Gene detail

Detailed information of OS493_008389-T1 in Lophelia pertusa

Genomic Location: scaffold_19:3205082...3206363
NR annotation: KAJ7393091.1, POU domain, class 4, transcription factor 2 [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
Q90435	POU domain, class 4, transcription factor 3 OS=Danio rerio OX=7955 GN=pou4f3 PE=2 SV=2
Q15319	POU domain, class 4, transcription factor 3 OS=Homo sapiens OX=9606 GN=POU4F3 PE=1 SV=1
Q63955	POU domain, class 4, transcription factor 3 OS=Mus musculus OX=10090 GN=Pou4f3 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006834 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan
PF00157 all species →	Pou	Pou domain - N-terminal to homeobox domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000327 all species →	Domain	POU-specific domain	Interproscan
IPR050255 all species →	Family	POU domain transcription factor	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR013847 all species →	Domain	POU domain	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan
IPR010982 all species →	Homologous_superfamily	Lambda repressor-like, DNA-binding domain superfamily	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11636 all species →	POU DOMAIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
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:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0003677 all species →	Molecular Function	DNA 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
K09366	POU4F, BRN3; POU domain transcription factor, class 4	-	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_008389-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

108.6Max TPM

37.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	41.43	99.58
polyp at pH7 6	18	18	32.72	59.29
coral polyp · control treatment	16	16	52.49	108.58
coral polyp · oil and dispersant treatment	16	16	27.81	60.19
coral polyp · oil treatment	16	16	37.08	74.11
coral polyp · dispersant treatment	16	16	29.28	60.08
Polyp	10	10	40.12	85.30

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	99.58
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	90.51
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	75.30
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	75.07
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.28
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.05
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.69
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.68
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.92
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.80
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.04
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.30
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.97
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.81
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.20
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.16
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.76
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.61
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.29
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.82
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.39
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.13
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.00
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.86
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.62
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.13
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.41
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.79
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.35
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.19
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.88
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.29
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.58
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.11
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.65
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.54
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	108.58
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	90.34
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	88.75
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.27
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.92
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.17
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.16
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.92
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.54
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.83
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.79
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.83
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.56
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.15
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.22
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.82
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.19
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.05
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.07
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.99
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.19
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.21
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.71
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.78
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.06
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.16
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.89
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.36
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.28
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.15
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.50
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.33
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	74.11
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.77
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	60.60
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.43
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.24
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.97
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.03
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.54
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.78
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.60
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.32
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.54
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.95
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.26
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.20
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.96
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.08
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.20
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.15
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.33
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.41
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.45
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.70
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.41
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.79
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.53
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.22
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.62
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.47
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.02
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.62
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.48
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	85.30
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	72.34
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	56.51
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	41.99
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	41.73
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	38.81
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	19.40
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	17.19
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	15.95
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	11.96

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.