Gene detail

Detailed information of OS493_002850-T1 in Lophelia pertusa

Genomic Location: scaffold_6:1088712...1089329
NR annotation: KAJ7340124.1, Proteasome subunit beta type-3 [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
O73817	Proteasome subunit beta type-3 OS=Oncorhynchus mykiss OX=8022 GN=psmb3 PE=2 SV=1
P49720	Proteasome subunit beta type-3 OS=Homo sapiens OX=9606 GN=PSMB3 PE=1 SV=2
Q9R1P1	Proteasome subunit beta type-3 OS=Mus musculus OX=10090 GN=Psmb3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009279 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00227 all species →	Proteasome	Proteasome subunit	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR023333 all species →	Family	Proteasome B-type subunit	Interproscan
IPR033811 all species →	Family	Proteasome beta 3 subunit	Interproscan
IPR016050 all species →	Conserved_site	Proteasome beta-type subunit, conserved site	Interproscan
IPR001353 all species →	Family	Proteasome, subunit alpha/beta	Interproscan
IPR029055 all species →	Homologous_superfamily	Nucleophile aminohydrolases, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR32194 all species →	METALLOPROTEASE TLDD	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0019774 all species →	Cellular Component	proteasome core complex, beta-subunit complex	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	Interproscan
GO:0005839 all species →	Cellular Component	proteasome core complex	Interproscan
GO:0051603 all species →	Biological Process	proteolysis involved in protein catabolic process	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
K02735	PSMB3; 20S proteasome subunit beta 3	EC:3.4.25.1	Proteasome	ko03051	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_002850-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

206.5Max TPM

82.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	54.78	105.23
polyp at pH7 6	18	18	65.55	92.49
coral polyp · control treatment	16	16	93.97	133.88
coral polyp · oil and dispersant treatment	16	16	152.63	206.54
coral polyp · oil treatment	16	16	80.25	115.60
coral polyp · dispersant treatment	16	16	73.20	168.98
Polyp	10	10	46.49	106.66

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	-	105.23
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	98.72
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.59
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.38
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.40
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.65
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.53
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.49
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.55
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.36
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.26
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.00
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.44
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.10
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.21
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.04
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.68
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.37
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	92.49
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	85.42
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	80.34
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	74.77
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	74.54
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	71.88
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	71.47
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.80
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	69.15
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.95
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.75
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.21
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.40
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.51
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.89
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.75
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.00
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.55
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	133.88
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	121.57
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	112.46
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	111.10
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	109.23
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.64
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	98.85
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	97.03
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	91.64
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	90.09
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.83
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.69
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	79.90
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	71.29
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.68
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.62
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	206.54
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	206.22
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	201.24
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	187.80
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	178.60
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	174.39
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	168.95
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	154.36
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	151.53
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	141.00
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	139.57
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	122.86
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	115.32
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	98.99
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	97.96
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	96.81
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	115.60
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	112.34
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	111.33
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	109.14
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	97.19
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	92.80
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	90.21
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	78.92
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	78.36
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.01
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	69.84
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	69.76
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.67
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.75
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.19
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.83
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	168.98
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	116.12
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	110.16
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	105.50
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	91.20
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.41
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.12
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	68.75
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.24
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.35
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.41
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.88
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.67
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.13
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.44
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.91
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	106.66
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	66.92
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	53.87
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	52.07
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	50.43
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	48.79
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	28.66
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	27.29
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	21.92
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	8.27

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.