RBPWorld - a comprehensive database of RNA Binding Proteins

Functions and Diseases

RBP Type	Canonical_RBPs
Diseases	Cancer Disease
Drug	N.A.
Main interacting RNAs	N.A.
Moonlighting functions	N.A.
Localizations	Stress granucle
BulkPerturb-seq	N.A.

Description

Ensembl ID	ENSG00000123200	Gene ID	23091	Accession	20368
Symbol	ZC3H13	Alias	Xio;KIAA0853	Full Name	zinc finger CCCH-type containing 13
Status	Confidence	Length	98295 bases	Strand	Minus strand
Position	13 : 45954465 - 46052759	RNA binding domain	zf-CCCH
Summary	Enables RNA binding activity. Involved in mRNA methylation. Located in nuclear speck. Part of RNA N6-methyladenosine methyltransferase complex. [provided by Alliance of Genome Resources, Apr 2022]

RNA binding domains (RBDs)

Search:

Protein	Domain	Pfam ID	E-value	Domain number
ENSP00000242848	zf-CCCH	PF00642	2.7e-06	1
ENSP00000282007	zf-CCCH	PF00642	2.5e-06	1
ENSP00000503994	zf-CCCH	PF00642	2.7e-06	1

Showing 1 to 3 of 3 entries

RNA binding proteomes (RBPomes)

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Pubmed ID	Full Name	Cell	Author	Time	Doi
22681889	RIC_PMID22681889_Hs_HEK293	HEK293	Alexander G Baltz	2012 Jun 8	doi: 10.1016/j.molcel.2012.05.021
30528433	XRNAX_PMID30528433_Hs_HEK293	HEK293	Jakob Trendel	2019 Jan 10	doi: 10.1016/j.cell.2018.11.004.?Epub 2018 Dec 6
30528433	XRNAX_PMID30528433_Hs_HeLa	HeLa	Jakob Trendel	2019 Jan 10	doi: 10.1016/j.cell.2018.11.004.?Epub 2018 Dec 6
30528433	XRNAX_PMID30528433_Hs_MCF7	MCF7	Jakob Trendel	2019 Jan 10	doi: 10.1016/j.cell.2018.11.004.?Epub 2018 Dec 6
30607034	RIC_PMID_30607034_Hs_HEK293	HEK293	Rayner M L Queiroz	2019 Feb	doi: 10.1038/s41587-018-0001-2.?Epub 2019 Jan 3
30607034	RIC_PMID30607034_Hs_OOPS_MCF10A	MCF10A	Rayner M L Queiroz	2019 Feb	doi: 10.1038/s41587-018-0001-2.?Epub 2019 Jan 3
31076284	R.Deep_PMID_31076284_Hs		Maiwen Caudron-Herger	2019 Jul 11	doi: 10.1016/j.molcel.2019.04.018.?Epub 2019 May 7
33235359	RIC_PMID33235359_humanRIC.superset.2021		Fatima Gebauer	2021 Mar	doi: 10.1038/s41576-020-00302-y

Showing 1 to 8 of 8 entries

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Literatures on RNA binding capacity

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Pubmed ID	Title	Author	Time	Journal
36882788	Recent advances in the plant epitranscriptome.	Lisha Shen	2023-03-07	Genome biology

Showing 1 to 1 of 1 entries

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Transcripts

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Name	Transcript ID	bp	Protein	Translation ID
ZC3H13-201	ENST00000242848	8018	1668aa	ENSP00000242848
ZC3H13-202	ENST00000282007	6412	1564aa	ENSP00000282007
ZC3H13-203	ENST00000428921	695	No protein	-
ZC3H13-204	ENST00000464597	535	116aa	ENSP00000480658
ZC3H13-205	ENST00000470308	795	No protein	-
ZC3H13-206	ENST00000679008	8024	1669aa	ENSP00000503994

Showing 1 to 6 of 6 entries

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Gene Model

Click here to download ENSG00000123200's gene model file

ensgID	Trait	pValue	Pubmed ID
No data available in table

GWAS

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ensgID	SNP	Chromosome	Position	Trait	PubmedID	Or or BEAT	EFO ID
ENSG00000123200	rs2094247	13	46028027	Blood protein levels	28240269		EFO_0008069
ENSG00000123200	rs9534288	13	46031306	Blood protein levels	28240269	0.5958	EFO_0008069
ENSG00000123200	rs12585823	13	45962156	Blood protein levels	28240269	0.5688	EFO_0008226
ENSG00000123200	rs5803322	13	46008320	Blood protein levels	29875488	0.2	EFO_0007937

Showing 1 to 4 of 4 entries

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Protein-Protein Interaction (PPI)

Click here to download ENSG00000123200'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
ENSG00000123200	homo_sapiens	ENSP00000503994	99.7603	99.281	nomascus_leucogenys	ENSNLEP00000024164	99.8201	99.3405
ENSG00000123200	homo_sapiens	ENSP00000503994	96.6447	95.746	pan_paniscus	ENSPPAP00000022546	98.1741	97.2611
ENSG00000123200	homo_sapiens	ENSP00000503994	99.5207	99.2211	pongo_abelii	ENSPPYP00000034270	99.5803	99.2806
ENSG00000123200	homo_sapiens	ENSP00000503994	99.8802	99.7603	pan_troglodytes	ENSPTRP00000058664	100	99.88
ENSG00000123200	homo_sapiens	ENSP00000503994	99.7004	99.2211	gorilla_gorilla	ENSGGOP00000005382	99.88	99.3998
ENSG00000123200	homo_sapiens	ENSP00000503994	71.7196	64.5896	ornithorhynchus_anatinus	ENSOANP00000024538	87.7566	79.0323
ENSG00000123200	homo_sapiens	ENSP00000503994	87.5974	79.988	sarcophilus_harrisii	ENSSHAP00000028092	87.2836	79.7015
ENSG00000123200	homo_sapiens	ENSP00000503994	50.8089	46.7945	notamacropus_eugenii	ENSMEUP00000006561	53.0331	48.843
ENSG00000123200	homo_sapiens	ENSP00000503994	78.0707	73.9964	choloepus_hoffmanni	ENSCHOP00000008612	79.1616	75.0304
ENSG00000123200	homo_sapiens	ENSP00000503994	94.308	89.7543	dasypus_novemcinctus	ENSDNOP00000004184	95.4518	90.8429

Showing 1 to 10 of 158 entries

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Gene Ontology

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Go ID	Go term	No. evidence	Entries	Species	Category
GO:0016607	is_active_in nuclear speck	2	IBA,IDA	Homo_sapiens(9606)	Component
GO:0036396	part_of RNA N6-methyladenosine methyltransferase complex	2	IDA,IPI	Homo_sapiens(9606)	Component
GO:0080009	involved_in mRNA methylation	2	IMP,NAS	Homo_sapiens(9606)	Process
GO:0003723	enables RNA binding	1	HDA	Homo_sapiens(9606)	Function
GO:0005515	enables protein binding	1	IPI	Homo_sapiens(9606)	Function
GO:0005634	located_in nucleus	1	NAS	Homo_sapiens(9606)	Component
GO:0005654	located_in nucleoplasm	1	IDA	Homo_sapiens(9606)	Component
GO:0006397	involved_in mRNA processing	1	IEA	Homo_sapiens(9606)	Process
GO:0008380	involved_in RNA splicing	1	IEA	Homo_sapiens(9606)	Process
GO:0046872	enables metal ion binding	1	IEA	Homo_sapiens(9606)	Function

Showing 1 to 10 of 11 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