Gene detail

Detailed information of OS493_005225-T1 in Lophelia pertusa

Genomic Location: scaffold_10:4176248...4185501
NR annotation: KAJ7374872.1, positive regulation of interleukin-13 biosynthetic process [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
Q98925	Interferon regulatory factor 2 OS=Gallus gallus OX=9031 GN=IRF2 PE=2 SV=1
P14316	Interferon regulatory factor 2 OS=Homo sapiens OX=9606 GN=IRF2 PE=1 SV=2
P23906	Interferon regulatory factor 2 OS=Mus musculus OX=10090 GN=Irf2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000568 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10401 all species →	IRF-3	Interferon-regulatory factor 3	Family	Interproscan
PF00605 all species →	IRF	Interferon regulatory factor transcription factor	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR017855 all species →	Homologous_superfamily	SMAD-like domain superfamily	Interproscan
IPR001346 all species →	Domain	Interferon regulatory factor, DNA-binding domain	Interproscan
IPR019471 all species →	Domain	Interferon regulatory factor-3	Interproscan
IPR008984 all species →	Homologous_superfamily	SMAD/FHA domain superfamily	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11949 all species →	INTERFERON REGULATORY FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000976 all species →	Molecular Function	transcription cis-regulatory region binding	Interproscan
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0002376 all species →	Biological Process	immune system process	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0005515 all species →	Molecular Function	protein 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
K10155	IRF8; interferon regulatory factor 8	-	Transcription factors	ko03000	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_005225-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

108TPM > 0

7Conditions

22.6Max TPM

7.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.43	13.88
polyp at pH7 6	18	18	8.28	14.51
coral polyp · control treatment	16	16	10.30	22.62
coral polyp · oil and dispersant treatment	16	15	5.08	11.16
coral polyp · oil treatment	16	16	4.89	13.64
coral polyp · dispersant treatment	16	16	10.84	21.54
Polyp	10	9	2.70	7.86

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	-	13.88
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.47
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.60
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.77
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.35
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.74
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.39
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.54
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.93
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.43
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.12
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.58
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.25
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.09
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.95
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.68
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.05
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.97
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.51
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.93
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.81
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.60
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.86
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.79
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.17
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.12
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.46
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.03
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.47
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.84
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.09
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.89
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.31
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.03
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.12
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.01
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.62
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.97
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.72
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.18
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.06
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.70
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.63
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.55
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.29
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.83
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.97
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.09
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.16
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.15
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.73
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.08
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.16
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.96
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.14
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.89
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.81
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.97
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.79
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.01
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.50
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.36
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.29
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.21
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.61
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.41
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.09
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.64
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.27
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.25
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.50
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.39
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.45
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.49
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.36
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.58
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.22
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.89
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.27
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.07
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.99
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.67
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.24
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.54
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.48
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.29
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.78
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.44
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.61
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.41
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.90
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.74
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.16
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.04
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.55
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.25
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.20
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.83
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.25
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	7.86
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.49
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.96
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.53
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.02
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.79
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.57
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.48
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.27
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.