Gene detail

Detailed information of OS493_001285-T1 in Lophelia pertusa

Genomic Location: scaffold_2:7665648...7693923
NR annotation: KAJ7387933.1, Transcription elongation factor SPT4 [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
P63271	Transcription elongation factor SPT4-A OS=Mus musculus OX=10090 GN=Supt4h1a PE=2 SV=1
Q3SYX6	Transcription elongation factor SPT4 OS=Bos taurus OX=9913 GN=SUPT4H1 PE=3 SV=1
P63272	Transcription elongation factor SPT4 OS=Homo sapiens OX=9606 GN=SUPT4H1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009629 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06093 all species →	Spt4	Spt4/RpoE2 zinc finger	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029040 all species →	Homologous_superfamily	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Interproscan
IPR038510 all species →	Homologous_superfamily	Spt4 superfamily	Interproscan
IPR022800 all species →	Domain	Spt4/RpoE2 zinc finger	Interproscan
IPR009287 all species →	Family	Transcription initiation Spt4	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12882 all species →	SUPPRESSOR OF TY 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0140673 all species →	Biological Process	transcription elongation-coupled chromatin remodeling	Interproscan
GO:0000993 all species →	Molecular Function	RNA polymerase II complex binding	Interproscan
GO:0006325 all species →	Biological Process	chromatin organization	Interproscan
GO:0032044 all species →	Cellular Component	DSIF complex	Interproscan
GO:0034243 all species →	Biological Process	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
K15171	SUPT4H1, SPT4; transcription elongation factor SPT4	-	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_001285-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

80.4Max TPM

36.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	26.72	37.27
polyp at pH7 6	18	17	27.95	42.93
coral polyp · control treatment	16	16	46.69	80.40
coral polyp · oil and dispersant treatment	16	16	51.59	68.96
coral polyp · oil treatment	16	16	41.36	56.66
coral polyp · dispersant treatment	16	16	35.78	51.91
Polyp	10	10	17.65	36.50

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.27
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.54
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.41
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.65
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.99
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.81
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.41
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.98
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.71
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.58
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.43
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.05
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.37
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.83
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.93
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.70
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.35
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.89
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.93
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.01
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.60
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.53
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.07
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.33
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.91
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.87
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.91
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.04
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.48
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.30
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.02
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.36
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.95
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.80
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	80.40
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.18
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.10
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.75
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.45
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.03
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.33
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.95
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.29
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.42
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.54
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.91
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.46
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.28
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.25
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.73
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.96
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.92
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.45
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.26
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.08
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.53
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.58
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.64
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.51
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.70
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.72
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.87
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.33
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.83
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.90
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.14
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.66
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.13
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.19
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.83
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.67
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.65
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.36
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.12
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.51
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.88
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.50
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.06
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.49
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.43
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.14
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.14
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.91
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.57
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.79
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.31
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.19
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.87
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.68
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.24
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.19
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.94
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.19
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.67
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.34
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.33
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.33
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.96
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	36.50
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	25.01
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	23.23
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	22.44
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	21.28
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	19.31
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	10.37
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.33
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.02
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.99

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.