Gene detail

Detailed information of OS493_022623-T1 in Lophelia pertusa

Genomic Location: scaffold_95:171981...181133
NR annotation: KAJ7357813.1, Visual system homeobox 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
O42250	Visual system homeobox 1 OS=Danio rerio OX=7955 GN=vsx1 PE=1 SV=2
Q61412	Visual system homeobox 2 OS=Mus musculus OX=10090 GN=Vsx2 PE=1 SV=1
Q9IAL1	Visual system homeobox 2 OS=Gallus gallus OX=9031 GN=VSX2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008160 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan
PF03826 all species →	OAR	OAR motif	Motif	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR052294 all species →	Family	Visual system homeobox transcriptional regulators	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR003654 all species →	Domain	OAR domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46892 all species →	VISUAL SYSTEM HOMEOBOX 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:1990837 all species →	Molecular Function	sequence-specific double-stranded DNA binding	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_022623-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_022623-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

86TPM > 0

7Conditions

2.9Max TPM

0.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	13	1.35	2.78
polyp at pH7 6	18	12	0.91	2.87
coral polyp · control treatment	16	16	0.85	2.03
coral polyp · oil and dispersant treatment	16	12	0.32	0.89
coral polyp · oil treatment	16	15	0.67	1.36
coral polyp · dispersant treatment	16	12	0.57	2.60
Polyp	10	6	0.62	2.28

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.78
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.77
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.67
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.45
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.99
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.92
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.74
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.66
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.38
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.37
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.36
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.32
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.84
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	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	-	2.87
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.47
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.90
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.66
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.23
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.22
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.16
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.04
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.95
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.89
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.63
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.39
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	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
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.03
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.42
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.37
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.25
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.20
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.16
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.86
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.81
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.74
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.58
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.55
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.54
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.48
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.32
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.17
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.13
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.89
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.87
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.60
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.58
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.48
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.31
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.29
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.26
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.26
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.24
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.16
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.15
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
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.36
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.30
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.18
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.14
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.05
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.76
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.62
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.55
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.54
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.44
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.41
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.39
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.37
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.32
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.23
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.60
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.97
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.87
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.80
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.68
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.56
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.48
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.43
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.43
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.43
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.41
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.39
SRR16705953	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
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.28
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.38
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.91
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.64
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.59
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.44
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	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.