Gene detail

Detailed information of OS493_003478-T1 in Lophelia pertusa

Genomic Location: scaffold_7:2044967...2052825
NR annotation: KAJ7393812.1, 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
Q80V94	AP-4 complex subunit epsilon-1 OS=Mus musculus OX=10090 GN=Ap4e1 PE=1 SV=3
Q9UPM8	AP-4 complex subunit epsilon-1 OS=Homo sapiens OX=9606 GN=AP4E1 PE=1 SV=2
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

Pfam accession	Pfam name	Description	Type	Source
PF01602 all species →	Adaptin_N	Adaptin N terminal region	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR050840 all species →	Family	Adaptor Complexes Large Subunit	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR002553 all species →	Domain	Clathrin/coatomer adaptor, adaptin-like, N-terminal	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
GO:0006886 all species →	Biological Process	intracellular protein transport	Interproscan
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0030117 all species →	Cellular Component	membrane coat	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_003478-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_003478-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

22.3Max TPM

8.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.97	11.12
polyp at pH7 6	18	18	7.53	13.30
coral polyp · control treatment	16	16	11.17	22.26
coral polyp · oil and dispersant treatment	16	16	9.25	12.25
coral polyp · oil treatment	16	16	9.32	12.68
coral polyp · dispersant treatment	16	16	10.82	17.94
Polyp	10	10	4.91	9.57

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.12
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.93
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.87
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.01
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.67
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.97
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.83
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.79
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.70
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.66
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.49
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.05
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.38
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.23
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.90
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.32
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.64
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.96
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.30
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.43
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.04
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.80
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.47
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.35
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.12
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.58
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.51
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.39
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.99
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.81
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.62
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.28
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.19
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.24
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.23
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.20
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.26
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.83
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.47
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.45
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.94
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.52
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.40
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.97
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.84
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.99
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.69
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.25
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.26
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.73
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.32
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.81
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.25
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.11
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.79
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.62
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.35
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.09
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.58
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.35
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.06
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.72
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.29
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.07
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.86
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.81
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.92
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.06
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.68
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.31
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.30
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.50
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.54
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.30
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.00
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.86
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.65
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.27
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.36
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.20
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.14
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.95
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.62
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.46
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.94
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.60
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.69
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.37
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.35
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.55
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.58
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.89
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.35
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.52
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.31
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.94
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.79
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.37
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.49
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.31
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.57
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	7.25
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	6.08
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.46
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.17
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.75
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.72
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.46
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.34
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.34

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.