Gene detail

Detailed information of OS493_007884-T1 in Lophelia pertusa

Genomic Location: scaffold_18:213939...220408
NR annotation: KAJ7337731.1, Ribosomal biogenesis protein las1l [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
Q9Y4W2	Ribosomal biogenesis protein LAS1L OS=Homo sapiens OX=9606 GN=LAS1L PE=1 SV=2
A2BE28	Ribosomal biogenesis protein LAS1L OS=Mus musculus OX=10090 GN=Las1l PE=1 SV=1
P36146	Protein LAS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=LAS1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008266 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04031 all species →	Las1	Las1-like	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007174 all species →	Family	Las1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15002 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004519 all species →	Molecular Function	endonuclease activity	Interproscan
GO:0006364 all species →	Biological Process	rRNA processing	Interproscan
GO:0090730 all species →	Cellular Component	Las1 complex	Interproscan
GO:0000460 all species →	Biological Process	maturation of 5.8S rRNA	Interproscan
GO:0000470 all species →	Biological Process	maturation of LSU-rRNA	Interproscan
GO:0030687 all species →	Cellular Component	preribosome, large subunit precursor	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_007884-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_007884-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

109TPM > 0

7Conditions

19.9Max TPM

5.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	5.81	9.39
polyp at pH7 6	18	18	7.53	13.57
coral polyp · control treatment	16	16	6.43	14.41
coral polyp · oil and dispersant treatment	16	16	5.48	19.92
coral polyp · oil treatment	16	16	4.91	8.84
coral polyp · dispersant treatment	16	16	4.47	11.06
Polyp	10	9	6.12	12.52

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.39
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.74
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.27
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.76
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.70
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.01
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.96
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.74
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.64
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.46
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.36
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.00
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.87
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.74
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.46
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.19
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.83
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.51
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.57
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.40
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.15
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.10
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.09
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.80
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.24
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.15
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.04
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.58
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.34
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.17
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.15
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.81
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.80
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.65
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.59
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.41
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.71
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.35
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.15
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.72
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.56
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.73
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.63
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.46
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.40
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.10
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.63
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.92
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.67
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.46
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.02
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.92
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.44
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.44
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.21
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.01
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.07
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.04
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.27
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.04
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.91
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.85
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.72
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.19
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.11
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.03
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.44
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.84
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.73
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.65
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.46
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.10
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.30
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.66
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.50
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.26
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.14
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.05
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.97
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.87
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.70
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.22
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.10
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.06
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.30
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.42
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.19
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.18
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.93
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.86
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.65
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.41
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.38
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.15
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.02
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.69
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.26
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.08
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	12.52
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.48
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	8.52
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.48
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	7.02
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.98
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.42
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.82
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.