Gene detail

Detailed information of OS493_013562-T1 in Lophelia pertusa

Genomic Location: scaffold_37:1390897...1393934
NR annotation: KAJ7392189.1, hypothetical protein OS493_013562 [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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003887 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_013562-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR000225 all species →	Repeat	Armadillo	Interproscan
IPR028435 all species →	Family	Plakophilin/Delta catenin	Interproscan
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10372 all species →	PLAKOPHILLIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0005912 all species →	Cellular Component	adherens junction	Interproscan
GO:0007043 all species →	Biological Process	cell-cell junction assembly	Interproscan
GO:0045296 all species →	Molecular Function	cadherin binding	Interproscan
GO:0098609 all species →	Biological Process	cell-cell adhesion	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
K08527	RARA, NR1B1; retinoic acid receptor alpha	-	Nuclear receptors	ko03310	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_013562-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

169.4Max TPM

51.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	46.97	70.77
polyp at pH7 6	18	18	41.89	66.23
coral polyp · control treatment	16	16	71.92	161.47
coral polyp · oil and dispersant treatment	16	16	47.99	99.02
coral polyp · oil treatment	16	16	56.04	84.14
coral polyp · dispersant treatment	16	16	59.72	169.41
Polyp	10	10	26.35	46.60

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	70.77
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	70.41
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.41
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.23
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.63
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.43
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.89
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.75
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.35
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.19
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.80
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.19
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.39
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.67
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.61
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.72
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.36
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.64
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.23
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.19
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.32
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.02
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.38
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.82
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.34
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.56
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.91
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.74
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.10
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.86
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.55
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.04
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.12
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.94
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.83
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	161.47
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	112.84
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	104.12
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.79
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	92.71
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	92.57
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	88.03
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.70
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.82
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.85
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.05
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.92
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.22
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.03
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.26
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.27
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	99.02
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.73
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.16
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.10
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.84
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.36
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.42
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.64
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.89
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.21
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.20
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.76
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.68
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.01
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.43
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.42
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	84.14
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.88
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	79.68
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	70.91
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	70.46
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.59
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.47
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.86
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.08
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.05
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.00
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.54
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.91
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.67
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.38
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	169.41
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	109.16
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	99.28
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	92.97
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	78.21
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.86
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.12
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.14
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.86
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.99
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.59
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.64
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.45
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.19
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.19
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.40
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	46.60
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	43.29
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	41.44
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	39.45
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	33.44
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	28.09
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	10.27
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.56
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	6.82
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.51

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.