Gene detail

Detailed information of OS493_022060-T1 in Lophelia pertusa

Genomic Location: scaffold_89:27928...28569
NR annotation: KAJ7358630.1, Y-box-binding protein 2 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
B5DE31	Y-box-binding protein 1 OS=Danio rerio OX=7955 GN=ybx1 PE=1 SV=1
Q06066	Y-box-binding protein 1 OS=Gallus gallus OX=9031 GN=YBX1 PE=2 SV=1
P62960	Y-box-binding protein 1 OS=Mus musculus OX=10090 GN=Ybx1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002091 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00313 all species →	CSD	'Cold-shock' DNA-binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002059 all species →	Domain	Cold-shock protein, DNA-binding	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR011129 all species →	Domain	Cold shock domain	Interproscan
IPR019844 all species →	Domain	Cold-shock (CSD) domain	Interproscan
IPR050181 all species →	Family	Cold shock domain-containing protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11544 all species →	COLD SHOCK DOMAIN CONTAINING PROTEINS	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0010468 all species →	Biological Process	regulation of gene expression	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

No KEGG orthology assignment for OS493_022060-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_022060-T1 across 110 RNA-seq samples of Lophelia pertusa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

110Samples

80TPM > 0

7Conditions

3.1Max TPM

0.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	1.57	3.06
polyp at pH7 6	18	18	1.26	2.68
coral polyp · control treatment	16	9	0.74	2.19
coral polyp · oil and dispersant treatment	16	9	0.33	2.16
coral polyp · oil treatment	16	9	0.61	2.49
coral polyp · dispersant treatment	16	8	0.23	1.26
Polyp	10	9	0.90	2.33

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.06
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.04
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.58
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.37
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.01
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.90
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.76
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.45
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.41
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.33
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.22
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.21
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.10
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.87
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.77
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.76
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.72
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.65
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.68
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.95
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.78
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.73
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.57
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.55
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.41
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.28
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.25
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.22
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.13
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.06
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.98
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.96
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.91
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.69
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.28
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.23
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.19
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.19
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.77
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.52
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.48
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.27
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.09
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.23
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.12
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.16
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.50
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.94
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.25
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.22
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.15
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.10
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.01
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.49
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.74
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.66
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.06
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.98
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.96
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.83
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.12
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.01
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.26
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.82
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.79
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.37
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.21
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.12
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.09
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.09
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.33
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.97
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.81
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.21
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.70
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.69
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.22
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.05
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.01
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.