Gene detail

Detailed information of OS493_017483-T1 in Lophelia pertusa

Genomic Location: scaffold_56:774483...780870
NR annotation: KAJ7385114.1, hypothetical protein OS493_017483 [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
P47238	Paired box protein Pax-6 OS=Coturnix japonica OX=93934 GN=PAX6 PE=2 SV=1
P55864	Paired box protein Pax-6 OS=Xenopus laevis OX=8355 GN=pax6 PE=2 SV=1
Q1LZF1	Paired box protein Pax-6 OS=Bos taurus OX=9913 GN=PAX6 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000410 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan
PF00292 all species →	PAX	'Paired box' domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR043565 all species →	Family	PAX family	Interproscan
IPR001523 all species →	Domain	Paired domain	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR043182 all species →	Domain	Paired DNA-binding domain	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45636 all species →	PAIRED BOX PROTEIN PAX-6-RELATED-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0048856 all species →	Biological Process	anatomical structure development	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_017483-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_017483-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

108TPM > 0

7Conditions

7.9Max TPM

2.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	3.30	5.05
polyp at pH7 6	18	18	3.23	6.48
coral polyp · control treatment	16	16	3.45	5.86
coral polyp · oil and dispersant treatment	16	15	1.91	3.83
coral polyp · oil treatment	16	16	3.10	7.94
coral polyp · dispersant treatment	16	16	1.58	4.35
Polyp	10	9	2.16	6.53

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.05
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.70
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.41
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.85
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.72
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.72
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.61
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.34
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.17
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.96
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.82
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.80
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.79
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.71
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.68
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.60
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.53
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.95
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.48
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.20
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.61
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.21
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.72
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.43
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.73
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.59
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.55
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.46
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.45
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.42
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.33
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.18
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.14
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.60
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.59
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.39
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.86
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.62
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.16
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.64
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.43
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.88
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.79
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.41
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.96
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.81
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.51
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.36
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.25
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.12
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.92
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.43
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.83
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.20
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.77
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.32
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.24
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.98
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.90
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.89
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.89
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.78
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.63
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.61
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.40
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.15
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.04
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.94
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.93
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.48
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.70
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.52
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.84
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.79
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.62
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.51
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.31
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.06
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.84
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.70
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.61
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.15
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.70
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.35
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.36
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.27
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.94
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.65
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.62
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.57
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.50
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.49
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.32
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.09
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.02
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.01
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.56
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.38
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.18
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.53
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.51
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.85
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.69
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.33
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.80
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.49
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.45
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.