Gene detail

Detailed information of OS493_024797-T1 in Lophelia pertusa

Genomic Location: scaffold_117:862670...864397
NR annotation: KAJ7378132.1, DNA repair protein Rad9,Rhp9 [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
P10040	Protein crumbs OS=Drosophila melanogaster OX=7227 GN=crb PE=1 SV=3
Q80YA8	Protein crumbs homolog 2 OS=Mus musculus OX=10090 GN=Crb2 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003182 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12661 all species →	hEGF	Human growth factor-like EGF	Domain	Interproscan
PF07645 all species →	EGF_CA	Calcium-binding EGF domain	Domain	Interproscan
PF00008 all species →	EGF	EGF-like domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000742 all species →	Domain	EGF-like domain	Interproscan
IPR000152 all species →	PTM	EGF-type aspartate/asparagine hydroxylation site	Interproscan
IPR013032 all species →	Conserved_site	EGF-like, conserved site	Interproscan
IPR051355 all species →	Family	Notch and Slit guidance protein	Interproscan
IPR049883 all species →	Domain	NOTCH1 EGF-like calcium-binding domain	Interproscan
IPR018097 all species →	Conserved_site	EGF-like calcium-binding, conserved site	Interproscan
IPR001881 all species →	Domain	EGF-like calcium-binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45836 all species →	SLIT HOMOLOG	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0007219 all species →	Biological Process	Notch signaling pathway	Interproscan
GO:0007411 all species →	Biological Process	axon guidance	Interproscan
GO:0009986 all species →	Cellular Component	cell surface	Interproscan
GO:0043235 all species →	Cellular Component	receptor complex	Interproscan
GO:0005509 all species →	Molecular Function	calcium ion 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

No KEGG orthology assignment for OS493_024797-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_024797-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

40.2Max TPM

10.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	6.65	13.73
polyp at pH7 6	18	18	6.93	13.36
coral polyp · control treatment	16	16	13.28	31.20
coral polyp · oil and dispersant treatment	16	16	16.13	27.78
coral polyp · oil treatment	16	16	11.17	22.67
coral polyp · dispersant treatment	16	16	12.35	40.15
Polyp	10	10	3.58	6.31

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	-	13.73
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.33
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.78
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.86
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.16
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.60
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.49
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.28
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.09
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.89
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.71
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.52
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.25
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.44
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.38
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.14
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.09
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.36
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.54
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.76
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.65
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.18
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.65
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.61
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.35
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.79
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.79
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.75
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.72
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.49
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.47
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.31
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.27
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.07
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.96
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.20
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.11
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.09
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.62
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.87
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.63
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.41
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.00
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.67
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.56
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.68
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.43
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.66
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.23
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.30
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.06
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.78
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.68
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.84
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.60
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.53
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.38
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.93
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.36
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.24
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.56
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.67
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.43
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.18
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.91
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.28
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.62
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.67
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.60
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.61
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.28
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.63
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.99
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.81
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.63
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.03
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.02
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.55
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.80
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.64
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.43
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.80
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.26
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.15
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.05
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.54
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.11
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.24
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.07
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.65
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.07
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.11
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.71
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.82
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.46
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.85
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.71
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.14
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.95
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.31
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.98
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.79
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.27
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.24
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.38
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.28
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.29
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.45
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.78

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.