Gene detail

Detailed information of OS493_031544-T1 in Lophelia pertusa

Genomic Location: scaffold_219:595598...606671
NR annotation: KAJ7376948.1, Programmed cell death protein 4 [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
Q98TX3	Programmed cell death protein 4 OS=Gallus gallus OX=9031 GN=PDCD4 PE=2 SV=1
Q61823	Programmed cell death protein 4 OS=Mus musculus OX=10090 GN=Pdcd4 PE=1 SV=1
Q9JID1	Programmed cell death protein 4 OS=Rattus norvegicus OX=10116 GN=Pdcd4 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005884 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02847 all species →	MA3	MA3 domain	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003891 all species →	Domain	Initiation factor eIF-4 gamma, MA3	Interproscan
IPR039778 all species →	Family	Programmed cell death protein 4	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12626 all species →	PROGRAMMED CELL DEATH 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0045892 all species →	Biological Process	negative regulation of DNA-templated transcription	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_031544-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_031544-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

625.5Max TPM

153.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	94.32	148.14
polyp at pH7 6	18	18	116.64	175.12
coral polyp · control treatment	16	16	159.97	325.66
coral polyp · oil and dispersant treatment	16	16	183.33	337.19
coral polyp · oil treatment	16	16	157.66	283.61
coral polyp · dispersant treatment	16	16	283.67	625.48
Polyp	10	10	53.03	83.95

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	-	148.14
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	138.55
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	137.18
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	135.69
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	105.77
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	101.57
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	100.95
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	99.27
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	94.72
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	93.69
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	85.62
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	84.13
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	78.56
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	77.61
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	68.83
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.75
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.71
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.07
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	175.12
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	174.16
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	169.32
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	166.39
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	164.50
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	159.60
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	141.29
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	138.98
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	132.14
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	131.81
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	88.86
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	80.82
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	78.23
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.04
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.75
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.96
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.46
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.09
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	325.66
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	299.20
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	204.88
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	188.61
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	171.76
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	168.82
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	167.63
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	162.95
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	142.38
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	134.76
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	124.87
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	116.16
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	112.33
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	94.29
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.27
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.92
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	337.19
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	267.43
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	252.54
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	244.52
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	224.21
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	212.62
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	193.75
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	188.73
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	168.84
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	165.64
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	151.34
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	135.23
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	117.70
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	113.68
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	112.69
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.16
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	283.61
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	276.23
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	214.59
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	189.29
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	185.50
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	176.02
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	175.52
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	173.94
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	152.11
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	149.29
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	144.25
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	113.19
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	112.91
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.44
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.70
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.93
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	625.48
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	432.71
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	389.92
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	360.22
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	350.33
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	347.72
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	325.91
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	325.39
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	294.02
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	220.28
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	219.00
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	211.62
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	191.29
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	168.41
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.20
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.20
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	83.95
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	80.13
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	74.74
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	74.41
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	67.99
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	59.08
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	29.11
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	25.68
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	24.95
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	10.30

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.