Gene detail

Detailed information of OS493_006587-T1 in Lophelia pertusa

Genomic Location: scaffold_13:4447702...4451544
NR annotation: KAJ7393601.1, 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
P21573	Y-box-binding protein 1 OS=Xenopus laevis OX=8355 GN=ybx1 PE=2 SV=1
P41824	Y-box factor homolog OS=Aplysia californica OX=6500 PE=2 SV=1
Q9JKB3	Y-box-binding protein 3 OS=Mus musculus OX=10090 GN=Ybx3 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002110 (this species only)

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
IPR050181 all species →	Family	Cold shock domain-containing protein	Interproscan
IPR019844 all species →	Domain	Cold-shock (CSD) domain	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K09276	YBX1, NSEP1; Y-box-binding protein 1	-	Spliceosome	ko03041	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_006587-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

110TPM > 0

7Conditions

2,100.8Max TPM

1,566.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	1,646.01	1,965.19
polyp at pH7 6	18	18	1,714.02	2,094.55
coral polyp · control treatment	16	16	1,826.78	2,100.80
coral polyp · oil and dispersant treatment	16	16	1,532.14	1,925.53
coral polyp · oil treatment	16	16	1,816.86	2,063.91
coral polyp · dispersant treatment	16	16	1,224.61	1,571.94
Polyp	10	10	944.01	1,203.19

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,965.19
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,961.78
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,791.79
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,782.04
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,776.93
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,748.16
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,745.91
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,717.89
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,663.04
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,647.85
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,553.69
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,552.68
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,535.55
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,527.28
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,521.58
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,520.78
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,339.40
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,276.72
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,094.55
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,058.84
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,032.77
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,946.30
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,861.16
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,855.54
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,729.27
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,717.16
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,670.04
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,662.72
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,642.98
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,629.05
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,597.86
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,582.02
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,495.36
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,441.49
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,418.73
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,416.60
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,100.80
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,087.44
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,039.07
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,997.14
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,971.63
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,942.14
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,922.80
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,920.95
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,885.61
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,840.43
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,768.73
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,584.31
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,575.54
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,554.73
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,545.50
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,491.63
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,925.53
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,873.04
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,627.41
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,623.28
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,603.98
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,603.93
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,578.23
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,570.79
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,559.21
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,557.53
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,434.11
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,410.98
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,389.84
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,318.77
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,271.81
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,165.82
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,063.91
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,047.80
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,047.45
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,046.02
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,927.53
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,925.71
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,922.83
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,893.11
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,879.18
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,808.53
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,747.66
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,677.89
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,620.72
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,617.41
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,541.26
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,302.76
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,571.94
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,570.65
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,556.13
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,474.60
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,450.75
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,347.16
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,327.21
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,317.78
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,258.16
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,216.45
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,157.48
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,091.77
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,021.34
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	972.12
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	803.42
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	456.80
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1,203.19
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1,135.86
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1,070.21
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1,060.54
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1,048.66
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	947.92
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	900.96
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	700.92
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	692.96
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	678.89

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.