Gene detail

Detailed information of OS493_012429-T1 in Lophelia pertusa

Genomic Location: scaffold_32:2215079...2219330
NR annotation: KAJ7386088.1, Paired box protein Pax-6 [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
P26630	Paired box protein Pax-6 OS=Danio rerio OX=7955 GN=pax6a PE=2 SV=1
O73917	Paired box protein Pax-6 OS=Oryzias latipes OX=8090 GN=pax6 PE=2 SV=1
P55864	Paired box protein Pax-6 OS=Xenopus laevis OX=8355 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
IPR001523 all species →	Domain	Paired domain	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan
IPR043182 all species →	Domain	Paired DNA-binding domain	Interproscan
IPR043565 all species →	Family	PAX family	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:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K08031	PAX6; paired box protein 6	-	Transcription factors	ko03000	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_012429-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

335.4Max TPM

46.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	17.38	28.93
polyp at pH7 6	18	18	18.98	34.99
coral polyp · control treatment	16	16	48.52	143.09
coral polyp · oil and dispersant treatment	16	16	98.22	335.43
coral polyp · oil treatment	16	16	52.76	124.48
coral polyp · dispersant treatment	16	16	73.09	210.32
Polyp	10	10	11.50	26.74

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	-	28.93
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.43
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.21
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.71
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.90
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.69
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.18
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.99
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.87
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.21
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.72
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.72
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.00
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.22
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.90
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.28
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.96
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.91
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.99
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.42
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.78
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.63
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.22
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.92
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.85
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.66
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.21
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.62
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.63
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.04
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.48
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.06
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.79
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.96
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.35
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.07
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	143.09
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	91.80
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.47
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.34
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.18
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.43
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.60
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.93
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.23
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.69
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.63
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.46
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.60
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.32
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.20
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.36
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	335.43
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	215.96
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	181.29
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	152.08
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	130.83
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	94.78
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	92.17
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.95
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	65.06
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.32
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.71
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.82
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.42
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.46
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.58
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.72
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	124.48
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	106.50
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	93.16
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	85.19
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.09
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.55
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.16
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.90
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.30
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.62
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.23
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.25
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.46
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.98
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.87
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.41
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	210.32
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	139.19
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	130.30
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	107.80
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	93.60
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	75.70
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.98
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.90
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.49
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.26
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.93
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.72
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.26
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.67
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.45
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.88
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	26.74
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	24.78
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	14.54
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.28
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.35
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	8.21
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.95
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.94
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.91
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.29

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.