Gene detail

Detailed information of OS493_003266-T1 in Lophelia pertusa

Genomic Location: scaffold_6:7088331...7108995
NR annotation: KAJ7340514.1, U3 snoRNP protein [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
Q8VCY6	U3 small nucleolar RNA-associated protein 6 homolog OS=Mus musculus OX=10090 GN=Utp6 PE=2 SV=1
Q9NYH9	U3 small nucleolar RNA-associated protein 6 homolog OS=Homo sapiens OX=9606 GN=UTP6 PE=1 SV=2
Q54WN5	U3 small nucleolar RNA-associated protein 6 homolog OS=Dictyostelium discoideum OX=44689 GN=utp6 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006535 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08640 all species →	U3_assoc_6	U3 small nucleolar RNA-associated protein 6	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR013949 all species →	Family	U3 small nucleolar RNA-associated protein 6	Interproscan
IPR003107 all species →	Repeat	HAT (Half-A-TPR) repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23271 all species →	HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN 66	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000462 all species →	Biological Process	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	Interproscan
GO:0030515 all species →	Molecular Function	snoRNA binding	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0032040 all species →	Cellular Component	small-subunit processome	Interproscan
GO:0034388 all species →	Cellular Component	Pwp2p-containing subcomplex of 90S preribosome	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
K14557	UTP6; U3 small nucleolar RNA-associated protein 6	-	Ribosome biogenesis	ko03009	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_003266-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

35.4Max TPM

9.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.90	11.88
polyp at pH7 6	18	18	10.30	14.38
coral polyp · control treatment	16	16	12.05	35.38
coral polyp · oil and dispersant treatment	16	16	8.75	35.27
coral polyp · oil treatment	16	16	8.63	17.38
coral polyp · dispersant treatment	16	16	7.50	16.80
Polyp	10	10	8.51	14.58

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.88
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.33
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.25
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.70
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.60
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.04
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.04
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.82
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.47
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.77
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.12
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.96
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.93
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.48
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.13
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.78
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.31
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.50
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.38
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.43
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.10
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.48
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.17
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.82
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.19
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.11
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.87
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.44
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.23
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.76
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.58
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.86
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.86
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.76
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.49
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.96
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.38
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.70
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.86
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.10
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.68
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.61
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.97
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.43
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.53
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.14
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.71
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.59
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.48
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.55
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.23
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.83
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.27
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.64
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.07
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.05
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.18
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.09
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.68
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.61
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.25
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.95
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.30
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.90
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.32
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.36
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.27
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.08
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.38
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.32
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.65
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.37
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.01
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.91
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.44
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.76
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.49
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.98
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.72
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.54
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.19
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.79
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.82
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.77
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.80
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.84
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.34
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.72
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.11
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.80
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.25
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.61
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.59
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.82
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.79
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.31
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.73
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.73
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.35
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.25
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	14.58
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	12.09
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.27
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.00
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	10.51
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.53
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.17
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.56
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.99
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.38

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.