Gene detail

Detailed information of OS493_017446-T1 in Lophelia pertusa

Genomic Location: scaffold_56:229364...233472
NR annotation: KAJ7385081.1, Sequestosome-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
O08623	Sequestosome-1 OS=Rattus norvegicus OX=10116 GN=Sqstm1 PE=1 SV=1
Q64337	Sequestosome-1 OS=Mus musculus OX=10090 GN=Sqstm1 PE=1 SV=1
Q13501	Sequestosome-1 OS=Homo sapiens OX=9606 GN=SQSTM1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003508 (this species only)
Ubiquitin family	ULD\|UFD\|PB1 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF16577 all species →	UBA_5	UBA domain	Domain	Interproscan
PF00569 all species →	ZZ	Zinc finger, ZZ type	Domain	Interproscan
PF00564 all species →	PB1	PB1 domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000433 all species →	Domain	Zinc finger, ZZ-type	Interproscan
IPR052260 all species →	Family	Autophagy Receptor and Signaling Regulator	Interproscan
IPR033741 all species →	Domain	Sequestosome-1, UBA domain	Interproscan
IPR034866 all species →	Domain	Sequestosome-1, PB1 domain	Interproscan
IPR000270 all species →	Domain	PB1 domain	Interproscan
IPR009060 all species →	Homologous_superfamily	UBA-like superfamily	Interproscan
IPR043145 all species →	Homologous_superfamily	Zinc finger, ZZ-type superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15090 all species →	SEQUESTOSOME 1-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0000423 all species →	Biological Process	mitophagy	Interproscan
GO:0005080 all species →	Molecular Function	protein kinase C binding	Interproscan
GO:0007032 all species →	Biological Process	endosome organization	Interproscan
GO:0016235 all species →	Cellular Component	aggresome	Interproscan
GO:0035973 all species →	Biological Process	aggrephagy	Interproscan
GO:0044753 all species →	Cellular Component	amphisome	Interproscan
GO:0070530 all species →	Molecular Function	K63-linked polyubiquitin modification-dependent protein binding	Interproscan
GO:0005515 all species →	Molecular Function	protein 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K14381	SQSTM1; sequestosome 1	-	Exosome	ko04147	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_017446-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

4,175.9Max TPM

695.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	272.52	395.38
polyp at pH7 6	18	18	312.75	419.08
coral polyp · control treatment	16	16	556.25	1,254.82
coral polyp · oil and dispersant treatment	16	16	1,885.16	4,175.93
coral polyp · oil treatment	16	16	580.05	1,246.50
coral polyp · dispersant treatment	16	16	953.58	3,460.43
Polyp	10	10	233.69	348.71

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	395.38
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	394.34
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	311.43
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	307.41
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	305.58
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	302.78
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	301.03
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	282.73
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	267.59
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	267.42
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	257.77
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	245.29
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	219.49
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	215.55
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	212.40
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	210.01
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	204.98
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	204.11
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	419.08
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	416.67
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	414.96
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	414.56
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	358.70
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	357.99
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	335.62
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	333.39
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	307.79
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	305.51
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	263.45
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	259.14
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	256.38
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	240.31
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	239.12
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	237.79
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	235.42
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	233.65
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,254.82
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,106.52
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	735.39
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	643.01
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	627.15
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	517.12
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	514.47
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	497.80
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	477.36
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	476.29
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	451.40
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	415.06
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	329.89
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	308.74
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	289.06
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	255.90
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4,175.93
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,277.14
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,741.43
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,381.41
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,302.41
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,066.54
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,009.65
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,877.99
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,819.11
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,424.95
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,377.86
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,242.16
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,158.49
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,117.00
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	755.12
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	435.42
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,246.50
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,121.95
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	900.45
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	896.69
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	896.34
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	749.49
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	441.70
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	433.34
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	427.90
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	382.08
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	363.14
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	314.55
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	309.24
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	292.66
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	271.51
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	233.18
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3,460.43
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,572.04
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,467.10
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,165.66
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,005.16
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	933.15
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	909.98
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	853.42
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	847.52
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	797.14
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	562.73
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	403.25
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	396.72
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	364.67
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	328.70
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	189.64
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	348.71
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	298.76
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	288.38
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	273.15
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	266.16
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	247.04
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	192.28
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	191.04
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	166.87
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	64.54

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.