Gene detail

Detailed information of OS493_006958-T1 in Lophelia pertusa

Genomic Location: scaffold_14:4399911...4404657
NR annotation: KAJ7386923.1, AMP deaminase [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
P79888	S-adenosylmethionine decarboxylase proenzyme OS=Xenopus laevis OX=8355 GN=amd1 PE=2 SV=1
P91931	S-adenosylmethionine decarboxylase proenzyme OS=Drosophila melanogaster OX=7227 GN=SamDC PE=2 SV=1
P17708	S-adenosylmethionine decarboxylase proenzyme OS=Rattus norvegicus OX=10116 GN=Amd1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003295 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01536 all species →	SAM_decarbox	Adenosylmethionine decarboxylase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018166 all species →	Conserved_site	S-adenosylmethionine decarboxylase, conserved site	Interproscan
IPR048283 all species →	Family	S-adenosylmethionine decarboxylase-like	Interproscan
IPR016067 all species →	Homologous_superfamily	S-adenosylmethionine decarboxylase, core	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11570 all species →	S-ADENOSYLMETHIONINE DECARBOXYLASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004014 all species →	Molecular Function	adenosylmethionine decarboxylase activity	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006597 all species →	Biological Process	spermine biosynthetic process	Interproscan
GO:0008295 all species →	Biological Process	spermidine biosynthetic process	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_006958-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_006958-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

104TPM > 0

7Conditions

33.5Max TPM

12.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	12.91	18.77
polyp at pH7 6	18	16	13.50	23.17
coral polyp · control treatment	16	16	14.81	33.49
coral polyp · oil and dispersant treatment	16	15	10.59	17.70
coral polyp · oil treatment	16	16	14.61	19.75
coral polyp · dispersant treatment	16	15	10.98	20.86
Polyp	10	8	8.44	22.24

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.77
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.73
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.76
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.30
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.17
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.79
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.71
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.82
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.14
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.52
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.08
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.58
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.54
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.04
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.89
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.23
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.62
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.68
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.17
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.09
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.41
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.07
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.40
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.92
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.84
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.05
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.79
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.15
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.79
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.94
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.31
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.35
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.34
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.45
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	33.49
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.66
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.45
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.28
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.76
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.52
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.37
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.65
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.21
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.21
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.73
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.47
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.05
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.57
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.11
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.50
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.70
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.69
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.76
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.46
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.39
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.31
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.97
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.11
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.73
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.51
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.31
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.31
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.41
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.06
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.75
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.75
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.74
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.64
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.56
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.63
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.51
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.53
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.35
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.13
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.60
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.03
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.41
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.77
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.63
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.91
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.49
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.86
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.84
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.68
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.69
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.66
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.88
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.36
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.24
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.91
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.71
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.59
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.30
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.52
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.96
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.51
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	22.24
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	15.76
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.86
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.87
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.10
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.31
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.91
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.34
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
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.