Gene detail

Detailed information of OS493_038168-T1 in Lophelia pertusa

Genomic Location: scaffold_522:42338...43228
NR annotation: KAJ7318259.1, 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)	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
IPR019844 all species →	Domain	Cold-shock (CSD) domain	Interproscan
IPR002059 all species →	Domain	Cold-shock protein, DNA-binding	Interproscan
IPR011129 all species →	Domain	Cold shock domain	Interproscan
IPR050181 all species →	Family	Cold shock domain-containing protein	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	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_038168-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_038168-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

54TPM > 0

7Conditions

2.7Max TPM

0.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	0.98	2.17
polyp at pH7 6	18	13	0.70	2.69
coral polyp · control treatment	16	8	0.13	0.54
coral polyp · oil and dispersant treatment	16	0	0.00	0.00
coral polyp · oil treatment	16	6	0.08	0.45
coral polyp · dispersant treatment	16	3	0.06	0.48
Polyp	10	8	0.36	1.18

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	-	2.17
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.83
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.67
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.27
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.03
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.01
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.00
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.98
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.94
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.92
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.91
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.76
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.76
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.74
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.68
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.69
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.41
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.25
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.14
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.02
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.02
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.98
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.85
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.75
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.53
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.50
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.33
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.18
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.54
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.51
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.47
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.20
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.15
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.14
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.11
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.03
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
SRR16705989	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
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
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705948	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
SRR16705979	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
SRR16705994	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
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.45
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.28
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.28
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.19
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.11
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.03
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
SRR16705961	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
SRR16705964	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
SRR16705998	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
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.48
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.40
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.07
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
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705956	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
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	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
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.18
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.59
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.49
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.39
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.39
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.29
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.21
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.08
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
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.