Gene detail

Detailed information of OS493_024167-T1 in Lophelia pertusa

Genomic Location: scaffold_111:607607...610573
NR annotation: KAJ7378219.1, hypothetical protein OS493_024167 [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
Q06615	Homeobox protein notochord OS=Xenopus laevis OX=8355 GN=noto PE=2 SV=1
Q91770	Homeobox protein not2 OS=Xenopus laevis OX=8355 GN=not2 PE=2 SV=1
Q26603	Homeobox protein SMOX-4 (Fragment) OS=Schistosoma mansoni OX=6183 GN=SMOX-4 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001829 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan
IPR050460 all species →	Family	Distal-less homeobox transcription factors	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24327 all species →	HOMEOBOX PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	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:0006357 all species →	Biological Process	regulation of transcription 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

No KEGG orthology assignment for OS493_024167-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_024167-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

94TPM > 0

7Conditions

5.5Max TPM

0.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	13	0.54	1.32
polyp at pH7 6	18	11	0.53	1.51
coral polyp · control treatment	16	16	1.49	3.15
coral polyp · oil and dispersant treatment	16	15	0.80	2.33
coral polyp · oil treatment	16	16	0.67	2.06
coral polyp · dispersant treatment	16	15	1.89	5.50
Polyp	10	8	0.62	1.26

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.32
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.32
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.27
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.09
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.98
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.95
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.72
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.60
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.51
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.33
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.25
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.20
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.12
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.40
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.29
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.99
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.90
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.86
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.76
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.63
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.52
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.50
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.26
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.15
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.98
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.18
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.18
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.81
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.65
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.63
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.59
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.20
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.12
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.09
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.95
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.80
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.66
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.61
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.16
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.33
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.38
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.26
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.23
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.05
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.91
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.82
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.76
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.62
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.61
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.59
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.49
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.43
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.19
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.17
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.06
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.46
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.32
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.69
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.69
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.68
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.65
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.60
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.59
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.49
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.42
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.34
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.25
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.19
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.18
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.17
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.50
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.08
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.95
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.60
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.23
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.61
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.54
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.48
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.42
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.34
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.29
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.09
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.96
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.78
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.40
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.26
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.25
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.06
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.75
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.72
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.53
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.44
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.22
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
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.