CDK5RAP1 (CDK5RAP1 mitochondrial tRNA methylthiotransferase)

Gene

• Entrez ID: 51654
• Gene name: CDK5RAP1 mitochondrial tRNA methylthiotransferase
• Gene symbol: CDK5RAP1
• Synonyms (NCBI Gene): C20orf34, C42, CGI-05, HSPC167
• Chromosome: 20
• Chromosome location: 20q11.21
• Summary: 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

miRNA

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

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005575	Component	Cellular_component	ND
GO:0005739	Component	Mitochondrion	IBA	21873635
GO:0005829	Component	Cytosol	IBA	21873635
GO:0007420	Process	Brain development	NAS	10915792
GO:0019901	Function	Protein kinase binding	NAS	10721722
GO:0035597	Function	N6-isopentenyladenosine methylthiotransferase activity	IBA	21873635
GO:0035600	Process	TRNA methylthiolation	IEA
GO:0044877	Function	Protein-containing complex binding	IEA
GO:0045664	Process	Regulation of neuron differentiation	NAS	10721722
GO:0045736	Process	Negative regulation of cyclin-dependent protein serine/threonine kinase activity	IBA	21873635
GO:0045736	Process	Negative regulation of cyclin-dependent protein serine/threonine kinase activity	IDA	11882646
GO:0045736	Process	Negative regulation of cyclin-dependent protein serine/threonine kinase activity	TAS	17491008
GO:0045903	Process	Positive regulation of translational fidelity	IEA
GO:0046872	Function	Metal ion 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	IEA

Other IDs

• MIM: 608200
• HGNC: 15880
• e!Ensembl: 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

Associated diseases

Causal
Disease term	Disease name	dbSNP ID	References
Melanoma	melanoma	rs121913315, rs121913323, rs137853080, rs137853081, rs121909232, rs121913388, rs104894094, rs104894095, rs104894097, rs104894098, rs104894099, rs104894109, rs137854599, rs11547328, rs104894340, rs398123152, rs587780668, rs587782083, rs587782206, rs587782792, rs180177042, rs121913381, rs730881675, rs730881674, rs730881677, rs730881673, rs1800586, rs768966657, rs587778189, rs786204195, rs121913321, rs45476696, rs864622636, rs864622263, rs869025340, rs876660436, rs876658534, rs876658556, rs878853647, rs878853644, rs878853650, rs886041162, rs121913389, rs1057519852, rs121913384, rs121913387, rs1060501266, rs1060501263, rs1060501262, rs749714198, rs1060501265, rs559848002, rs1064794292, rs1131691187, rs1131691186, rs199907548, rs1554654052, rs1554656411, rs1554656624, rs1554653915, rs1554653956, rs1554656253, rs1554654224, rs754806883, rs1057520039, rs1563889584, rs1563889685, rs1287464120, rs1563888944, rs1563892715, rs1563889847, rs141798398, rs1587332338, rs1587340291, rs11552823, rs561034503, rs138677674, rs1819962958, rs1820531050	18488026

Unknown
Disease term	Disease name	Evidence	References	Source
Diabetes	Diabetes			GWAS

Associations from Text Mining
Disease Name	Relationship Type	References
Breast Neoplasms	Associate	9460986