Gene detail

Detailed information of OS493_001449-T1 in Lophelia pertusa

Genomic Location: scaffold_3:1747601...1761959
NR annotation: KAJ7381326.1, hypothetical protein OS493_001449 [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
P32232	Cystathionine beta-synthase OS=Rattus norvegicus OX=10116 GN=Cbs PE=1 SV=3
Q58H57	Cystathionine beta-synthase OS=Macaca fascicularis OX=9541 GN=CBS PE=2 SV=3
P35520	Cystathionine beta-synthase OS=Homo sapiens OX=9606 GN=CBS PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004906 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00291 all species →	PALP	Pyridoxal-phosphate dependent enzyme	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036052 all species →	Homologous_superfamily	Tryptophan synthase beta chain-like, PALP domain superfamily	Interproscan
IPR050214 all species →	Family	Cysteine Synthase/Cystathionine Beta-Synthase	Interproscan
IPR001926 all species →	Domain	Tryptophan synthase beta chain-like, PALP domain	Interproscan
IPR005857 all species →	Family	Cystathionine beta-synthase	Interproscan
IPR001216 all species →	Binding_site	Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10314 all species →	CYSTATHIONINE BETA-SYNTHASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004122 all species →	Molecular Function	cystathionine beta-synthase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006535 all species →	Biological Process	cysteine biosynthetic process from serine	Interproscan
GO:0019344 all species →	Biological Process	cysteine biosynthetic process	Interproscan
GO:0019343 all species →	Biological Process	cysteine biosynthetic process via cystathionine	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_001449-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_001449-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

118.9Max TPM

35.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	22.54	43.85
polyp at pH7 6	18	18	23.45	35.88
coral polyp · control treatment	16	16	44.92	75.13
coral polyp · oil and dispersant treatment	16	16	47.00	82.24
coral polyp · oil treatment	16	16	27.92	51.81
coral polyp · dispersant treatment	16	16	64.76	118.94
Polyp	10	10	15.35	30.75

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	-	43.85
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.08
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.58
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.50
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.77
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.16
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.70
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.10
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.88
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.52
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.27
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.03
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.77
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.39
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.82
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.45
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.22
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.69
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.88
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.93
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.08
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.36
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.95
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.57
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.19
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.34
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.46
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.94
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.63
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.55
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.20
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.66
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.52
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.50
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.43
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	75.13
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.65
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.56
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.03
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.09
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.94
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.92
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.05
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.45
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.34
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.77
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.58
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.55
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.90
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.77
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.99
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.24
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	78.21
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.59
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.53
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.36
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.89
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.40
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.17
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.54
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.99
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.76
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.75
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.90
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.86
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.64
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.18
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.81
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.12
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.78
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.51
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.80
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.94
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.48
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.63
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.41
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.99
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.67
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.51
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.31
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.66
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.98
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.07
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	118.94
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	103.17
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	92.70
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.07
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	80.73
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	77.74
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.25
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.64
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.60
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.31
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.64
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.91
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.52
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.51
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.91
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.45
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	30.75
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	24.11
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	18.51
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	16.21
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	15.14
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	14.05
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	10.74
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	10.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	9.82
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.18

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.