Gene detail

Detailed information of OS493_010013-T1 in Lophelia pertusa

Genomic Location: scaffold_24:1830233...1833178
NR annotation: KAJ7337159.1, Partitioning defective 6 beta [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
Q9JK83	Partitioning defective 6 homolog beta OS=Mus musculus OX=10090 GN=Pard6b PE=1 SV=2
Q9JK84	Partitioning defective 6 homolog gamma OS=Mus musculus OX=10090 GN=Pard6g PE=2 SV=1
Q9BYG4	Partitioning defective 6 homolog gamma OS=Homo sapiens OX=9606 GN=PARD6G PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007863 (this species only) · gene tree & orthology
Ubiquitin family	ULD\|UFD\|PB1 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00564 all species →	PB1	PB1 domain	Domain	Interproscan
PF00595 all species →	PDZ	PDZ domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001478 all species →	Domain	PDZ domain	Interproscan
IPR000270 all species →	Domain	PB1 domain	Interproscan
IPR034868 all species →	Domain	Partitioning defective protein 6, PB1 domain	Interproscan
IPR051741 all species →	Family	Partitioning defective 6 homolog protein	Interproscan
IPR036034 all species →	Homologous_superfamily	PDZ superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14102 all species →	PAR-6-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0007098 all species →	Biological Process	centrosome cycle	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
K06093	PARD6; partitioning defective protein 6	-	Chromosome and associated proteins	ko03036	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_010013-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

138.5Max TPM

28.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	14.81	23.62
polyp at pH7 6	18	18	14.59	22.03
coral polyp · control treatment	16	16	24.01	48.13
coral polyp · oil and dispersant treatment	16	16	40.11	74.60
coral polyp · oil treatment	16	16	23.96	49.23
coral polyp · dispersant treatment	16	16	64.34	138.47
Polyp	10	10	10.82	18.17

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.62
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.21
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.33
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.18
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.00
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.28
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.03
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.19
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.59
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.80
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.49
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.21
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.21
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.72
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.54
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.18
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.44
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.62
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.03
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.74
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.08
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.37
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.23
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.01
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.32
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.13
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.52
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.24
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.56
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.81
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.76
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.36
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.61
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.13
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.79
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.87
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.13
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.69
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.28
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.44
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.36
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.69
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.99
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.43
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.39
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.94
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.84
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.69
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.29
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.59
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.04
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.30
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.60
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.93
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.51
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.62
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.86
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.67
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.53
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.88
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.65
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.37
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.54
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.18
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.36
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.20
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.63
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.22
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.23
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.71
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.58
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.08
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.05
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.23
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.75
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.12
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.64
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.37
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.71
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.47
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.30
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.76
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.75
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.62
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	138.47
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	126.61
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	104.23
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	87.89
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	87.35
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	71.12
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.13
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.03
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.83
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.78
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.67
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.08
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.15
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.31
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.78
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.93
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	18.17
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	18.05
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	16.17
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	13.26
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.57
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	7.49
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.45
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.43
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.41
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.23

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.