EuRBPDB

Description

Ensembl ID: ENSG00000005156 (Gene tree)
Gene ID: 3980
Gene Symbol: LIG3
Alias: LIG3alpha|LIG2
Full Name: DNA ligase 3
Gene Type: protein_coding
Species: Homo_sapiens
Status: putative
Strand: Plus strand
Length: 29,250 bases
Position: chr17:34,980,494-35,009,743
Accession: 6600
RBP type: non-canonical RBP
Summary: This gene is a member of the DNA ligase family. Each member of this family encodes a protein that catalyzes the joining of DNA ends but they each have a distinct role in DNA metabolism. The protein encoded by this gene is involved in excision repair and is located in both the mitochondria and nucleus, with translation initiation from the upstream start codon allowing for transport to the mitochondria and translation initiation from a downstream start codon allowing for transport to the nucleus. Additionally, alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & HEK293	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
29431736	Capturing the interactome of newly transcribed RNA	RICK & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000586407	LIG3-208	815	-	-	- (aa)	-	-
ENST00000592690	LIG3-215	722	-	ENSP00000467063	207 (aa)	-	K7ENR9
ENST00000262327	LIG3-201	3055	XM_006721896	ENSP00000262327	949 (aa)	XP_006721959	P49916
ENST00000378526	LIG3-202	8400	XM_005257970	ENSP00000367787	1009 (aa)	XP_005258027	P49916
ENST00000586119	LIG3-207	565	-	-	- (aa)	-	-
ENST00000585370	LIG3-203	235	-	ENSP00000465288	36 (aa)	-	K7EJR4
ENST00000592244	LIG3-214	440	-	-	- (aa)	-	-
ENST00000586435	LIG3-209	588	-	-	- (aa)	-	-
ENST00000585740	LIG3-204	887	-	ENSP00000467757	185 (aa)	-	K7EQB6
ENST00000593099	LIG3-216	4664	-	-	- (aa)	-	-
ENST00000588713	LIG3-211	467	-	-	- (aa)	-	-
ENST00000590181	LIG3-212	1156	-	-	- (aa)	-	-
ENST00000586058	LIG3-206	581	-	-	- (aa)	-	-
ENST00000590630	LIG3-213	904	-	-	- (aa)	-	-
ENST00000588109	LIG3-210	592	-	ENSP00000466278	38 (aa)	-	K7ELY6
ENST00000585941	LIG3-205	1699	-	ENSP00000468479	545 (aa)	-	K7ERZ5

Gene Model

Pathways

Pathway ID	Pathway Name	Source
hsa03410	Base excision repair	KEGG

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000005156	Electrocardiography	6E-12	19305408
ENSG00000005156	Electrocardiography	6E-25	24952745

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000005156	rs1052536	17	35004556	C	QT interval	24952745	[0.78-1.18] unit increase	0.98	EFO_0004682
ENSG00000005156	rs2074518	17	34997363	T	QT interval	19305408	[0.71-1.39] msec decrease	1.05	EFO_0004682
ENSG00000005156	rs145583519	17	34981227	G	Macrophage inflammatory protein 1b levels	27989323	[0.29-0.52] SD units increase	0.4044	EFO_0008219
ENSG00000005156	rs3135977	17	34990229	?	Adolescent idiopathic scoliosis	30019117			EFO_0005423
ENSG00000005156	rs3135967	17	34986710	A	Pulse pressure	30224653	[0.079-0.147] unit increase	0.1128	EFO_0005763
ENSG00000005156	rs2074518	17	34997363	T	QT interval	30679814	[0.97-1.69] unit decrease	1.33	EFO_0004682

Protein-Protein Interaction (PPI)

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

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000724	double-strand break repair via homologous recombination	-	TAS	Process
GO:0003677	DNA binding	-	IEA	Function
GO:0003909	DNA ligase activity	9809069.	IDA	Function
GO:0003909	DNA ligase activity	-	TAS	Function
GO:0003910	DNA ligase (ATP) activity	21873635.	IBA	Function
GO:0005515	protein binding	15744309.24407287.25609649.	IPI	Function
GO:0005524	ATP binding	-	IEA	Function
GO:0005634	nucleus	21873635.	IBA	Component
GO:0005654	nucleoplasm	-	IDA	Component
GO:0005654	nucleoplasm	-	TAS	Component
GO:0005737	cytoplasm	21873635.	IBA	Component
GO:0005739	mitochondrion	21873635.	IBA	Component
GO:0006273	lagging strand elongation	21873635.	IBA	Process
GO:0006283	transcription-coupled nucleotide-excision repair	-	TAS	Process
GO:0006288	base-excision repair, DNA ligation	21873635.	IBA	Process
GO:0006288	base-excision repair, DNA ligation	19589734.	IDA	Process
GO:0006288	base-excision repair, DNA ligation	-	TAS	Process
GO:0006297	nucleotide-excision repair, DNA gap filling	-	TAS	Process
GO:0006302	double-strand break repair	19589734.	IDA	Process
GO:0007049	cell cycle	-	IEA	Process
GO:0008270	zinc ion binding	-	IEA	Function
GO:0033151	V(D)J recombination	9809069.	IDA	Process
GO:0043504	mitochondrial DNA repair	21873635.	IBA	Process
GO:0051301	cell division	-	IEA	Process
GO:0071897	DNA biosynthetic process	-	IEA	Process
GO:0090298	negative regulation of mitochondrial DNA replication	21878356.	IMP	Process
GO:0097681	double-strand break repair via alternative nonhomologous end joining	21873635.	IBA	Process