Gene detail

Detailed information of OS493_017021-T1 in Lophelia pertusa

Genomic Location: scaffold_53:2164337...2175418
NR annotation: KAJ7360388.1, hypothetical protein OS493_017021 [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
P0CB38	Polyadenylate-binding protein 4-like OS=Homo sapiens OX=9606 GN=PABPC4L PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006185 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR033102 all species →	Family	Negative elongation factor E	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR17250 all species →	NEGATIVE ELONGATION FACTOR E	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0032021 all species →	Cellular Component	NELF complex	Interproscan
GO:0034244 all species →	Biological Process	negative regulation of transcription elongation by RNA polymerase II	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid 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
K15182	RDBP, NELFE; negative elongation factor E	-	Transcription machinery	ko03021	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_017021-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

59.0Max TPM

27.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	23.84	31.39
polyp at pH7 6	18	18	24.32	33.10
coral polyp · control treatment	16	16	34.84	45.69
coral polyp · oil and dispersant treatment	16	16	34.90	58.96
coral polyp · oil treatment	16	16	35.32	44.38
coral polyp · dispersant treatment	16	16	17.38	23.87
Polyp	10	9	22.86	33.97

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.39
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.21
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.20
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.51
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.26
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.06
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.93
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.28
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.26
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.08
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.48
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.33
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.92
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.64
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.39
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.30
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.20
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.65
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.10
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.84
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.05
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.52
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.36
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.11
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.35
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.72
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.60
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.26
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.01
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.48
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.16
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.92
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.90
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.31
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.49
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.69
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.42
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.16
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.65
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.63
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.48
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.23
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.43
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.33
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.30
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.58
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.10
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.19
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.85
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.50
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.94
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.96
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.20
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.22
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.18
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.74
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.09
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.39
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.59
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.14
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.10
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.78
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.62
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.65
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.15
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.45
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.18
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.38
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.18
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.96
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.22
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.08
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.84
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.08
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.92
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.62
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.49
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.05
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.57
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.37
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.64
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.73
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.87
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.23
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.74
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.94
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.81
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.77
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.42
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.94
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.83
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.03
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.28
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.74
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.34
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.99
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.25
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.92
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	33.97
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	31.78
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	30.42
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	30.35
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	29.29
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	27.40
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	18.94
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	16.19
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	10.23
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.