Cdk13 cyclin-dependent kinase 13 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cdk13provided by RGD
Official Full Name: cyclin-dependent kinase 13provided by RGD
Primary source: RGD:1311226
See related: EnsemblRapid:ENSRNOG00000013620 AllianceGenome:RGD:1311226
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Cdc2l5
Summary: Predicted to enable RNA polymerase II CTD heptapeptide repeat kinase activity; cyclin binding activity; and protein kinase binding activity. Predicted to be involved in several processes, including alternative mRNA splicing, via spliceosome; hemopoiesis; and positive regulation of transcription elongation by RNA polymerase II. Predicted to act upstream of or within negative regulation of stem cell differentiation. Predicted to be located in Golgi apparatus; cytosol; and nuclear speck. Predicted to be part of cyclin K-CDK13 complex and cyclin/CDK positive transcription elongation factor complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in congenital heart defects, dysmorphic facial features, and intellectual developmental disorder; hepatocellular carcinoma; intellectual disability; and prostate carcinoma. Orthologous to human CDK13 (cyclin dependent kinase 13). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 250.0), Spleen (RPKM 226.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 17q11

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	17	NC_086035.1 (51945975..52040218)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	17	NC_051352.1 (47251145..47344675)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	17	NC_005116.4 (49833194..49922932)

Chromosome 17 - NC_086035.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

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Markers

RH139622 (e-PCR)
- UniSTS:221706

CDC2L5_3913 (e-PCR)
- UniSTS:462093

D17Rat74 (e-PCR), detects polymorphism
- UniSTS:226895

RH132491 (e-PCR)
- UniSTS:215774

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II CTD heptapeptide repeat kinase activity	ISO Inferred from Sequence Orthology more info
enables cyclin binding	IBA Inferred from Biological aspect of Ancestor more info
enables cyclin binding	ISO Inferred from Sequence Orthology more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in alternative mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in hemopoiesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of stem cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription elongation by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription elongation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of signal transduction	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
part_of cyclin K-CDK13 complex	ISO Inferred from Sequence Orthology more info
part_of cyclin/CDK positive transcription elongation factor complex	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
part_of nuclear cyclin-dependent protein kinase holoenzyme complex	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: cyclin-dependent kinase 13

Names: cell division cycle 2-like 5 (cholinesterase-related cell division controller); cell division protein kinase 13

NP_001258224.2

EC 2.7.11.22

NP_001258225.2

EC 2.7.11.22

XP_038951649.1

EC 2.7.11.22

XP_038951650.1

EC 2.7.11.22

XP_038951651.1

EC 2.7.11.22

XP_038951652.1

EC 2.7.11.22

XP_038951653.1

EC 2.7.11.22

XP_063132528.1

EC 2.7.11.22

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.

mRNA and Protein(s)

NM_001271295.2 → NP_001258224.2 cyclin-dependent kinase 13 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

JAXUCZ010000017

UniProtKB/TrEMBL

F1M1X9

Related

ENSRNOP00000018431.8, ENSRNOT00000018431.9

Conserved Domains (1) summary

cd07864
Location:697 → 998

STKc_CDK12; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 12
NM_001271296.2 → NP_001258225.2 cyclin-dependent kinase 13 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

JAXUCZ010000017

Conserved Domains (1) summary

cd07864
Location:697 → 998

STKc_CDK12; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 12

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086035.1 Reference GRCr8

Range

51945975..52040218

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039095721.2 → XP_038951649.1 cyclin-dependent kinase 13 isoform X1

UniProtKB/TrEMBL

A0A8I6AEX0

Related

ENSRNOP00000091047.1, ENSRNOT00000107948.2

Conserved Domains (1) summary

cd07864
Location:697 → 998

STKc_CDK12; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 12
XM_039095722.2 → XP_038951650.1 cyclin-dependent kinase 13 isoform X2

Conserved Domains (1) summary

cd07864
Location:697 → 998

STKc_CDK12; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 12
XM_039095724.2 → XP_038951652.1 cyclin-dependent kinase 13 isoform X5

Conserved Domains (1) summary

cl21453
Location:697 → 867

PKc_like; Protein Kinases, catalytic domain
XM_039095723.2 → XP_038951651.1 cyclin-dependent kinase 13 isoform X4

Conserved Domains (1) summary

cl21453
Location:697 → 862

PKc_like; Protein Kinases, catalytic domain
XM_039095725.2 → XP_038951653.1 cyclin-dependent kinase 13 isoform X6

Conserved Domains (1) summary

cl21453
Location:697 → 784

PKc_like; Protein Kinases, catalytic domain
XM_063276458.1 → XP_063132528.1 cyclin-dependent kinase 13 isoform X3