Gene detail

Detailed information of OS493_016467-T1 in Lophelia pertusa

Genomic Location: scaffold_50:1727834...1731590
NR annotation: KAJ7385386.1, hypothetical protein OS493_016467 [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
O42567	Retinal homeobox protein Rx-B OS=Xenopus laevis OX=8355 GN=rax-b PE=2 SV=2
O42356	Retinal homeobox protein Rx1 OS=Danio rerio OX=7955 GN=rx1 PE=2 SV=2
Q9I9A2	Retinal homeobox protein Rx2 OS=Oryzias latipes OX=8090 GN=rx2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000383 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03826 all species →	OAR	OAR motif	Motif	Interproscan
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR050649 all species →	Family	Paired Homeobox Transcription Factors	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR003654 all species →	Domain	OAR domain	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24329 all species →	HOMEOBOX PROTEIN ARISTALESS	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000977 all species →	Molecular Function	RNA polymerase II transcription 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
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	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
K09332	RAX, RX; retina and anterior neural fold homeobox protein	-	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_016467-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

101TPM > 0

7Conditions

39.7Max TPM

3.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	1.52	3.99
polyp at pH7 6	18	15	10.47	39.68
coral polyp · control treatment	16	16	2.94	8.02
coral polyp · oil and dispersant treatment	16	15	2.42	10.76
coral polyp · oil treatment	16	15	3.13	23.41
coral polyp · dispersant treatment	16	15	1.40	6.04
Polyp	10	9	1.22	5.84

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	-	3.99
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.31
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.25
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.52
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.51
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.42
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.83
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.81
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.27
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.14
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.82
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.73
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.69
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.45
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.39
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.26
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.68
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.17
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.73
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.45
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.76
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.73
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.62
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.72
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.16
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.98
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.94
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.75
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.73
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.28
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.83
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
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.02
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.85
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.73
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.75
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.63
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.25
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.16
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.05
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.61
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.34
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.23
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.06
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.95
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.72
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.44
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.23
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.76
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.78
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.56
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.18
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.94
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.26
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.09
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.72
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.15
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.03
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.89
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.81
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.67
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.49
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.42
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	23.41
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.95
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.12
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.89
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.74
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.44
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.40
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.38
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.36
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.25
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.83
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.74
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.65
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.63
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.36
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.04
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.72
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.53
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.21
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.19
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.45
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.39
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.99
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.80
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.77
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.44
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.43
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.27
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.11
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.08
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.84
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.42
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.29
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.04
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.86
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.50
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.46
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.43
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.33
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.