Gene detail

Detailed information of OS493_001701-T1 in Lophelia pertusa

Genomic Location: scaffold_4:209697...216420
NR annotation: KAJ7374975.1, Proteasome subunit beta type-2 [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
P49721	Proteasome subunit beta type-2 OS=Homo sapiens OX=9606 GN=PSMB2 PE=1 SV=1
Q9R1P3	Proteasome subunit beta type-2 OS=Mus musculus OX=10090 GN=Psmb2 PE=1 SV=1
P40307	Proteasome subunit beta type-2 OS=Rattus norvegicus OX=10116 GN=Psmb2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007962 (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
IPR050115 all species →	Family	Proteasome subunit alpha	Interproscan
IPR029055 all species →	Homologous_superfamily	Nucleophile aminohydrolases, N-terminal	Interproscan
IPR035206 all species →	Family	Proteasome subunit beta 2	Interproscan
IPR001353 all species →	Family	Proteasome, subunit alpha/beta	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11599 all species →	PROTEASOME SUBUNIT ALPHA/BETA	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0010498 all species →	Biological Process	proteasomal protein catabolic process	Interproscan
GO:0019774 all species →	Cellular Component	proteasome core complex, beta-subunit complex	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
K02734	PSMB2; 20S proteasome subunit beta 4	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_001701-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

223.6Max TPM

97.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	71.47	109.71
polyp at pH7 6	18	18	75.81	103.26
coral polyp · control treatment	16	16	99.28	131.87
coral polyp · oil and dispersant treatment	16	16	147.18	218.55
coral polyp · oil treatment	16	16	90.43	135.68
coral polyp · dispersant treatment	16	16	81.89	173.62
Polyp	10	10	140.46	223.61

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	-	109.71
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	102.38
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	94.28
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	86.70
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	84.36
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	78.82
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	78.22
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	78.08
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	69.77
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	68.41
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.82
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.36
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.77
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.67
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.45
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.10
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.96
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.59
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	103.26
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	97.50
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	96.61
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	93.96
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	92.52
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	92.10
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	90.83
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	88.93
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	77.94
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	76.42
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	72.23
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.17
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.97
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.63
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.91
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.35
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.98
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.28
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	131.87
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	131.28
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	124.66
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	124.34
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	108.88
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	108.75
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	105.02
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	103.51
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.66
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	99.61
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	90.11
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	84.82
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	75.70
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	71.88
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.98
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.36
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	218.55
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	202.73
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	193.24
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	189.53
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	166.01
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	163.33
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	147.22
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	142.30
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	128.10
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	125.10
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	119.49
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	117.41
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	116.80
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	112.95
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	110.45
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	101.65
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	135.68
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	119.07
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	106.39
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	102.11
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	98.39
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	93.37
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	92.30
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	87.15
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.02
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	82.66
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	82.60
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	82.39
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	81.02
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	75.63
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	67.13
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.03
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	173.62
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	120.31
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	117.22
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	96.31
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	91.77
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	89.06
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	84.16
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	83.97
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	77.79
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.08
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.61
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.38
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.62
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.39
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.63
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.30
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	223.61
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	216.19
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	200.30
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	193.80
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	125.61
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	119.40
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	98.68
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	92.72
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	74.04
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	60.26

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.