Gene detail

Detailed information of OS493_010850-T1 in Lophelia pertusa

Genomic Location: scaffold_27:1064305...1067869
NR annotation: KAJ7380139.1, protein with role in RNA processing [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
Q0VCF9	Protein LSM12 OS=Bos taurus OX=9913 GN=LSM12 PE=2 SV=2
Q3MHD2	Protein LSM12 OS=Homo sapiens OX=9606 GN=LSM12 PE=1 SV=2
Q9D0R8	Protein LSM12 OS=Mus musculus OX=10090 GN=Lsm12 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008737 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21166 all species →	LSM12_LSM	LSM12, LSM domain	Domain	Interproscan
PF09793 all species →	AD	Anticodon-binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039683 all species →	Family	Protein Lsm12-like	Interproscan
IPR048478 all species →	Domain	LSM12, LSM domain	Interproscan
IPR019181 all species →	Domain	LSM12, anticodon-binding domain	Interproscan
IPR047574 all species →	Domain	AD domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13542 all species →	LSM12 HOMOLOG	Interproscan

Gene Ontology

No Gene Ontology signature was detected for OS493_010850-T1. This gene does have a gene model — the search simply returned no hit.

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
K23643	LSM12; protein LSM12	-	Circadian rhythm - fly	ko04711	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_010850-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

115.5Max TPM

37.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	20.90	36.31
polyp at pH7 6	18	18	35.27	83.21
coral polyp · control treatment	16	16	44.23	109.18
coral polyp · oil and dispersant treatment	16	16	64.08	115.46
coral polyp · oil treatment	16	16	36.95	73.63
coral polyp · dispersant treatment	16	16	32.59	61.50
Polyp	10	10	29.09	53.65

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.31
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.90
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.84
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.69
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.57
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.43
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.03
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.61
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.41
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.02
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.66
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.11
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.83
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.99
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.72
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.25
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.71
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.17
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	83.21
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	71.99
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.01
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.73
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.52
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.78
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.48
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.10
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.78
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.61
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.15
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.77
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.38
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.01
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.44
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.57
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.80
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.57
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	109.18
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	86.72
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.74
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.60
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.09
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.69
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.25
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.89
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.96
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.17
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.67
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.88
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.36
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.36
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.40
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.79
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	115.46
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	107.66
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	105.39
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	91.98
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.53
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.58
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.42
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.66
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.93
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.71
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.94
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.97
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.14
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.53
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.87
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.54
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.63
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.54
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.73
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.37
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.18
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.19
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.19
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.07
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.62
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.95
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.66
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.29
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.35
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.20
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.80
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.43
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.50
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.28
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.46
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.08
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.37
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.74
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.51
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.96
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.74
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.36
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.46
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.89
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.60
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.98
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.91
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.62
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	53.65
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	50.87
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	40.27
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	38.17
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	32.67
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	24.31
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	19.56
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	12.25
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.99
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.13

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.