Gene detail

Detailed information of OS493_005834-T1 in Lophelia pertusa

Genomic Location: scaffold_12:1542127...1548063
NR annotation: KAJ7339436.1, hypothetical protein OS493_005834 [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
Q16526	Cryptochrome-1 OS=Homo sapiens OX=9606 GN=CRY1 PE=1 SV=1
Q8WP19	Cryptochrome-1 OS=Macaca fascicularis OX=9541 GN=CRY1 PE=2 SV=1
Q32Q86	Cryptochrome-1 OS=Rattus norvegicus OX=10116 GN=Cry1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001198 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03441 all species →	FAD_binding_7	FAD binding domain of DNA photolyase	Domain	Interproscan
PF00875 all species →	DNA_photolyase	DNA photolyase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036155 all species →	Homologous_superfamily	Cryptochrome/photolyase, N-terminal domain superfamily	Interproscan
IPR005101 all species →	Domain	Cryptochrome/DNA photolyase, FAD-binding domain	Interproscan
IPR006050 all species →	Domain	DNA photolyase, N-terminal	Interproscan
IPR014729 all species →	Homologous_superfamily	Rossmann-like alpha/beta/alpha sandwich fold	Interproscan
IPR036134 all species →	Homologous_superfamily	Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily	Interproscan
IPR002081 all species →	Family	Cryptochrome/DNA photolyase class 1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11455 all species →	CRYPTOCHROME	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003904 all species →	Molecular Function	deoxyribodipyrimidine photo-lyase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0032922 all species →	Biological Process	circadian regulation of gene expression	Interproscan
GO:0043153 all species →	Biological Process	entrainment of circadian clock by photoperiod	Interproscan
GO:0071949 all species →	Molecular Function	FAD binding	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K02295	CRY; cryptochrome	-	Circadian rhythm	ko04710	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_005834-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

105TPM > 0

7Conditions

12.6Max TPM

1.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	1.08	2.56
polyp at pH7 6	18	16	1.28	3.89
coral polyp · control treatment	16	16	2.10	7.90
coral polyp · oil and dispersant treatment	16	16	1.84	12.63
coral polyp · oil treatment	16	15	1.33	2.69
coral polyp · dispersant treatment	16	15	1.20	2.70
Polyp	10	10	1.89	3.11

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	-	2.56
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.67
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.46
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.43
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.35
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.31
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.24
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.21
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.11
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.02
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.95
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.88
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.71
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.67
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.65
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.61
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.53
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.89
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.19
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.91
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.90
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.77
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.70
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.62
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.43
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.42
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.05
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.90
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.87
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.68
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.56
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.55
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.54
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.90
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.52
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.66
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.44
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.44
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.11
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.09
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.86
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.81
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.57
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.29
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.14
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.90
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.90
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.75
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.20
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.63
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.39
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.89
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.79
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.61
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.47
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.34
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.15
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.12
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.06
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.91
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.74
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.53
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.32
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.28
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.21
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.69
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.58
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.53
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.41
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.24
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.75
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.64
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.35
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.00
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.98
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.69
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.69
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.33
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.28
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.08
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.70
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.58
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.22
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.09
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.82
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.48
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.46
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.43
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.80
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.62
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.62
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.62
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.30
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.24
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.16
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.11
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.06
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.06
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.50
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.97
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.64
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.34
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.05
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.74
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.40

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.