Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	51654
Gene name Gene Name - the full gene name approved by the HGNC.	CDK5RAP1 mitochondrial tRNA methylthiotransferase
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	CDK5RAP1
Synonyms (NCBI Gene) Gene synonyms aliases	C20orf34, C42, CGI-05, HSPC167
Chromosome Chromosome number	20
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	20q11.21
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a regulator of cyclin-dependent kinase 5 activity. This protein has also been reported to modify RNA by adding a methylthio-group and may thus have a dual function as an RNA methylthiotransferase and as an inhibitor of cyclin-dependent k

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miRTarBase ID	miRNA	Experiments	Reference
MIRT001473	hsa-miR-16-5p	pSILAC	18668040
MIRT001473	hsa-miR-16-5p	Proteomics;Other	18668040
MIRT2197784	hsa-miR-142-5p	CLIP-seq
MIRT2197785	hsa-miR-21	CLIP-seq
MIRT2197786	hsa-miR-561	CLIP-seq
MIRT2197787	hsa-miR-590-5p	CLIP-seq
MIRT2446709	hsa-miR-2110	CLIP-seq
MIRT2446710	hsa-miR-3127-3p	CLIP-seq
MIRT2446711	hsa-miR-3147	CLIP-seq
MIRT2446712	hsa-miR-3150a-3p	CLIP-seq
MIRT2446713	hsa-miR-3175	CLIP-seq
MIRT2446714	hsa-miR-3667-3p	CLIP-seq
MIRT2446715	hsa-miR-4425	CLIP-seq
MIRT2446716	hsa-miR-939	CLIP-seq
MIRT2501054	hsa-miR-1207-5p	CLIP-seq
MIRT2501055	hsa-miR-1238	CLIP-seq
MIRT2501056	hsa-miR-1301	CLIP-seq
MIRT2197784	hsa-miR-142-5p	CLIP-seq
MIRT2501057	hsa-miR-205	CLIP-seq
MIRT2197785	hsa-miR-21	CLIP-seq
MIRT2446709	hsa-miR-2110	CLIP-seq
MIRT2446710	hsa-miR-3127-3p	CLIP-seq
MIRT2446711	hsa-miR-3147	CLIP-seq
MIRT2446712	hsa-miR-3150a-3p	CLIP-seq
MIRT2446713	hsa-miR-3175	CLIP-seq
MIRT2501058	hsa-miR-3661	CLIP-seq
MIRT2446714	hsa-miR-3667-3p	CLIP-seq
MIRT2501059	hsa-miR-3691-3p	CLIP-seq
MIRT2501060	hsa-miR-3921	CLIP-seq
MIRT2501061	hsa-miR-3977	CLIP-seq
MIRT2501062	hsa-miR-433	CLIP-seq
MIRT2446715	hsa-miR-4425	CLIP-seq
MIRT2501063	hsa-miR-4653-5p	CLIP-seq
MIRT2501064	hsa-miR-4660	CLIP-seq
MIRT2501065	hsa-miR-4736	CLIP-seq
MIRT2501066	hsa-miR-4742-5p	CLIP-seq
MIRT2501067	hsa-miR-4763-3p	CLIP-seq
MIRT2501068	hsa-miR-5047	CLIP-seq
MIRT2197786	hsa-miR-561	CLIP-seq
MIRT2197787	hsa-miR-590-5p	CLIP-seq
MIRT2501069	hsa-miR-631	CLIP-seq
MIRT2446716	hsa-miR-939	CLIP-seq
MIRT2501054	hsa-miR-1207-5p	CLIP-seq
MIRT2501055	hsa-miR-1238	CLIP-seq
MIRT2501056	hsa-miR-1301	CLIP-seq
MIRT2197784	hsa-miR-142-5p	CLIP-seq
MIRT2501057	hsa-miR-205	CLIP-seq
MIRT2197785	hsa-miR-21	CLIP-seq
MIRT2446709	hsa-miR-2110	CLIP-seq
MIRT2446710	hsa-miR-3127-3p	CLIP-seq
MIRT2446711	hsa-miR-3147	CLIP-seq
MIRT2446712	hsa-miR-3150a-3p	CLIP-seq
MIRT2446713	hsa-miR-3175	CLIP-seq
MIRT2501058	hsa-miR-3661	CLIP-seq
MIRT2446714	hsa-miR-3667-3p	CLIP-seq
MIRT2501059	hsa-miR-3691-3p	CLIP-seq
MIRT2501060	hsa-miR-3921	CLIP-seq
MIRT2501061	hsa-miR-3977	CLIP-seq
MIRT2501062	hsa-miR-433	CLIP-seq
MIRT2446715	hsa-miR-4425	CLIP-seq
MIRT2677902	hsa-miR-4529-5p	CLIP-seq
MIRT2677903	hsa-miR-4649-3p	CLIP-seq
MIRT2501063	hsa-miR-4653-5p	CLIP-seq
MIRT2501064	hsa-miR-4660	CLIP-seq
MIRT2501065	hsa-miR-4736	CLIP-seq
MIRT2501066	hsa-miR-4742-5p	CLIP-seq
MIRT2501067	hsa-miR-4763-3p	CLIP-seq
MIRT2501068	hsa-miR-5047	CLIP-seq
MIRT2197786	hsa-miR-561	CLIP-seq
MIRT2197787	hsa-miR-590-5p	CLIP-seq
MIRT2501069	hsa-miR-631	CLIP-seq
MIRT2446716	hsa-miR-939	CLIP-seq

Show/Hide all(33)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003824	Function	Catalytic activity	IEA
GO:0005654	Component	Nucleoplasm	IDA	22422838
GO:0005654	Component	Nucleoplasm	IDA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	IDA	22422838
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	IDA	22422838
GO:0005829	Component	Cytosol	IDA
GO:0006400	Process	TRNA modification	IEA
GO:0007420	Process	Brain development	NAS	10915792
GO:0008033	Process	TRNA processing	IEA
GO:0009451	Process	RNA modification	IMP	22422838
GO:0016740	Function	Transferase activity	IEA
GO:0019901	Function	Protein kinase binding	NAS	10721722
GO:0035596	Function	Methylthiotransferase activity	IEA
GO:0035597	Function	TRNA-2-methylthio-N(6)-dimethylallyladenosine(37) synthase activity	IBA
GO:0035597	Function	TRNA-2-methylthio-N(6)-dimethylallyladenosine(37) synthase activity	IEA
GO:0035597	Function	TRNA-2-methylthio-N(6)-dimethylallyladenosine(37) synthase activity	IMP	22422838
GO:0035600	Process	TRNA methylthiolation	IEA
GO:0045664	Process	Regulation of neuron differentiation	NAS	10721722
GO:0045736	Process	Negative regulation of cyclin-dependent protein serine/threonine kinase activity	IDA	11882646
GO:0045786	Process	Negative regulation of cell cycle	TAS	17491008
GO:0045903	Process	Positive regulation of translational fidelity	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0051246	Process	Regulation of protein metabolic process	IEA
GO:0051536	Function	Iron-sulfur cluster binding	IEA
GO:0051539	Function	4 iron, 4 sulfur cluster binding	IEA
GO:0070131	Process	Positive regulation of mitochondrial translation	IEA
GO:0070900	Process	Mitochondrial tRNA modification	IBA
GO:0070900	Process	Mitochondrial tRNA modification	IEA

MIM	HGNC	e!Ensembl
608200	15880	ENSG00000101391

Protein

UniProt ID

Q96SZ6

Protein name

Mitochondrial tRNA methylthiotransferase CDK5RAP1 (EC 2.8.4.3) (CDK5 activator-binding protein C42) (CDK5 regulatory subunit-associated protein 1) (mt-tRNA-2-methylthio-N6-dimethylallyladenosine synthase) (mt-tRNA-N6-(dimethylallyl)adenosine(37) methylthi

Protein function

Methylthiotransferase that catalyzes the conversion of N6-(dimethylallyl)adenosine (i(6)A) to 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 (adjacent to the 3'-end of the anticodon) of four mitochondrial DNA-encoded tRNAs

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00919	UPF0004	101 → 204	Uncharacterized protein family UPF0004	Family
PF04055	Radical_SAM	252 → 461	Radical SAM superfamily	Domain
PF01938	TRAM	515 → 589	TRAM domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas (PubMed:10721722). Expressed in neurons of central nervous tissue (PubMed:10721722, PubMed:11882646). {ECO:0000269|PubMed:10721722, ECO:0000269|PubM

Sequence

MHPLQCVLQVQRSLGWGPLASVSWLSLRMCRAHSSLSSTMCPSPERQEDGARKDFSSRLA
AGPTFQHFLKSASAPQEKLSSEVEDPPPYLMMDELLGRQRKVYLETYGCQMNVNDTEIAW
SILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKALKTRRPRSRVPLRIGI
LGCMAERLKEEILNREKMVDILAGPDAYRDLPRLLAVAESGQQAANVLLSLDETYADVMP
VQTSASATSAFVSIMRGCDNMCSYCIVPFTRGRERSRPIASILEEVKKLSEQVFLPPRPP
KVLGLQGLKEVTLLGQNVNSFRDNSEVQFNSAVPTNLSRGFTTNYKTKQGGLRFAHLLDQ
VSRVDPEMRIRFTSPHPKDFPDEVLQLIHERDNICKQIHLPAQSGSSRVLEAMRRGYSRE
AYVELVHHIRESIPGVSLSSDFIAGFCGETEEDHVQTVSLLREVQYNMGFLFAYSMRQKT
RAYHRLKDDVPEEVKLRRLEELITIFREEATKANQTSVGCTQLVLVEGLSKRSATDLCGR
NDGNLKVIFPDAEMEDVNNPGLRVRAQPGDYVLVKITSASSQTLRGHVLCRTTLRDSSAY
C

Sequence length

601

Interactions

View interactions

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Diabetes	Type 2 diabetes (adjusted for BMI)	N/A	N/A	GWAS

Show/Hide Text Mining Associations (1)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Breast Neoplasms	Associate	9460986

CDK5RAP1 (CDK5RAP1 mitochondrial tRNA methylthiotransferase)