RBPWorld - a comprehensive database of RNA Binding Proteins

Functions and Diseases

RBP Type	Canonical_RBPs
Diseases	CancerSARS-COV-OC43
Drug	N.A.
Main interacting RNAs	mRNA
Moonlighting functions	N.A.
Localizations	Stress granule or P-body
BulkPerturb-seq	N.A.

Description

Ensembl ID	ENSG00000132300	Gene ID	55037	Accession	24717
Symbol	PTCD3	Alias	mS39;COXPD51;MRP-S39	Full Name	pentatricopeptide repeat domain 3
Status	Confidence	Length	35935 bases	Strand	Plus strand
Position	2 : 86106223 - 86142157	RNA binding domain	PPR_3 , PPR_long
Summary	Enables rRNA binding activity and ribosomal small subunit binding activity. Involved in mitochondrial translation. Located in several cellular components, including cytosol; mitochondrion; and nucleoplasm. Implicated in combined oxidative phosphorylation deficiency 51. [provided by Alliance of Genome Resources, Apr 2022]

RNA binding domains (RBDs)

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Protein	Domain	Pfam ID	E-value	Domain number
ENSP00000254630	PPR_3	PF13812	4.3e-13	1
ENSP00000254630	PPR_3	PF13812	4.3e-13	2
ENSP00000254630	PPR_long	PF17177	1.2e-07	3

Showing 1 to 3 of 3 entries

RNA binding proteomes (RBPomes)

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Pubmed ID	Full Name	Cell	Author	Time	Doi
22658674	RIC_PMID22658674_Hela_human	Hela	Alfredo Castello	2012 Jun 8	doi: 10.1016/j.cell.2012.04.031.?Epub 2012 May 31
22658674	RIC_PMID22658674_Hs_HeLa	HeLa	Alfredo Castello?	2012 Jun 8	doi: 10.1016/j.cell.2012.04.031.?Epub 2012 May 31
22681889	RIC_PMID22681889_Hs_HEK293	HEK293	Alexander G Baltz	2012 Jun 8	doi: 10.1016/j.molcel.2012.05.021
25173706	Pclap_PMID25173706_Hs_HEK293	HEK293	Katharina Kramer	2014 Oct;11	doi: 10.1038/nmeth.3092.?Epub 2014 Aug 31
25843628	ChIRP.MS_PMID25843628_Hela_human	Hela	Ci Chu	2015 Apr 9	doi: 10.1016/j.cell.2015.03.025.?Epub 2015 Apr 2
26632259	RIC_PMID26632259._Hs_HuH7	HuH7	Benedikt M Beckmann	2015 Dec 3	doi: 10.1038/ncomms10127.
27040163	serIC_PMID27040163_Hs_K562.1	K562	Thomas Conrad?	2016 Apr 4	doi: 10.1038/ncomms11212
27453046	RBDmap_PMID_27453046_Hs_HeLa	HeLa	Alfredo Castello	2016 Aug 18	doi: 10.1016/j.molcel.2016.06.029.?Epub 2016 Jul 21
28431233	RIC_PMID28431233_Hs_microRNA		Thomas Treiber	2017 Apr 20	doi: 10.1016/j.molcel.2017.03.014
29431736	RICK_PMID29431736_Hela_human	Hela	Xichen Bao	2018 Mar	doi: 10.1038/nmeth.4595.?Epub 2018 Feb 12

Showing 1 to 10 of 30 entries

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Literatures on RNA binding capacity

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Pubmed ID	Title	Author	Time	Journal
19427859	Pentatricopeptide repeat domain protein 3 associates with the mitochondrial small ribosomal subunit and regulates translation.	K M Stefan Davies	2009-06-18	FEBS letters
21278163	TEFM (c17orf42) is necessary for transcription of human mtDNA.	Michal Minczuk	2011-05-01	Nucleic acids research
23635806	Human pentatricopeptide proteins: only a few and what do they do?	N Robert Lightowlers	2013-01-01	RNA biology
23908630	Identification and characterization of CHCHD1, AURKAIP1, and CRIF1 as new members of the mammalian mitochondrial ribosome.	C Emine Koc	2013-01-01	Frontiers in physiology
27411691	The process of mammalian mitochondrial protein synthesis.	Nicole Mai	2017-01-01	Cell and tissue research
30132530	Elevated expression of PTCD3 correlates with tumor progression and predicts poor prognosis in patients with prostate cancer.	Yiqiao Huang	2018-10-01	Molecular medicine reports
35884802	Mitochondrial Ribosome Dysfunction in Human Alveolar Type II Cells in Emphysema.	Loukmane Karim	2022-06-24	Biomedicines

Showing 1 to 7 of 7 entries

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Transcripts

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Name	Transcript ID	bp	Protein	Translation ID
PTCD3-201	ENST00000254630	6681	689aa	ENSP00000254630
PTCD3-202	ENST00000409326	522	78aa	ENSP00000386963
PTCD3-203	ENST00000409783	587	187aa	ENSP00000386922
PTCD3-204	ENST00000418628	532	69aa	ENSP00000394441
PTCD3-205	ENST00000464541	890	No protein	-
PTCD3-206	ENST00000465560	747	No protein	-
PTCD3-207	ENST00000467273	757	No protein	-
PTCD3-208	ENST00000469585	885	No protein	-
PTCD3-209	ENST00000472044	293	No protein	-
PTCD3-210	ENST00000473829	587	No protein	-

Showing 1 to 10 of 20 entries

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Gene Model

Click here to download ENSG00000132300's gene model file

Phenotypes

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ensgID	Trait	pValue	Pubmed ID
12441	Breast Neoplasms	1.5950000E-004	17529973
12443	Breast Neoplasms	1.5870000E-004	17529973
12456	Breast Neoplasms	2.0880000E-004	17529973
91047	Methylphenidate	3E-6	21130132

Showing 1 to 4 of 4 entries

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GWAS

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ensgID	SNP	Chromosome	Position	Trait	PubmedID	Or or BEAT	EFO ID
ENSG00000132300	rs2241437	2	86133450	Response to methylphenidate treatment in attention-deficit/hyperactivity disorder (blood pressure)	21130132		GO_0036271
ENSG00000132300	rs10184246	2	86114205	Lung function (FEV1/FVC)	30595370		EFO_0004713
ENSG00000132300	rs3731818	2	86141681	Diastolic blood pressure	27841878	0.117	EFO_0006336
ENSG00000132300	rs3731818	2	86141681	Systolic blood pressure	27841878	0.24	EFO_0006335
ENSG00000132300	rs3731818	2	86141681	Pulse pressure	27841878	0.127	EFO_0005763

Showing 1 to 5 of 5 entries

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Protein-Protein Interaction (PPI)

Click here to download ENSG00000132300's PPI file

Orthologs

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Ensembl ID	Source				Target
Ensembl ID	Species	Protein ID	Perc_pos	Perc_id	Species	Protein ID	Perc_pos	Perc_id
ENSG00000132300	homo_sapiens	ENSP00000254630	97.0972	94.9202	nomascus_leucogenys	ENSNLEP00000003128	97.0972	94.9202
ENSG00000132300	homo_sapiens	ENSP00000254630	99.4194	98.984	pan_paniscus	ENSPPAP00000008678	99.4194	98.984
ENSG00000132300	homo_sapiens	ENSP00000254630	97.5327	96.0813	pongo_abelii	ENSPPYP00000013622	97.5327	96.0813
ENSG00000132300	homo_sapiens	ENSP00000254630	99.4194	99.1292	pan_troglodytes	ENSPTRP00000040563	99.4194	99.1292
ENSG00000132300	homo_sapiens	ENSP00000254630	99.2743	98.6938	gorilla_gorilla	ENSGGOP00000001769	99.2743	98.6938
ENSG00000132300	homo_sapiens	ENSP00000254630	77.6488	62.8447	ornithorhynchus_anatinus	ENSOANP00000019594	77.6488	62.8447
ENSG00000132300	homo_sapiens	ENSP00000254630	73.1495	57.0392	sarcophilus_harrisii	ENSSHAP00000017202	72.6225	56.6282
ENSG00000132300	homo_sapiens	ENSP00000254630	56.6038	44.5573	notamacropus_eugenii	ENSMEUP00000010688	64.1447	50.4934
ENSG00000132300	homo_sapiens	ENSP00000254630	73.5849	66.6183	choloepus_hoffmanni	ENSCHOP00000003342	80.8612	73.2057
ENSG00000132300	homo_sapiens	ENSP00000254630	83.7446	74.0203	dasypus_novemcinctus	ENSDNOP00000006417	83.3815	73.6994

Showing 1 to 10 of 203 entries

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Gene Ontology

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Go ID	Go term	No. evidence	Entries	Species	Category
GO:0032543	involved_in mitochondrial translation	3	IBA,IMP,NAS	Homo_sapiens(9606)	Process
GO:0005739	is_active_in mitochondrion	2	IBA,IDA	Homo_sapiens(9606)	Component
GO:0005743	located_in mitochondrial inner membrane	2	NAS,TAS	Homo_sapiens(9606)	Component
GO:0019843	enables rRNA binding	2	IBA,IDA	Homo_sapiens(9606)	Function
GO:0043024	enables ribosomal small subunit binding	2	IBA,IDA	Homo_sapiens(9606)	Function
GO:0003723	enables RNA binding	1	HDA	Homo_sapiens(9606)	Function
GO:0005515	enables protein binding	1	IPI	Homo_sapiens(9606)	Function
GO:0005654	located_in nucleoplasm	1	IDA	Homo_sapiens(9606)	Component
GO:0005763	part_of mitochondrial small ribosomal subunit	1	NAS	Homo_sapiens(9606)	Component
GO:0005829	located_in cytosol	1	IDA	Homo_sapiens(9606)	Component

Showing 1 to 10 of 12 entries

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Welcome to

RBP World!

Functions and Diseases

Description

RNA binding domains (RBDs)

RNA binding proteomes (RBPomes)

Literatures on RNA binding capacity

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

Protein-Protein Interaction (PPI)

Paralogs

Orthologs

Gene Ontology

Expression