Gene detail

Detailed information of OS493_001415-T1 in Lophelia pertusa

Genomic Location: scaffold_3:1019779...1025513
NR annotation: KAJ7381294.1, 26S proteasome complex subunit SEM1 [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
Q3ZBR6	26S proteasome complex subunit SEM1 OS=Bos taurus OX=9913 GN=SEM1 PE=3 SV=1
P60896	26S proteasome complex subunit SEM1 OS=Homo sapiens OX=9606 GN=SEM1 PE=1 SV=1
P60897	26S proteasome complex subunit SEM1 OS=Mus musculus OX=10090 GN=Sem1 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0010383 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05160 all species →	DSS1_SEM1	DSS1/SEM1 family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007834 all species →	Family	DSS1/SEM1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR16771 all species →	26 PROTEASOME COMPLEX SUBUNIT DSS1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006406 all species →	Biological Process	mRNA export from nucleus	Interproscan
GO:0008541 all species →	Cellular Component	proteasome regulatory particle, lid subcomplex	Interproscan
GO:0043248 all species →	Biological Process	proteasome assembly	Interproscan
GO:0000502 all species →	Cellular Component	proteasome complex	Interproscan
GO:0000724 all species →	Biological Process	double-strand break repair via homologous recombination	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
K10881	SHFM1, DSS1, RPN15; 26 proteasome complex subunit DSS1	-	DNA repair and recombination proteins	ko03400	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_001415-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

1,136.6Max TPM

180.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	246.32	327.70
polyp at pH7 6	18	18	312.08	767.72
coral polyp · control treatment	16	16	73.90	149.33
coral polyp · oil and dispersant treatment	16	16	111.67	218.73
coral polyp · oil treatment	16	16	75.11	107.27
coral polyp · dispersant treatment	16	16	67.27	208.47
Polyp	10	10	452.31	1,136.64

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	327.70
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	320.93
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	317.27
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	311.50
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	288.60
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	286.06
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	285.11
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	261.77
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	241.94
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	239.47
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	238.37
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	235.96
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	232.32
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	221.73
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	186.77
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	182.66
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	131.73
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	123.91
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	767.72
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	731.60
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	476.34
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	424.51
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	295.15
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	284.32
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	261.64
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	259.71
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	256.12
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	246.47
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	245.38
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	237.18
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	196.07
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	195.89
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	192.81
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	190.09
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	188.14
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	168.23
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	149.33
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	144.99
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	102.19
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.10
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.92
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	68.42
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.06
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.62
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.13
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.01
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.57
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.55
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.29
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.19
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.44
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.55
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	218.73
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	156.73
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	143.39
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	141.70
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	118.60
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	112.18
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	109.70
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	108.70
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	102.96
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.31
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	91.34
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.75
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	83.94
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.76
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.47
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.49
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	107.27
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	102.72
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	91.89
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	91.58
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	88.48
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	82.64
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	78.83
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.66
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.22
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.02
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.99
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.87
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	60.26
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.38
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.15
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.82
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	208.47
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	154.43
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	84.83
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	78.48
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.87
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.46
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.64
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.97
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.60
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.49
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.37
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.62
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.82
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.01
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.38
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.85
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1,136.64
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	939.13
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	531.53
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	494.83
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	381.89
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	276.93
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	239.15
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	193.17
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	190.55
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	139.33

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.