Gene detail

Detailed information of OS493_003477-T1 in Lophelia pertusa

Genomic Location: scaffold_7:2032461...2044639
NR annotation: KAJ7393811.1, AP-4 complex subunit epsilon-1 [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
Q9UPM8	AP-4 complex subunit epsilon-1 OS=Homo sapiens OX=9606 GN=AP4E1 PE=1 SV=2
Q80V94	AP-4 complex subunit epsilon-1 OS=Mus musculus OX=10090 GN=Ap4e1 PE=1 SV=3
Q8L7A9	AP-4 complex subunit epsilon OS=Arabidopsis thaliana OX=3702 GN=At1g31730 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002707 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_003477-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR050840 all species →	Family	Adaptor Complexes Large Subunit	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22780 all species →	ADAPTIN, ALPHA/GAMMA/EPSILON	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0030124 all species →	Cellular Component	AP-4 adaptor complex	Interproscan
GO:0140312 all species →	Molecular Function	cargo adaptor 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_003477-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_003477-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

35.3Max TPM

14.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	14.60	21.25
polyp at pH7 6	18	18	14.47	21.60
coral polyp · control treatment	16	16	17.40	35.28
coral polyp · oil and dispersant treatment	16	16	14.19	23.13
coral polyp · oil treatment	16	16	15.01	19.04
coral polyp · dispersant treatment	16	16	11.07	16.46
Polyp	10	10	13.22	20.29

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	-	21.25
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.19
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.60
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.11
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.04
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.96
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.26
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.25
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.21
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.66
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.59
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.40
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.64
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.35
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.79
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.29
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.78
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.34
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.60
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.61
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.91
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.85
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.08
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.64
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.42
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.64
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.86
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.31
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.94
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.85
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.75
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.28
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.11
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.06
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.84
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.75
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.28
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.17
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.44
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.30
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.52
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.76
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.42
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.23
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.14
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.87
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.27
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.03
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.25
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.09
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.34
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.25
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.13
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.69
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.96
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.35
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.07
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.40
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.88
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.05
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.91
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.26
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.16
SRR16705979	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	10.92
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.84
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.24
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.50
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.04
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.66
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.41
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.10
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.97
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.91
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.14
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.64
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.09
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.66
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.61
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.44
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.43
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.95
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.28
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.90
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.46
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.15
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.55
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.31
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.92
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.44
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.56
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.13
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.40
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.57
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.34
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.77
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.00
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.04
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.83
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.62
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	20.29
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	20.19
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	19.89
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	18.38
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	13.03
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.23
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	8.45
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.91
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.24
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.63

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.