Gene detail

Detailed information of OS493_005023-T1 in Lophelia pertusa

Genomic Location: scaffold_10:2004071...2016026
NR annotation: KAJ7374681.1, hypothetical protein OS493_005023 [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
Q8IXH7	Negative elongation factor C/D OS=Homo sapiens OX=9606 GN=NELFCD PE=1 SV=2
Q5RFA0	Negative elongation factor D OS=Pongo abelii OX=9601 GN=NELFCD PE=2 SV=1
A5GFY4	Negative elongation factor D OS=Sus scrofa OX=9823 GN=NELFCD PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005020 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04858 all species →	TH1	TH1 protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006942 all species →	Family	TH1 protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12144 all species →	NEGATIVE ELONGATION FACTOR D	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0045892 all species →	Biological Process	negative regulation of DNA-templated transcription	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	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

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
K15181	TH1L, NELFD; negative elongation factor C/D	-	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_005023-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

61.5Max TPM

22.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	27.84	37.45
polyp at pH7 6	18	18	29.62	43.63
coral polyp · control treatment	16	16	22.85	61.46
coral polyp · oil and dispersant treatment	16	16	15.74	45.02
coral polyp · oil treatment	16	16	19.79	30.81
coral polyp · dispersant treatment	16	16	11.11	20.39
Polyp	10	10	32.00	58.94

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	-	37.45
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.53
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.43
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.49
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.17
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.73
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.16
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.92
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.88
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.52
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.34
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.06
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.01
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.58
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.41
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.31
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.84
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.27
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.63
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.20
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.63
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.08
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.06
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.90
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.12
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.67
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.78
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.66
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.19
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.62
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.11
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.82
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.81
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.37
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.26
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.18
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.46
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.21
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.95
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.04
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.22
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.93
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.06
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.22
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.25
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.98
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.44
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.50
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.97
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.93
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.37
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.02
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.23
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.75
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.09
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.15
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.83
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.92
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.70
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.33
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.98
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.67
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.13
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.80
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.16
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.08
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.98
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.81
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.05
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.27
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.42
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.14
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.03
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.90
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.72
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.86
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.02
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.92
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.44
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.54
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.22
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.77
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.53
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.39
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.92
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.81
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.30
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.68
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.50
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.27
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.26
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.59
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.70
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.61
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.14
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.29
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.51
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.96
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.86
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	58.94
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	46.75
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	33.73
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	31.05
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	29.66
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	27.09
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	26.57
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	24.55
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	20.86
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	20.80

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.