Gene detail

Detailed information of OS493_024015-T1 in Lophelia pertusa

Genomic Location: scaffold_109:1278037...1283014
NR annotation: KAJ7390625.1, C-1-tetrahydrofolate synthase, cytoplasmic [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
P28723	Formate--tetrahydrofolate ligase OS=Spinacia oleracea OX=3562 PE=1 SV=3
Q9SPK5	Formate--tetrahydrofolate ligase OS=Arabidopsis thaliana OX=3702 GN=THFS PE=2 SV=1
P11586	C-1-tetrahydrofolate synthase, cytoplasmic OS=Homo sapiens OX=9606 GN=MTHFD1 PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001689 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01268 all species →	FTHFS	Formate--tetrahydrofolate ligase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR020628 all species →	Conserved_site	Formate-tetrahydrofolate ligase, FTHFS, conserved site	Interproscan
IPR000559 all species →	Family	Formate-tetrahydrofolate ligase, FTHFS	Interproscan

PANTHER

No PANTHER signature was detected for OS493_024015-T1. This gene does have a gene model — the search simply returned no hit.

Gene Ontology

GO term	Category	Description	Source
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0004329 all species →	Molecular Function	formate-tetrahydrofolate ligase 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_024015-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_024015-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

86.5Max TPM

35.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	22.45	33.82
polyp at pH7 6	18	18	28.08	46.70
coral polyp · control treatment	16	16	45.65	86.46
coral polyp · oil and dispersant treatment	16	16	45.85	71.49
coral polyp · oil treatment	16	16	35.51	73.72
coral polyp · dispersant treatment	16	16	46.75	78.76
Polyp	10	10	17.24	29.79

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	-	33.82
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.89
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.50
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.88
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.35
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.26
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.06
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.46
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.95
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.76
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.45
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.96
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.89
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.78
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.31
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.63
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.26
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.85
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.70
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.07
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.16
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.10
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.87
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.80
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.25
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.05
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.43
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.19
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.20
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.33
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.03
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.13
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.87
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.01
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.29
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	86.46
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	68.92
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.68
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.16
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.41
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.28
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.63
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.43
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.70
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.87
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.86
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.42
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.28
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.05
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.52
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.80
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.49
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.03
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.66
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.44
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.87
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.66
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.21
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.53
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.41
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.34
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.26
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.76
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.70
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.73
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.23
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.27
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.72
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	60.29
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.56
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.31
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.77
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.66
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.83
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.33
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.35
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.98
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.79
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.52
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.26
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.14
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.49
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.15
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	78.76
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.22
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.12
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.11
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.53
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.10
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.95
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.18
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.62
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.87
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.46
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.29
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.06
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.46
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.38
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.89
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	29.79
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	25.54
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	23.44
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	18.99
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	16.68
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	15.20
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	13.01
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	12.44
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	9.92
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.42

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.