Gene detail

Detailed information of OS493_011342-T1 in Lophelia pertusa

Genomic Location: scaffold_28:3000370...3003011
NR annotation: KAJ7373733.1, hypothetical protein OS493_011342 [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
Q2S1V4	Tryptophanase OS=Salinibacter ruber (strain DSM 13855 / M31) OX=309807 GN=tnaA PE=3 SV=1
Q0C406	Tryptophanase OS=Hyphomonas neptunium (strain ATCC 15444) OX=228405 GN=tnaA PE=3 SV=1
O30971	Tryptophanase OS=Rhodobacter capsulatus OX=1061 GN=tnaA PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003246 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01212 all species →	Beta_elim_lyase	Beta-eliminating lyase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015421 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, major domain	Interproscan
IPR001597 all species →	Domain	Aromatic amino acid beta-eliminating lyase/threonine aldolase	Interproscan
IPR015422 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, small domain	Interproscan
IPR015424 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR32325 all species →	BETA-ELIMINATING LYASE-LIKE PROTEIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006520 all species →	Biological Process	amino acid metabolic process	Interproscan
GO:0016829 all species →	Molecular Function	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

No KEGG orthology assignment for OS493_011342-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_011342-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

34.5Max TPM

6.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.30	9.61
polyp at pH7 6	18	18	4.86	9.13
coral polyp · control treatment	16	16	9.16	24.66
coral polyp · oil and dispersant treatment	16	16	10.37	34.54
coral polyp · oil treatment	16	16	7.56	24.64
coral polyp · dispersant treatment	16	16	7.86	23.87
Polyp	10	10	3.52	8.49

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.61
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.74
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.88
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.50
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.25
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.15
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.87
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.81
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.70
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.69
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.83
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.75
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.60
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.28
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.42
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.48
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.18
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.59
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.13
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.94
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.33
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.50
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.48
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.52
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.44
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.26
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.15
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.90
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.81
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.60
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.15
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.12
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.49
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.37
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.28
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.06
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.66
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.48
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.29
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.08
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.07
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.69
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.76
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.34
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.88
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.61
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.91
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.28
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.56
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.88
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.34
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.74
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.54
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.09
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.88
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.88
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.81
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.51
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.98
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.37
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.82
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.47
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.68
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.41
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.30
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.12
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.68
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.34
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.64
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.20
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.37
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.48
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.63
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.98
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.03
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.55
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.43
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.09
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.61
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.32
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.98
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.35
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.12
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.13
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.87
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.14
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.21
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.71
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.64
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.53
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.26
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.55
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.36
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.36
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.93
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.81
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.77
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.56
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.64
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.47
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	8.49
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.13
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.92
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.03
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.72
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.30
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.15
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.95
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.45
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.11

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.