Gene detail

Detailed information of OS493_003156-T1 in Lophelia pertusa

Genomic Location: scaffold_6:5845242...5862203
NR annotation: KAJ7340410.1, radical S-adenosyl methionine domain-containing protein 1 [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
Q9HA92	Radical S-adenosyl methionine domain-containing protein 1, mitochondrial OS=Homo sapiens OX=9606 GN=RSAD1 PE=1 SV=2
A4IGH2	Radical S-adenosyl methionine domain-containing protein 1, mitochondrial OS=Danio rerio OX=7955 GN=rsad1 PE=2 SV=1
A5D7B1	Radical S-adenosyl methionine domain-containing protein 1, mitochondrial OS=Bos taurus OX=9913 GN=RSAD1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004534 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06969 all species →	HemN_C	HemN C-terminal domain	Domain	Interproscan
PF04055 all species →	Radical_SAM	Radical SAM superfamily	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR034505 all species →	Family	Anaerobic coproporphyrinogen-III oxidase	Interproscan
IPR006638 all species →	Domain	Elp3/MiaA/NifB-like, radical SAM core domain	Interproscan
IPR010723 all species →	Domain	HemN, C-terminal	Interproscan
IPR007197 all species →	Domain	Radical SAM	Interproscan
IPR013785 all species →	Homologous_superfamily	Aldolase-type TIM barrel	Interproscan
IPR004559 all species →	Family	Heme chaperone HemW-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13932 all species →	COPROPORPHYRINIGEN III OXIDASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0006779 all species →	Biological Process	porphyrin-containing compound biosynthetic process	Interproscan
GO:0051539 all species →	Molecular Function	4 iron, 4 sulfur cluster binding	Interproscan
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0051536 all species →	Molecular Function	iron-sulfur cluster binding	Interproscan
GO:0004109 all species →	Molecular Function	coproporphyrinogen oxidase 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_003156-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_003156-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

109TPM > 0

7Conditions

70.4Max TPM

13.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	13.27	18.78
polyp at pH7 6	18	18	14.11	21.31
coral polyp · control treatment	16	16	15.19	59.68
coral polyp · oil and dispersant treatment	16	16	11.45	70.44
coral polyp · oil treatment	16	16	14.04	22.21
coral polyp · dispersant treatment	16	16	7.39	14.19
Polyp	10	9	17.87	30.16

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.78
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.47
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.70
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.41
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.89
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.62
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.58
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.24
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.01
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.33
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.30
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.00
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.84
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.77
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.53
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.44
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.23
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.69
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.31
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.41
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.23
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.20
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.65
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.17
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.05
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.86
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.76
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.45
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.37
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.15
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.33
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.10
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.02
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.86
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.69
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.32
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.68
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.83
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.84
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.35
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.99
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.94
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.41
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.88
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.44
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.15
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.10
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.60
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.54
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.06
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.39
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.79
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	70.44
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.01
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.75
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.33
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.02
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.50
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.44
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.71
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.65
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.62
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.92
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.83
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.40
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.15
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.68
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.72
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.21
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.58
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.24
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.20
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.90
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.06
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.95
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.11
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.07
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.60
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.99
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.85
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.71
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.38
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.75
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.03
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.19
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.18
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.92
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.18
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.53
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.72
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.60
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.13
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.83
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.83
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.74
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.69
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.41
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.30
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.06
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.95
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	30.16
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	25.36
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	23.53
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	22.27
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	22.11
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	22.07
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	12.38
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.90
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.90
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.