EuRBPDB

Description

RBDs

RBPome

Literatures

Expression

Transcripts

Gene Model

Phenotypes

GWAS

PPI

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000106246 (Gene tree)
Gene ID: 26024
Gene Symbol: PTCD1
Alias: KIAA0632
Full Name: pentatricopeptide repeat domain 1
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Minus strand
Length: 49,425 bases
Position: chr7:99,416,739-99,466,163
Accession: 22198
RBP type: canonical RBP
Summary: This gene encodes a mitochondrial protein that binds leucine tRNAs and other mitochondrial RNAs and plays a role in the regulation of translation. Increased expression of this gene results in decreased mitochondrial leucine tRNA levels. Naturally occurring read-through transcription exists between upstream ATP5J2 (ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2) and this gene. [provided by RefSeq, Aug 2015]

RNA binding domains(RBDs)

Protein ID	Domain	Pfam ID	E-value	Domain number	Total number
ENSP00000292478	PPR	PF01535.20	6.6e-15	1	2
ENSP00000292478	PPR	PF01535.20	6.6e-15	2	2

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
22681889	The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts	4SURIC & HEK293	2012 May	Baltz AG	DOI: 10.1016/j.molcel.2012.05.021
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & HEK293	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
29431736	Capturing the interactome of newly transcribed RNA	RIC & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595
22658674	Insights into RNA biology from an atlas of mammalian mRNA-binding proteins	RIC & Hela	2012 May 31	Castello A	DOI: 10.1016/j.cell.2012.04.031
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & Hela	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & MCF7	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
27812116	Ancient Out-of-Africa Mitochondrial DNA Variants Associate with Distinct Mitochondrial Gene Expression Patterns.	PLoS Genet	2016 Nov 3	Cohen T	doi: 10.1371/journal.pgen.1006407
19651879	Pentatricopeptide repeat domain protein 1 lowers the levels of mitochondrial leucine tRNAs in cells.	Nucleic Acids Res	2009 Sep	Rackham O	doi: 10.1093/nar/gkp627

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000419981	PTCD1-202	533	-	ENSP00000401600	106 (aa)	-	C9JWL7
ENST00000430982	PTCD1-204	571	-	ENSP00000390530	164 (aa)	-	C9JGL8
ENST00000485746	PTCD1-205	721	-	-	- (aa)	-	-
ENST00000430029	PTCD1-203	556	-	ENSP00000408059	144 (aa)	-	C9JQN9
ENST00000292478	PTCD1-201	5582	-	ENSP00000292478	700 (aa)	-	O75127

Gene Model

Click here to download ENSG00000106246's gene model file

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000106246	Blood Pressure	2.1560000E-005	-
ENSG00000106246	Blood Pressure	4.1160000E-005	-

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000106246	rs13243267	7	99455691	?	Serum metabolite levels	23093944	[NR] unit decrease	0.1191	EFO_0005653
ENSG00000106246	rs2293256	7	99460078	?	Serum metabolite levels	23093944	[NR] unit decrease	0.2122	EFO_0005653
ENSG00000106246	rs883403	7	99450355	T	Smoking status (ever vs never smokers)	30643258	[0.012-0.023] unit increase	0.017332198	EFO_0004318
ENSG00000106246	rs10215854	7	99439297	?	White blood cell count	30595370			EFO_0004308

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000106246's network

* RBP PPI network refers to all genes directly bind to RBP

Orthologs

Ensembl ID	Gene Symbol	Coverage	Identiy	Ortholog	Gene Symbol	Coverage	Identiy	Species
ENSG00000106246	PTCD1	81	45.709	ENSAPOG00000010679	ptcd1	85	46.237	Acanthochromis_polyacanthus
ENSG00000106246	PTCD1	100	77.042	ENSAMEG00000006224	-	93	76.901	Ailuropoda_melanoleuca
ENSG00000106246	PTCD1	85	48.350	ENSACIG00000017861	ptcd1	85	48.264	Amphilophus_citrinellus
ENSG00000106246	PTCD1	92	46.024	ENSAOCG00000020741	-	80	48.718	Amphiprion_ocellaris
ENSG00000106246	PTCD1	88	45.367	ENSAOCG00000022617	ptcd1	81	48.029	Amphiprion_ocellaris
ENSG00000106246	PTCD1	92	45.649	ENSAPEG00000022632	ptcd1	84	47.308	Amphiprion_percula
ENSG00000106246	PTCD1	84	49.497	ENSATEG00000007016	ptcd1	80	49.743	Anabas_testudineus
ENSG00000106246	PTCD1	84	60.606	ENSAPLG00000006862	-	93	60.606	Anas_platyrhynchos
ENSG00000106246	PTCD1	99	54.908	ENSACAG00000012871	-	92	54.765	Anolis_carolinensis
ENSG00000106246	PTCD1	98	88.792	ENSANAG00000035790	-	100	88.792	Aotus_nancymaae
ENSG00000106246	PTCD1	83	49.233	ENSACLG00000002824	ptcd1	80	49.147	Astatotilapia_calliptera
ENSG00000106246	PTCD1	87	47.188	ENSAMXG00000037292	ptcd1	91	46.799	Astyanax_mexicanus
ENSG00000106246	PTCD1	100	77.305	ENSBTAG00000020440	-	87	77.589	Bos_taurus
ENSG00000106246	PTCD1	100	88.905	ENSCJAG00000015815	-	100	88.905	Callithrix_jacchus
ENSG00000106246	PTCD1	100	76.521	ENSCAFG00000015055	-	93	76.379	Canis_familiaris
ENSG00000106246	PTCD1	100	76.521	ENSCAFG00020014480	-	93	76.379	Canis_lupus_dingo
ENSG00000106246	PTCD1	100	76.705	ENSCHIG00000027000	-	99	76.989	Capra_hircus
ENSG00000106246	PTCD1	100	79.915	ENSTSYG00000029495	-	100	79.774	Carlito_syrichta
ENSG00000106246	PTCD1	94	74.355	ENSCAPG00000014660	-	99	74.203	Cavia_aperea
ENSG00000106246	PTCD1	100	73.625	ENSCPOG00000001780	-	100	73.484	Cavia_porcellus
ENSG00000106246	PTCD1	100	87.216	ENSCCAG00000034025	-	100	87.216	Cebus_capucinus
ENSG00000106246	PTCD1	100	93.581	ENSCATG00000040859	-	100	93.581	Cercocebus_atys
ENSG00000106246	PTCD1	98	76.934	ENSCLAG00000006354	-	100	76.023	Chinchilla_lanigera
ENSG00000106246	PTCD1	100	87.879	ENSCSAG00000017794	-	95	93.760	Chlorocebus_sabaeus
ENSG00000106246	PTCD1	97	54.047	ENSCPBG00000020866	-	97	54.184	Chrysemys_picta_bellii
ENSG00000106246	PTCD1	82	31.588	ENSCING00000007717	-	97	31.695	Ciona_intestinalis
ENSG00000106246	PTCD1	100	92.867	ENSCANG00000023441	-	100	92.867	Colobus_angolensis_palliatus
ENSG00000106246	PTCD1	100	73.400	ENSCGRG00001023686	Ptcd1	100	73.400	Cricetulus_griseus_chok1gshd
ENSG00000106246	PTCD1	99	73.126	ENSCGRG00000015031	Ptcd1	100	73.126	Cricetulus_griseus_crigri
ENSG00000106246	PTCD1	84	47.906	ENSCSEG00000002378	ptcd1	80	48.387	Cynoglossus_semilaevis
ENSG00000106246	PTCD1	83	47.412	ENSCVAG00000015826	ptcd1	81	47.315	Cyprinodon_variegatus
ENSG00000106246	PTCD1	85	47.117	ENSCVAG00000003621	ptcd1	88	46.634	Cyprinodon_variegatus
ENSG00000106246	PTCD1	87	49.521	ENSDARG00000076176	ptcd1	88	49.839	Danio_rerio
ENSG00000106246	PTCD1	100	73.174	ENSDNOG00000009957	-	100	73.455	Dasypus_novemcinctus
ENSG00000106246	PTCD1	99	73.381	ENSDORG00000000740	Ptcd1	99	73.381	Dipodomys_ordii
ENSG00000106246	PTCD1	90	41.033	ENSEBUG00000014515	ptcd1	99	41.833	Eptatretus_burgeri
ENSG00000106246	PTCD1	100	79.213	ENSEASG00005002480	-	100	79.073	Equus_asinus_asinus
ENSG00000106246	PTCD1	100	79.213	ENSECAG00000016617	-	100	79.073	Equus_caballus
ENSG00000106246	PTCD1	84	46.955	ENSELUG00000016517	ptcd1	82	46.945	Esox_lucius
ENSG00000106246	PTCD1	100	76.695	ENSFCAG00000015069	-	100	76.554	Felis_catus
ENSG00000106246	PTCD1	93	57.965	ENSFALG00000013803	-	92	59.077	Ficedula_albicollis
ENSG00000106246	PTCD1	100	75.921	ENSFDAG00000006393	-	100	75.779	Fukomys_damarensis
ENSG00000106246	PTCD1	74	47.429	ENSFHEG00000012491	ptcd1	92	46.098	Fundulus_heteroclitus
ENSG00000106246	PTCD1	82	48.700	ENSGMOG00000007639	ptcd1	91	48.700	Gadus_morhua
ENSG00000106246	PTCD1	87	59.076	ENSGALG00000004711	-	95	56.459	Gallus_gallus
ENSG00000106246	PTCD1	86	46.721	ENSGAFG00000013175	ptcd1	85	46.721	Gambusia_affinis
ENSG00000106246	PTCD1	86	48.849	ENSGACG00000016607	ptcd1	89	49.744	Gasterosteus_aculeatus
ENSG00000106246	PTCD1	92	54.273	ENSGAGG00000021832	-	99	54.573	Gopherus_agassizii
ENSG00000106246	PTCD1	99	100.000	ENSGGOG00000015123	-	99	98.426	Gorilla_gorilla
ENSG00000106246	PTCD1	83	49.063	ENSHBUG00000018275	ptcd1	80	48.976	Haplochromis_burtoni
ENSG00000106246	PTCD1	100	76.662	ENSHGLG00000017621	-	100	76.521	Heterocephalus_glaber_female
ENSG00000106246	PTCD1	100	76.662	ENSHGLG00100007218	-	100	76.521	Heterocephalus_glaber_male
ENSG00000106246	PTCD1	83	47.521	ENSHCOG00000010784	ptcd1	82	47.766	Hippocampus_comes
ENSG00000106246	PTCD1	100	74.017	ENSSTOG00000001682	-	100	73.876	Ictidomys_tridecemlineatus
ENSG00000106246	PTCD1	100	72.727	ENSJJAG00000000319	Ptcd1	100	72.727	Jaculus_jaculus
ENSG00000106246	PTCD1	83	47.466	ENSKMAG00000008708	ptcd1	80	47.377	Kryptolebias_marmoratus
ENSG00000106246	PTCD1	88	47.452	ENSLBEG00000008061	ptcd1	83	48.203	Labrus_bergylta
ENSG00000106246	PTCD1	87	58.039	ENSLACG00000011172	ptcd1	86	58.333	Latimeria_chalumnae
ENSG00000106246	PTCD1	86	54.366	ENSLOCG00000004833	ptcd1	93	54.849	Lepisosteus_oculatus
ENSG00000106246	PTCD1	100	70.968	ENSLAFG00000002588	-	100	70.968	Loxodonta_africana
ENSG00000106246	PTCD1	100	93.438	ENSMFAG00000041324	-	100	93.438	Macaca_fascicularis
ENSG00000106246	PTCD1	100	93.295	ENSMMUG00000030408	-	100	93.295	Macaca_mulatta
ENSG00000106246	PTCD1	100	93.438	ENSMNEG00000043786	-	100	93.438	Macaca_nemestrina
ENSG00000106246	PTCD1	100	86.585	ENSMLEG00000031179	-	100	73.466	Mandrillus_leucophaeus
ENSG00000106246	PTCD1	90	48.571	ENSMAMG00000007623	ptcd1	85	48.571	Mastacembelus_armatus
ENSG00000106246	PTCD1	87	47.164	ENSMZEG00005012722	ptcd1	83	47.078	Maylandia_zebra
ENSG00000106246	PTCD1	99	55.524	ENSMGAG00000004211	-	93	55.664	Meleagris_gallopavo
ENSG00000106246	PTCD1	100	77.151	ENSMICG00000017428	-	100	77.606	Microcebus_murinus
ENSG00000106246	PTCD1	90	45.639	ENSMMOG00000020243	ptcd1	88	47.700	Mola_mola
ENSG00000106246	PTCD1	98	58.436	ENSMODG00000001350	-	99	58.436	Monodelphis_domestica
ENSG00000106246	PTCD1	84	49.583	ENSMALG00000018442	ptcd1	80	49.412	Monopterus_albus
ENSG00000106246	PTCD1	99	74.170	MGP_CAROLIEiJ_G0028011	Ptcd1	99	74.170	Mus_caroli
ENSG00000106246	PTCD1	99	73.882	ENSMUSG00000029624	Ptcd1	99	73.882	Mus_musculus
ENSG00000106246	PTCD1	99	74.315	MGP_PahariEiJ_G0024580	Ptcd1	99	74.315	Mus_pahari
ENSG00000106246	PTCD1	99	74.170	MGP_SPRETEiJ_G0029012	Ptcd1	99	74.170	Mus_spretus
ENSG00000106246	PTCD1	100	75.530	ENSMPUG00000016518	-	100	75.389	Mustela_putorius_furo
ENSG00000106246	PTCD1	100	78.622	ENSMLUG00000010994	-	94	78.481	Myotis_lucifugus
ENSG00000106246	PTCD1	85	48.339	ENSNBRG00000010079	ptcd1	84	48.247	Neolamprologus_brichardi
ENSG00000106246	PTCD1	100	92.612	ENSNLEG00000011060	-	100	92.612	Nomascus_leucogenys
ENSG00000106246	PTCD1	97	62.518	ENSMEUG00000006930	-	99	62.518	Notamacropus_eugenii
ENSG00000106246	PTCD1	89	76.815	ENSOPRG00000013647	-	89	76.815	Ochotona_princeps
ENSG00000106246	PTCD1	83	46.880	ENSONIG00000003168	ptcd1	95	46.791	Oreochromis_niloticus
ENSG00000106246	PTCD1	80	57.549	ENSOANG00000007728	-	73	57.838	Ornithorhynchus_anatinus
ENSG00000106246	PTCD1	99	73.429	ENSOCUG00000010584	-	97	73.429	Oryctolagus_cuniculus
ENSG00000106246	PTCD1	85	47.776	ENSORLG00000009275	ptcd1	85	47.848	Oryzias_latipes
ENSG00000106246	PTCD1	85	47.282	ENSORLG00020000988	ptcd1	85	47.351	Oryzias_latipes_hni
ENSG00000106246	PTCD1	85	47.360	ENSORLG00015010557	ptcd1	85	47.430	Oryzias_latipes_hsok
ENSG00000106246	PTCD1	87	47.471	ENSOMEG00000020627	ptcd1	88	47.619	Oryzias_melastigma
ENSG00000106246	PTCD1	99	75.286	ENSOGAG00000010877	-	100	75.143	Otolemur_garnettii
ENSG00000106246	PTCD1	100	72.766	ENSOARG00000018676	-	100	73.050	Ovis_aries
ENSG00000106246	PTCD1	100	98.429	ENSPPAG00000036024	-	100	98.429	Pan_paniscus
ENSG00000106246	PTCD1	100	76.879	ENSPPRG00000003478	-	100	76.738	Panthera_pardus
ENSG00000106246	PTCD1	100	98.429	ENSPTRG00000019452	-	100	98.429	Pan_troglodytes
ENSG00000106246	PTCD1	100	93.438	ENSPANG00000016730	-	100	93.438	Papio_anubis
ENSG00000106246	PTCD1	96	48.830	ENSPKIG00000014215	ptcd1	97	48.763	Paramormyrops_kingsleyae
ENSG00000106246	PTCD1	85	57.973	ENSPSIG00000011184	-	100	58.472	Pelodiscus_sinensis
ENSG00000106246	PTCD1	73	41.333	ENSPMAG00000009667	ptcd1	99	41.333	Petromyzon_marinus
ENSG00000106246	PTCD1	99	58.457	ENSPCIG00000024778	-	99	58.457	Phascolarctos_cinereus
ENSG00000106246	PTCD1	86	45.677	ENSPFOG00000004458	ptcd1	82	46.812	Poecilia_formosa
ENSG00000106246	PTCD1	86	45.990	ENSPLAG00000011051	ptcd1	85	46.645	Poecilia_latipinna
ENSG00000106246	PTCD1	86	46.166	ENSPMEG00000020547	ptcd1	85	45.120	Poecilia_mexicana
ENSG00000106246	PTCD1	85	46.777	ENSPREG00000000059	ptcd1	84	46.777	Poecilia_reticulata
ENSG00000106246	PTCD1	95	96.979	ENSPPYG00000017377	-	100	96.979	Pongo_abelii
ENSG00000106246	PTCD1	81	72.644	ENSPCAG00000001852	-	88	72.644	Procavia_capensis
ENSG00000106246	PTCD1	99	78.602	ENSPCOG00000018596	-	99	78.917	Propithecus_coquereli
ENSG00000106246	PTCD1	100	62.805	ENSPVAG00000007529	-	72	88.000	Pteropus_vampyrus
ENSG00000106246	PTCD1	83	48.893	ENSPNYG00000019993	ptcd1	80	48.805	Pundamilia_nyererei
ENSG00000106246	PTCD1	92	49.924	ENSPNAG00000014931	ptcd1	93	49.618	Pygocentrus_nattereri
ENSG00000106246	PTCD1	98	73.799	ENSRNOG00000000987	Ptcd1	98	73.799	Rattus_norvegicus
ENSG00000106246	PTCD1	100	93.295	ENSRBIG00000043393	-	100	93.295	Rhinopithecus_bieti
ENSG00000106246	PTCD1	100	93.153	ENSRROG00000036420	-	100	93.153	Rhinopithecus_roxellana
ENSG00000106246	PTCD1	100	88.319	ENSSBOG00000024114	-	100	88.319	Saimiri_boliviensis_boliviensis
ENSG00000106246	PTCD1	98	56.749	ENSSHAG00000011376	-	98	61.957	Sarcophilus_harrisii
ENSG00000106246	PTCD1	85	53.871	ENSSFOG00015007909	ptcd1	81	54.295	Scleropages_formosus
ENSG00000106246	PTCD1	87	46.141	ENSSMAG00000000218	ptcd1	94	46.440	Scophthalmus_maximus
ENSG00000106246	PTCD1	88	46.975	ENSSDUG00000015671	ptcd1	86	47.164	Seriola_dumerili
ENSG00000106246	PTCD1	88	46.975	ENSSLDG00000014261	ptcd1	86	46.955	Seriola_lalandi_dorsalis
ENSG00000106246	PTCD1	99	52.789	ENSSPUG00000003540	-	98	53.701	Sphenodon_punctatus
ENSG00000106246	PTCD1	84	49.249	ENSSPAG00000011049	ptcd1	80	49.327	Stegastes_partitus
ENSG00000106246	PTCD1	93	77.948	ENSSSCG00000007622	-	99	77.410	Sus_scrofa
ENSG00000106246	PTCD1	87	60.359	ENSTGUG00000007563	-	99	61.258	Taeniopygia_guttata
ENSG00000106246	PTCD1	87	47.742	ENSTRUG00000013471	ptcd1	79	48.562	Takifugu_rubripes
ENSG00000106246	PTCD1	84	48.993	ENSTNIG00000008271	ptcd1	83	49.236	Tetraodon_nigroviridis
ENSG00000106246	PTCD1	100	74.194	ENSTBEG00000011021	-	100	74.053	Tupaia_belangeri
ENSG00000106246	PTCD1	100	74.716	ENSTTRG00000003006	-	100	74.716	Tursiops_truncatus
ENSG00000106246	PTCD1	100	76.901	ENSUAMG00000008049	-	100	76.761	Ursus_americanus
ENSG00000106246	PTCD1	99	76.420	ENSVVUG00000008836	-	100	76.278	Vulpes_vulpes
ENSG00000106246	PTCD1	86	52.310	ENSXETG00000009891	ptcd1	88	52.138	Xenopus_tropicalis
ENSG00000106246	PTCD1	86	47.039	ENSXMAG00000015540	ptcd1	84	47.204	Xiphophorus_maculatus

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000049	tRNA binding	21873635.	IBA	Function
GO:0000049	tRNA binding	19651879.	IDA	Function
GO:0003723	RNA binding	22658674.22681889.	HDA	Function
GO:0005739	mitochondrion	19651879.	IDA	Component
GO:0005759	mitochondrial matrix	21873635.	IBA	Component
GO:0005759	mitochondrial matrix	-	ISS	Component
GO:0042780	tRNA 3'-end processing	21873635.	IBA	Process
GO:0042780	tRNA 3'-end processing	21857155.	IDA	Process