Gene detail

Detailed information of OS493_003600-T1 in Lophelia pertusa

Genomic Location: scaffold_7:3543731...3550280
NR annotation: KAJ7393931.1, AP-3 complex subunit sigma-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
Q2YDH6	AP-3 complex subunit sigma-1 OS=Bos taurus OX=9913 GN=AP3S1 PE=2 SV=1
Q92572	AP-3 complex subunit sigma-1 OS=Homo sapiens OX=9606 GN=AP3S1 PE=1 SV=1
Q9DCR2	AP-3 complex subunit sigma-1 OS=Mus musculus OX=10090 GN=Ap3s1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009295 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01217 all species →	Clat_adaptor_s	Clathrin adaptor complex small chain	Domain	Interproscan
PF09032 all species →	Siah-Interact_N	Siah interacting protein, N terminal	Domain	Interproscan
PF05002 all species →	SGS	SGS domain	Domain	Interproscan
PF04969 all species →	CS	CS domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR052289 all species →	Family	Calcyclin-binding ubiquitin ligase bridge	Interproscan
IPR007699 all species →	Domain	SGS domain	Interproscan
IPR022775 all species →	Domain	AP complex, mu/sigma subunit	Interproscan
IPR015120 all species →	Domain	Siah interacting protein, N-terminal	Interproscan
IPR008978 all species →	Homologous_superfamily	HSP20-like chaperone	Interproscan
IPR000804 all species →	Conserved_site	Clathrin adaptor complex, small chain	Interproscan
IPR037893 all species →	Domain	Calcyclin-binding Protein, CS domain	Interproscan
IPR007052 all species →	Domain	CS domain	Interproscan
IPR027155 all species →	Family	AP-3 complex subunit sigma	Interproscan
IPR011012 all species →	Homologous_superfamily	Longin-like domain superfamily	Interproscan
IPR037201 all species →	Homologous_superfamily	Calcyclin-binding protein, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13164 all species →	CALICYLIN BINDING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	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
GO:0015631 all species →	Molecular Function	tubulin binding	Interproscan
GO:0031625 all species →	Molecular Function	ubiquitin protein ligase binding	Interproscan
GO:0044548 all species →	Molecular Function	S100 protein binding	Interproscan
GO:0006896 all species →	Biological Process	Golgi to vacuole transport	Interproscan
GO:0030123 all species →	Cellular Component	AP-3 adaptor complex	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_003600-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_003600-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

109TPM > 0

7Conditions

42.4Max TPM

19.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	14.69	30.98
polyp at pH7 6	18	18	17.13	21.83
coral polyp · control treatment	16	16	24.88	39.81
coral polyp · oil and dispersant treatment	16	16	27.93	42.41
coral polyp · oil treatment	16	16	19.82	31.89
coral polyp · dispersant treatment	16	16	15.49	24.43
Polyp	10	9	12.46	26.01

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.98
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.70
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.42
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.21
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.93
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.86
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.02
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.93
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.33
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.79
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.17
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.14
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.08
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.06
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.98
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.99
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.75
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.13
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.83
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.44
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.35
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.95
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.58
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.54
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.33
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.86
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.58
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.32
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.83
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.07
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.35
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.14
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.17
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.11
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.16
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.80
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.81
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.34
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.16
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.46
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.52
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.20
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.70
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.64
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.83
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.80
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.51
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.05
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.88
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.69
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.30
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.23
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.41
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.35
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.82
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.11
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.45
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.57
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.64
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.48
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.65
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.13
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.18
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.01
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.91
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.13
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.36
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.70
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.89
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.76
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.31
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.82
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.20
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.16
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.75
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.92
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.92
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.91
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.15
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.71
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.03
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.96
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.33
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.33
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.43
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.43
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.09
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.58
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.01
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.11
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.99
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.30
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.16
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.75
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.68
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.64
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.62
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.98
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.33
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.75
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	26.01
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	19.21
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	16.50
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	15.75
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	10.57
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.41
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	9.60
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.01
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.56
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.