Gene detail

Detailed information of OS493_004432-T1 in Lophelia pertusa

Genomic Location: scaffold_8:6461468...6467041
NR annotation: KAJ7387435.1, hypothetical protein OS493_004432 [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
Q8WPW2	Pyridoxal 5'-phosphate synthase subunit SNZERR OS=Suberites domuncula OX=55567 GN=SNZERR PE=2 SV=2
A5UY94	Pyridoxal 5'-phosphate synthase subunit PdxS OS=Roseiflexus sp. (strain RS-1) OX=357808 GN=pdxS PE=3 SV=1
Q5SKD9	Pyridoxal 5'-phosphate synthase subunit PdxS OS=Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) OX=300852 GN=pdxS PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006083 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01680 all species →	SOR_SNZ	SOR/SNZ family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001852 all species →	Family	Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ	Interproscan
IPR033755 all species →	Domain	PdxS/SNZ N-terminal domain	Interproscan
IPR011060 all species →	Homologous_superfamily	Ribulose-phosphate binding barrel	Interproscan
IPR013785 all species →	Homologous_superfamily	Aldolase-type TIM barrel	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR31829 all species →	PYRIDOXAL 5'-PHOSPHATE SYNTHASE SUBUNIT SNZ1-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0042819 all species →	Biological Process	vitamin B6 biosynthetic process	Interproscan
GO:0042823 all species →	Biological Process	pyridoxal phosphate biosynthetic process	Interproscan
GO:0006520 all species →	Biological Process	amino acid metabolic process	Interproscan
GO:0008615 all species →	Biological Process	pyridoxine biosynthetic process	Interproscan
GO:0016843 all species →	Molecular Function	amine-lyase activity	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
K06215	pdxS, pdx1; pyridoxal 5'-phosphate synthase pdxS subunit	EC:4.3.3.6	Vitamin B6 metabolism	ko00750	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_004432-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

215.3Max TPM

38.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	20.21	36.48
polyp at pH7 6	18	18	25.04	34.25
coral polyp · control treatment	16	16	52.68	215.34
coral polyp · oil and dispersant treatment	16	16	50.06	101.10
coral polyp · oil treatment	16	16	26.31	49.60
coral polyp · dispersant treatment	16	16	59.01	134.48
Polyp	10	10	37.77	85.44

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	-	36.48
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.76
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.57
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.51
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.81
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.59
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.39
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.14
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.07
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.67
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.92
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.78
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.69
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.29
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.64
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.35
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.96
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.19
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.25
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.28
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.86
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.54
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.10
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.85
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.71
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.19
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.88
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.17
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.33
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.18
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.80
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.57
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.31
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.96
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.25
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.47
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	215.34
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.66
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	71.29
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.65
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.00
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.13
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.30
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.37
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.94
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.90
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.55
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.04
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.46
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.01
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.29
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.04
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	101.10
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.91
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.67
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.91
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.78
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.66
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.84
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.17
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.75
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.28
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.90
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.18
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.44
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.98
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.06
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.29
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.60
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.88
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.15
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.37
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.10
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.07
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.92
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.04
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.87
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.42
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.42
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.07
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.18
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.06
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.42
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.41
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	134.48
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	88.78
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	84.41
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	78.57
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.90
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.11
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.22
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.09
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.06
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.28
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.81
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.63
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.08
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.99
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.59
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.11
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	85.44
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	63.52
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	54.79
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	51.59
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	33.59
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	28.24
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	22.10
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.42
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	13.33
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.63

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.