Gene detail

Detailed information of OS493_022619-T1 in Lophelia pertusa

Genomic Location: scaffold_95:137749...145184
NR annotation: KAJ7357809.1, hypothetical protein OS493_022619 [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
Q32PI6	Large ribosomal subunit protein uL4m OS=Bos taurus OX=9913 GN=MRPL4 PE=1 SV=1
Q9BYD3	Large ribosomal subunit protein uL4m OS=Homo sapiens OX=9606 GN=MRPL4 PE=1 SV=1
Q503X2	Large ribosomal subunit protein uL4m OS=Danio rerio OX=7955 GN=mrpl4 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004676 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00573 all species →	Ribosomal_L4	Ribosomal protein L4/L1 family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR023574 all species →	Homologous_superfamily	Large ribosomal subunit protein uL4 domain superfamily	Interproscan
IPR002136 all species →	Family	Large ribosomal subunit protein uL4	Interproscan
IPR013005 all species →	Family	Large ribosomal subunit protein uL4-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10746 all species →	50S RIBOSOMAL PROTEIN L4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003735 all species →	Molecular Function	structural constituent of ribosome	Interproscan
GO:0005840 all species →	Cellular Component	ribosome	Interproscan
GO:0006412 all species →	Biological Process	translation	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_022619-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_022619-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

107TPM > 0

7Conditions

43.4Max TPM

9.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	10.59	24.23
polyp at pH7 6	18	16	13.81	28.09
coral polyp · control treatment	16	16	7.20	17.34
coral polyp · oil and dispersant treatment	16	16	5.33	26.65
coral polyp · oil treatment	16	16	6.48	12.95
coral polyp · dispersant treatment	16	16	4.57	11.31
Polyp	10	10	24.18	43.43

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	-	24.23
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.61
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.67
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.95
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.09
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.00
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.88
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.88
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.29
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.82
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.17
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.51
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.50
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.28
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.29
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.06
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.45
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.09
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.11
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.21
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.25
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.43
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.88
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.66
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.25
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.84
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.59
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.56
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.67
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.82
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.62
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.24
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.33
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.34
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.79
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.30
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.12
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.39
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.70
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.03
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.87
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.78
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.63
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.31
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.29
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.19
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.94
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.02
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.50
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.65
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.11
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.83
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.00
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.63
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.91
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.84
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.42
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.19
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.89
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.87
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.82
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.79
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.70
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.64
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.96
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.95
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.67
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.40
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.93
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.06
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.92
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.75
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.67
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.57
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.55
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.54
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.31
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.10
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.10
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.66
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.48
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.31
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.11
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.55
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.23
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.79
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.19
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.77
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.68
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.52
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.36
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.22
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.78
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.44
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.12
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.01
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.97
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	43.43
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	40.89
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	38.05
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	31.68
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	18.97
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	17.66
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	15.65
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	13.26
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	12.06
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.17

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.