniProtKB/TrEMBL

B3KQ08

Conserved Domains (1) summary

cl40454
Location:1 → 95

CYCLIN_SF; Cyclin box fold superfamily
NM_001350497.2 → NP_001337426.1 cyclin-L2 isoform C

Status: REVIEWED

Description

Transcript Variant: This variant (6) has multiple differences, compared to variant 1. These differences cause translation initiation at a downstream start codon, compared to variant 1. The resulting isoform (C) is shorter at the N-terminus compared to isoform A. Variants 3, 4, 6, and 7 encode the same isoform (C).

Source sequence(s)

AL391244, CR628411

UniProtKB/TrEMBL

B3KQ08

Conserved Domains (1) summary

cl40454
Location:1 → 95

CYCLIN_SF; Cyclin box fold superfamily
NM_001350498.2 → NP_001337427.1 cyclin-L2 isoform C

Status: REVIEWED

Description

Transcript Variant: This variant (7) contains an alternate exon compared to variant 1. The resulting isoform (C) is shorter at the N-terminus compared to isoform A. Variants 3, 4, 6, and 7 encode the same isoform (C).

Source sequence(s)

AK000685, AK056120, AK057133, AK074112, HY002650

UniProtKB/TrEMBL

B3KQ08

Conserved Domains (1) summary

cl40454
Location:1 → 95

CYCLIN_SF; Cyclin box fold superfamily
NM_001350499.2 → NP_001337428.1 cyclin-L2 isoform D

Status: REVIEWED

Description

Transcript Variant: This variant (8) contains two consecutive alternate exons, resulting in use of an alternate start codon, compared to variant 1. The resulting isoform (D) has a shorter but distinct N-terminus compared to isoform A. Variants 8 and 9 both encode the same isoform (D).

Source sequence(s)

AK000685, AK056120, AK074112, CN402151, DA944374, HY002650

Conserved Domains (1) summary

smart00385
Location:90 → 151

CYCLIN; domain present in cyclins, TFIIB and Retinoblastoma
NM_001350500.2 → NP_001337429.1 cyclin-L2 isoform D

Status: REVIEWED

Description

Transcript Variant: This variant (9) contains two consecutive alternate exons, resulting in use of an alternate start codon, compared to variant 1. The resulting isoform (D) has a shorter but distinct N-terminus compared to isoform A. Variants 8 and 9 both encode the same isoform (D).

Source sequence(s)

AK000685, AK056120, AK074112, CN402151, DA944374, HY002650

Conserved Domains (1) summary

smart00385
Location:90 → 151

CYCLIN; domain present in cyclins, TFIIB and Retinoblastoma
NM_030937.6 → NP_112199.2 cyclin-L2 isoform A

See identical proteins and their annotated locations for NP_112199.2

Status: REVIEWED

Description

Transcript Variant: This variant (1, also known as L2alpha or T2) encodes the longest isoform (A, also known as L2alpha) containing a cyclin box in the N-terminus and RS domain in the C-terminus.

Source sequence(s)

AK000685, AL834432, AY037150, HY002650

Consensus CDS

CCDS30557.1

UniProtKB/Swiss-Prot

A0A024R072, A0A024R077, A0A0C4DGC4, A8K8A3, B1B152, F2Z3J5, Q5T2N5, Q5T2N6, Q6IQ12, Q7Z4Z8, Q8N3C9, Q8N3D5, Q8NHE3, Q8TEL0, Q96B00, Q96S94

Related

ENSP00000383611.3, ENST00000400809.8

Conserved Domains (2) summary

smart00385
Location:200 → 282

CYCLIN; domain present in cyclins, TFIIB and Retinoblastoma

cd00043
Location:77 → 150

CYCLIN; Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB ...

RNA

NR_135154.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) contains two alternate exons and uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK000685, AK074112, HY172534

Related

ENST00000496007.5
NR_146722.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (10) contains multiple internal alternate exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD)

Source sequence(s)

AK000685, AK056120, AK074112, DA944374, DA954161, DN994809, HY002650
NR_146723.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (11) contains multiple internal alternate exons and uses an alternate splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK000685, AK056120, AK074112, DA944374, HY002650

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

1385711..1399335 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011542216.4 → XP_011540518.1 cyclin-L2 isoform X1

Conserved Domains (2) summary

smart00385
Location:233 → 315

CYCLIN; domain present in cyclins, TFIIB and Retinoblastoma

COG5333
Location:69 → 306

CCL1; Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
XM_047431297.1 → XP_047287253.1 cyclin-L2 isoform X2
XM_047431301.1 → XP_047287257.1 cyclin-L2 isoform X3

Related

ENSP00000423734.1, ENST00000481223.6

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

817645..832544 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054338927.1 → XP_054194902.1 cyclin-L2 isoform X4

UniProtKB/Swiss-Prot

A0A024R072, A0A024R077, A0A0C4DGC4, A8K8A3, B1B152, F2Z3J5, Q5T2N5, Q5T2N6, Q6IQ12, Q7Z4Z8, Q8N3C9, Q8N3D5, Q8NHE3, Q8TEL0, Q96B00, Q96S94
XM_054338926.1 → XP_054194901.1 cyclin-L2 isoform X1
XM_054338928.1 → XP_054194903.1 cyclin-L2 isoform X2
XM_054338929.1 → XP_054194904.1 cyclin-L2 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001144867.1: Suppressed sequence

Description

NM_001144867.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
NM_001144868.1: Suppressed sequence

Description

NM_001144868.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.