Gene detail

Detailed information of OS493_002411-T1 in Lophelia pertusa

Genomic Location: scaffold_5:1844571...1847490
NR annotation: KAJ7365696.1, Paired box protein Pax-7 [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
P47239	Paired box protein Pax-7 OS=Mus musculus OX=10090 GN=Pax7 PE=1 SV=2
P23760	Paired box protein Pax-3 OS=Homo sapiens OX=9606 GN=PAX3 PE=1 SV=2
P24610	Paired box protein Pax-3 OS=Mus musculus OX=10090 GN=Pax3 PE=1 SV=2

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
IPR001523 all species →	Domain	Paired domain	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR043565 all species →	Family	PAX family	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan
IPR043182 all species →	Domain	Paired DNA-binding domain	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	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: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: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
K09381	PAX3_7; paired box protein 3/7	-	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_002411-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

620.8Max TPM

73.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.92	22.08
polyp at pH7 6	18	18	37.45	105.24
coral polyp · control treatment	16	16	131.47	332.11
coral polyp · oil and dispersant treatment	16	16	98.52	301.38
coral polyp · oil treatment	16	16	65.26	249.55
coral polyp · dispersant treatment	16	16	135.15	620.84
Polyp	10	10	30.74	107.49

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.08
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.96
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.14
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.07
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.51
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.35
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.75
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.74
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.70
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.29
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.52
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.25
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.71
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.14
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.90
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.54
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.17
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.80
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	105.24
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	100.83
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.31
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.33
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.41
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.09
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.89
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.19
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.16
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.73
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.16
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.77
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.73
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.22
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.41
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.64
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.34
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.63
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	332.11
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	255.63
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	241.31
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	219.82
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	194.63
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	189.29
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	152.22
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	132.33
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	123.07
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.74
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.26
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.97
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.00
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.55
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.80
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.87
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	301.38
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	235.19
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	177.20
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	140.71
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	118.77
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	107.70
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	100.62
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.34
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.26
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.95
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.34
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.34
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.64
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.41
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.77
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.65
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	249.55
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	133.33
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	125.19
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.64
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	75.69
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.56
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	67.45
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.78
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.99
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.99
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.87
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.75
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.18
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.54
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.26
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.42
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	620.84
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	267.59
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	210.29
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	206.20
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	130.07
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	116.37
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	108.47
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	106.42
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	97.73
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	88.91
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.91
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.68
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.18
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.95
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.31
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.40
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	107.49
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	57.84
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	34.62
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	26.97
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	25.20
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	24.93
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	16.80
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.00
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.41
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.18

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.