Gene detail

Detailed information of OS493_009513-T1 in Lophelia pertusa

Genomic Location: scaffold_22:3589360...3596219
NR annotation: KAJ7374171.1, Transcription elongation factor A protein 1 [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
Q148K0	Transcription elongation factor A protein 2 OS=Bos taurus OX=9913 GN=TCEA2 PE=2 SV=1
Q9QVN7	Transcription elongation factor A protein 2 OS=Mus musculus OX=10090 GN=Tcea2 PE=2 SV=2
Q63799	Transcription elongation factor A protein 2 OS=Rattus norvegicus OX=10116 GN=Tcea2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006396 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08711 all species →	Med26	TFIIS helical bundle-like domain	Domain	Interproscan
PF07500 all species →	TFIIS_M	Transcription factor S-II (TFIIS), central domain	Domain	Interproscan
PF01096 all species →	TFIIS_C	Transcription factor S-II (TFIIS)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001222 all species →	Domain	Zinc finger, TFIIS-type	Interproscan
IPR003618 all species →	Domain	Transcription elongation factor S-II, central domain	Interproscan
IPR036575 all species →	Homologous_superfamily	Transcription elongation factor S-II, central domain superfamily	Interproscan
IPR017923 all species →	Domain	Transcription factor IIS, N-terminal	Interproscan
IPR003617 all species →	Domain	Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type	Interproscan
IPR035100 all species →	Family	Transcription elongation factor, IIS-type	Interproscan
IPR035441 all species →	Homologous_superfamily	TFIIS/LEDGF domain superfamily	Interproscan
IPR006289 all species →	Family	Transcription elongation factor, TFIIS	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11477 all species →	TRANSCRIPTION FACTOR S-II ZINC FINGER DOMAIN-CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0006351 all species →	Biological Process	DNA-templated transcription	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006368 all species →	Biological Process	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
K03145	TFIIS; transcription elongation factor S-II	-	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_009513-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

43.2Max TPM

22.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	21.21	28.58
polyp at pH7 6	18	18	22.13	32.39
coral polyp · control treatment	16	16	25.12	38.43
coral polyp · oil and dispersant treatment	16	16	26.14	43.17
coral polyp · oil treatment	16	16	22.93	38.70
coral polyp · dispersant treatment	16	16	16.26	36.20
Polyp	10	10	18.91	32.33

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.58
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.53
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.50
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.91
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.05
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.92
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.50
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.95
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.87
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.36
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.13
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.10
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.24
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.99
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.65
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.14
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.85
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.43
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.39
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.93
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.52
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.42
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.52
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.09
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.85
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.29
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.25
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.65
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.11
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.53
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.32
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.29
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.31
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.60
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.92
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.41
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.43
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.03
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.71
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.47
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.91
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.18
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.70
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.57
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.87
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.83
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.52
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.61
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.37
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.60
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.95
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.18
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.17
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.74
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.55
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.21
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.70
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.18
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.89
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.19
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.22
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.48
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.47
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.43
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.11
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.61
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.09
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.21
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.70
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.92
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.20
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.50
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.30
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.43
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.15
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.66
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.52
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.73
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.70
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.67
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.71
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.42
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.74
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.52
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.20
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.64
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.90
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.14
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.75
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.41
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.87
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.66
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.05
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.12
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.07
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.38
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.85
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.15
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.71
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.30
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	32.33
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	23.45
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	21.78
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	21.48
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	20.95
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	19.43
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	14.93
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	14.12
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	10.63
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.97

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.