Gene detail

Detailed information of OS493_012791-T1 in Lophelia pertusa

Genomic Location: scaffold_33:3116674...3119268
NR annotation: KAJ7380029.1, Programmed cell death protein 2 [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
P46718	Programmed cell death protein 2 OS=Mus musculus OX=10090 GN=Pdcd2 PE=2 SV=2
Q16342	Programmed cell death protein 2 OS=Homo sapiens OX=9606 GN=PDCD2 PE=1 SV=2
Q2YDC9	Programmed cell death protein 2 OS=Bos taurus OX=9913 GN=PDCD2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006728 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01753 all species →	zf-MYND	MYND finger	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002893 all species →	Domain	Zinc finger, MYND-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12298 all species →	PCDC2 PROGRAMMED CELL DEATH PROTEIN 2 -RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	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_012791-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_012791-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

105TPM > 0

7Conditions

12.2Max TPM

4.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	3.49	5.67
polyp at pH7 6	18	15	3.78	6.86
coral polyp · control treatment	16	16	6.07	12.19
coral polyp · oil and dispersant treatment	16	16	3.94	10.63
coral polyp · oil treatment	16	16	5.87	11.46
coral polyp · dispersant treatment	16	15	3.33	8.29
Polyp	10	9	2.00	3.81

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	-	5.67
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.64
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.27
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.31
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.04
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.96
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.63
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.57
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.41
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.07
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.05
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.88
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.84
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.54
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.42
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.37
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.20
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.86
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.08
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.95
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.65
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.45
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.10
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.04
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.73
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.11
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.90
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.54
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.43
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.05
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.77
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.44
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.19
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.73
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.90
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.94
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.98
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.47
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.77
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.70
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.37
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.80
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.31
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.24
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.53
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.96
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.79
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.43
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.63
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.30
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.99
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.99
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.84
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.66
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.15
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.98
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.84
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.55
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.19
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.12
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.05
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.93
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.92
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.89
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.46
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.28
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.34
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.12
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.81
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.69
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.55
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.37
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.31
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.17
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.78
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.63
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.29
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.28
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.16
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.61
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.29
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.06
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.08
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.27
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.16
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.63
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.43
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.22
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.13
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.02
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.56
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.31
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.79
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.44
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.91
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.81
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.81
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.49
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.27
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.26
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.17
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.81
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.90
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.50
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.