Gene detail

Detailed information of OS493_000054-T1 in Lophelia pertusa

Genomic Location: scaffold_1:578358...582286
NR annotation: KAJ7394252.1, adherens junction organization [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
P55196	Afadin OS=Homo sapiens OX=9606 GN=AFDN PE=1 SV=3
Q9QZQ1	Afadin OS=Mus musculus OX=10090 GN=Afdn PE=1 SV=3
O35889	Afadin OS=Rattus norvegicus OX=10116 GN=Afdn PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004405 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00498 all species →	FHA	FHA domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR008984 all species →	Homologous_superfamily	SMAD/FHA domain superfamily	Interproscan
IPR028842 all species →	Family	Afadin	Interproscan
IPR000253 all species →	Domain	Forkhead-associated (FHA) domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10398 all species →	AFADIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005911 all species →	Cellular Component	cell-cell junction	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_000054-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_000054-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

67.9Max TPM

20.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	16.96	31.10
polyp at pH7 6	18	18	15.49	24.82
coral polyp · control treatment	16	16	22.61	42.67
coral polyp · oil and dispersant treatment	16	16	24.93	45.84
coral polyp · oil treatment	16	16	21.47	44.52
coral polyp · dispersant treatment	16	16	34.25	67.86
Polyp	10	10	5.20	10.61

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.10
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.70
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.59
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.78
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.10
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.06
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.61
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.24
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.09
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.02
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.65
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.85
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.16
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.95
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.88
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.61
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.59
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.27
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.82
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.54
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.45
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.26
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.22
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.00
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.96
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.06
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.52
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.29
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.69
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.58
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.55
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.28
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.08
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.68
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.58
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.17
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.67
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.20
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.89
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.97
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.62
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.60
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.28
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.97
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.75
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.74
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.09
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.10
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.33
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.12
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.63
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.79
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.84
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.59
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.50
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.85
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.17
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.53
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.50
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.15
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.23
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.59
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.41
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.41
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.41
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.95
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.67
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.07
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.52
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.37
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.32
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.90
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.16
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.92
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.72
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.13
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.03
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.90
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.88
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.12
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.10
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.21
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.25
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.97
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.86
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.69
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.46
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.31
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.85
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.64
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.99
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.89
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.81
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.36
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.54
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.41
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.35
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.72
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.31
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.75
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	10.61
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.19
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.13
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.98
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.66
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.15
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.07
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.91
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.72
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.54

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.