XRN1

General Information

Gene Name : XRN1
Gene ID : ENSG00000114127.10
Essential Gene : No

Functions

RNA stability & decay
Viral RNA regulation

Localization(RBPImage: XRN1)

Cytoplasm
Compartment/Organelle
P bodies
Cytoskeleton
Actin

Domains (AlphaFold: XRN1)

Nuclease

Antibody Validation

Bethyl Labs: A300-443A

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	XRN1	ENSG00000114127.10	18.20	11.41	14.80	ENCSR000AEF
HepG2	XRN1	ENSG00000114127.10	3.13	5.48	4.30	ENCSR985KAT
K562	XRN1	ENSG00000114127.10	8.92	7.76	8.34	ENCSR000AEO

Assays

2 Released experiments are available on ENCORE database.

Assay Type	Exp_Name	ENCODE ID	Target label	Biosample	Status	Linked Antibody	Controls	Method	Note
knockdown followed by RNA-seq	XRN1-BGKLV38-K562	ENCSR949RMX	XRN1	K562	Released		ENCSR260BQC	shRNA	KD% = 91.5,93.8
knockdown followed by RNA-seq	XRN1-BGHLV37-HepG2	ENCSR676SDU	XRN1	HepG2	Released		ENCSR225PRV	shRNA	KD% = 79.8,85.7

eCLIP

No eCLIP experiment available

Antibody Validation

GeneName	Antibody_DCC_ID	Product_ID	Lot_ID	Phosphate	HepG2 Primary Validation	K562 Primary Validation	HepG2 Secondary Validation	K562 Secondary Validation
XRN1	ENCAB231MQI	A300-443A	3				BGHLV37-99, Released, ENCODE3	BGKLV38-129, Released, ENCODE3

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project
XRN1	K562	shRNA			BGKLV38-125,BGKLV38-126	BGKLV38-1,BGKLV38-2		NotSatisfied	ENCODE3
XRN1	K562	shRNA			BGKLV38-127,BGKLV38-128	BGKLV38-1,BGKLV38-2		NotSatisfied	ENCODE3
XRN1	K562	shRNA	ENCSR949RMX	ENCSR260BQC	XRN1-BGKLV38-129C,XRN1-BGKLV38-130C	NT-BGKLV38-1C,NT-BGKLV38-2C	91.5,93.8	Released	ENCODE4
XRN1	K562	shRNA			BGKLV38-131,BGKLV38-132	BGKLV38-1,BGKLV38-2	91.7,89.3	NotSatisfied	ENCODE3
XRN1	HepG2	shRNA			BGHLV23-59,BGHLV23-60	BGHLV23-1,BGHLV23-2	redo transfection,redo transfection	NotSatisfied	ENCODE3
XRN1	HepG2	shRNA			BGHLV37-97,BGHLV37-98	BGHLV37-1,BGHLV37-2		NotSatisfied	ENCODE3
XRN1	HepG2	shRNA	ENCSR676SDU	ENCSR225PRV	XRN1-BGHLV37-99C,XRN1-BGHLV37-100C	non-target-BGHLV37-1C,non-target-BGHLV37-2C	79.8,85.7	Released	ENCODE4
XRN1	HepG2	shRNA			BGHLV37-101,BGHLV37-102	BGHLV37-1,BGHLV37-2	99.5,99.5	NotSatisfied	ENCODE3
XRN1	HepG2	shRNA			BGHLV37-103,BGHLV37-104	BGHLV37-1,BGHLV37-2		NotSatisfied	ENCODE3

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

XRN1: Click to RBP Image Database

Cytoplasm

Compartment/Organelle

P bodies

Cytoskeleton

Actin

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
XRN1	Product_ID: A300-443A Lot_ID: 3 Source: Bethyl Labs Target Name: XRN1-human

Summary
Proteins Bound to RBP RNA

RNA Targets

eCLIP assay for XRN1 is not avaliable on ENCORE database.

Proteins bound to RNA

XRN1 RNA is bound by 23 proteins.

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eCLIP assay for XRN1 is not avaliable on ENCORE database.

23 proteins are bound to XRN1 RNA:

Show entries

Search:

Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr3	142094749	142094839	-	CDS,intron-Distal,intron-Proximal	5.27685	21.95813	K562	TARDBP
chr3	142095923	142096052	-	intron-Distal	4.73042	20.33936	K562	KHSRP
chr3	142144912	142145025	-	intron-Distal	5.45966	18.13366	HepG2	QKI
chr3	142141528	142141672	-	3'-UTR,CDS,intron-Distal,intron-Proximal	4.42135	17.08595	K562	EFTUD2
chr3	142096219	142096285	-	intron-Distal	5.00400	16.87092	K562	KHSRP
chr3	142090080	142090146	-	CDS,intron-Distal,intron-Proximal	5.36309	15.86994	HepG2	BCLAF1
chr3	142103432	142103499	-	CDS,intron-Distal	5.37603	15.18966	HepG2	BCLAF1
chr3	142123851	142123919	-	CDS,intron-Distal,intron-Proximal	3.99134	15.00162	HepG2	BCLAF1
chr3	142096099	142096185	-	intron-Distal	4.19486	14.75316	K562	KHSRP
chr3	142151643	142151722	-	3'-UTR,CDS,intron-Distal	5.05410	14.51064	HepG2	BCLAF1
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 126 entries

eCLIP assay for XRN1 is not avaliable on ENCORE database.

Diffrential Expression

The Knockdown/knockout assay for XRN1 is not available on ENCORE database.
111 RBPs can affect the levels of XRN1.

CanvasJS.com

The Knockdown/knockout RNA-Seq assay for XRN1 is not available on ENCORE database.

111 RBPs can affect the gene expression of XRN1 :

Show entries

Search:

Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
XRN1	ENSG00000114127.6	1269.53900	2184.61340	-0.78310	20.83810	18.08660	K562	CPEB4
XRN1	ENSG00000114127.6	721.30600	1245.91530	-0.78850	16.83060	15.53770	HepG2	UTP3
XRN1	ENSG00000114127.6	3743.68260	2129.09170	0.81410	14.84170	13.63310	K562	AQR
XRN1	ENSG00000114127.6	552.71350	949.32330	-0.78040	14.65940	13.35690	HepG2	HNRNPU
XRN1	ENSG00000114127.6	601.74590	985.94080	-0.71230	14.52420	13.23070	HepG2	SMN1
XRN1	ENSG00000114127.6	1356.34110	2065.16410	-0.60650	13.41650	12.26830	K562	AGGF1
XRN1	ENSG00000114127.6	1482.99980	1001.21600	0.56670	11.50050	10.51150	HepG2	SRSF9
XRN1	ENSG00000114127.6	853.28090	1375.73470	-0.68910	12.03560	10.35520	K562	EIF3G
XRN1	ENSG00000114127.6	1695.90530	1106.21050	0.61630	11.12140	10.11600	HepG2	TAF15
XRN1	ENSG00000114127.6	728.95060	1112.93440	-0.61050	10.20190	9.15300	HepG2	PCBP1
Gene Name	Gene ID	KDMean	CNMean	log2(fold change)	-log(pval)	-log(padj)	Cell Line	Affected by RBP	Bound by RBP

Showing 1 to 10 of 123 entries

*: "Inf" was shown as "99999.99999" and "-Inf" was shown as "-99999.99999".
**: "-log(0)" was displayed as "99999.99999".

The Knockdown/knockout RNA-Seq assay for XRN1 is not available on ENCORE database.

10 RBPs can affect the splicing of XRN1 :

Show entries

Search:

Event Type	Gene Name	Gene ID	chr	Strand	ExonStart	ExonEnd	upstreamES	upstreamEE	downstreamES	downstreamEE	dPSI	p-value	FDR	is_included	Cell Line	Affected by RBP
SE	XRN1	ENSG00000114127.6	chr3	-	142066075	142066184	142054289	142054351	142074242	142074338	-0.22000	0.00000	0.00001	excluded	K562	AQR
SE	XRN1	ENSG00000114127.6	chr3	-	142145585	142145683	142142332	142142484	142151502	142151735	-0.47700	0.00000	0.00001	excluded	K562	AQR
SE	XRN1	ENSG00000114127.6	chr3	-	142037631	142037745	142037488	142037536	142048275	142048479	0.25300	0.00000	0.01292	included	HepG2	RBM5
A3SS	XRN1	ENSG00000114127.6	chr3	-	142078703	142078802	142078703	142078773	142083888	142084021	0.25400	0.00000	0.00004	longer	K562	AQR
A3SS	XRN1	ENSG00000114127.6	chr3	-	142132976	142133168	142132976	142133133	142135981	142136214	0.22700	0.00007	0.00062	longer	K562	AQR
A3SS	XRN1	ENSG00000114127.6	chr3	-	142090080	142090195	142090080	142090170	142094639	142094734	0.10900	0.00012	0.00102	longer	K562	AQR
SE	XRN1	ENSG00000114127.6	chr3	-	142095538	142095637	142095090	142095436	142098923	142099022	0.25700	0.00027	0.00924	included	HepG2	HNRNPK
SE	XRN1	ENSG00000114127.6	chr3	-	142145585	142145683	142142401	142142484	142151502	142151735	-0.21500	0.00030	0.02841	excluded	K562	HNRNPUL1
SE	XRN1	ENSG00000114127.6	chr3	-	142037631	142037745	142037488	142037536	142048275	142048457	-0.33800	0.00036	0.01146	excluded	HepG2	HNRNPK
SE	XRN1	ENSG00000114127.6	chr3	-	142066075	142066184	142054289	142054351	142074242	142074338	-0.16100	0.00048	0.01555	excluded	K562	AGGF1

Showing 1 to 10 of 24 entries

*: "Inf" was shown as "99999.99999" and "-Inf" was shown as "-99999.99999".
**: "-log(0)" was displayed as "99999.99999".

XRN1

General Information

Functions

Localization(RBPImage: XRN1)

Domains (AlphaFold: XRN1)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

eCLIP assay for XRN1 is not avaliable on ENCORE database.

23 proteins are bound to XRN1 RNA:

eCLIP assay for XRN1 is not avaliable on ENCORE database.

Diffrential Expression

The Knockdown/knockout RNA-Seq assay for XRN1 is not available on ENCORE database.

111 RBPs can affect the gene expression of XRN1 :

The Knockdown/knockout RNA-Seq assay for XRN1 is not available on ENCORE database.

10 RBPs can affect the splicing of XRN1 :

The Knockdown/knockout RNA-Seq assay for XRN1 is not avaliable on ENCORE database.