Gene detail

Detailed information of OS493_013704-T1 in Lophelia pertusa

Genomic Location: scaffold_38:313800...314156
NR annotation: KAJ7385676.1, LSM domain [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
Q8QZX5	U7 snRNA-associated Sm-like protein LSm10 OS=Mus musculus OX=10090 GN=Lsm10 PE=1 SV=1
Q969L4	U7 snRNA-associated Sm-like protein LSm10 OS=Homo sapiens OX=9606 GN=LSM10 PE=1 SV=1
Q54F84	Putative uncharacterized protein DDB_G0291015 OS=Dictyostelium discoideum OX=44689 GN=DDB_G0291015 PE=4 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0010077 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01423 all species →	LSM	LSM domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR052840 all species →	Family	U7 snRNA-associated Sm-like	Interproscan
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan
IPR047575 all species →	Domain	Sm domain	Interproscan
IPR001163 all species →	Domain	Sm domain, eukaryotic/archaea-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21196 all species →	U7 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM10	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006398 all species →	Biological Process	mRNA 3'-end processing by stem-loop binding and cleavage	Interproscan
GO:0016604 all species →	Cellular Component	nuclear body	Interproscan
GO:0071208 all species →	Molecular Function	histone pre-mRNA DCP binding	Interproscan
GO:0071209 all species →	Molecular Function	U7 snRNA binding	Interproscan
GO:0071254 all species →	Cellular Component	cytoplasmic U snRNP body	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	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
K25591	LSM10; U7 snRNA-associated Sm-like protein LSm10	-	Messenger RNA biogenesis	ko03019	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_013704-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

56.4Max TPM

7.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	6.85	9.76
polyp at pH7 6	18	18	7.09	10.17
coral polyp · control treatment	16	16	10.17	28.93
coral polyp · oil and dispersant treatment	16	16	8.24	56.38
coral polyp · oil treatment	16	16	8.68	15.34
coral polyp · dispersant treatment	16	16	4.14	10.81
Polyp	10	10	6.48	14.72

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.76
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.66
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.54
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.99
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.98
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.70
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.07
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.63
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.60
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.30
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.29
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.18
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.15
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.13
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.03
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.41
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.02
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.79
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.17
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.05
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.49
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.13
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.81
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.77
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.78
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.23
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.05
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.04
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.62
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.16
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.01
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.48
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.12
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.85
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.81
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.10
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.93
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.77
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.39
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.28
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.99
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.27
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.14
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.05
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.21
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.76
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.36
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.85
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.45
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.71
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.98
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.66
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.38
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.25
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.88
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.57
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.73
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.53
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.53
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.10
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.61
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.58
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.84
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.83
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.01
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.77
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.76
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.48
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.34
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.59
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.56
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.75
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.74
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.60
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.70
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.25
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.75
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.73
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.66
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.76
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.33
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.81
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.03
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.30
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.81
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.33
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.85
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.14
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.68
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.30
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.11
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.83
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.28
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.09
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.97
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.96
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.34
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.38
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.87
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.29
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	14.72
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.94
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	10.39
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	10.16
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	7.55
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.73
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.21
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.07
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.74
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.25

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.