Gene detail

Detailed information of OS493_037418-T1 in Lophelia pertusa

Genomic Location: scaffold_423:117443...118601
NR annotation: KAJ7376025.1, Homeobox protein DLX-4 [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
Q98879	Homeobox protein Dlx4a OS=Danio rerio OX=7955 GN=dlx4a PE=2 SV=1
P53775	Homeobox protein DLL-4 OS=Xenopus laevis OX=8355 GN=dll4 PE=2 SV=1
P20009	Homeotic protein distal-less OS=Drosophila melanogaster OX=7227 GN=Dll PE=2 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006415 (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
IPR020479 all species →	Domain	Homeobox domain, metazoa	Interproscan
IPR000047 all species →	Conserved_site	Helix-turn-helix motif	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan
IPR050460 all species →	Family	Distal-less homeobox transcription factors	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	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
GO:0009790 all species →	Biological Process	embryo development	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	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
K18488	DLX2; homeobox protein DLX2	-	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_037418-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

22.5Max TPM

5.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.67	7.84
polyp at pH7 6	18	18	7.01	14.62
coral polyp · control treatment	16	16	6.28	12.31
coral polyp · oil and dispersant treatment	16	15	3.27	6.80
coral polyp · oil treatment	16	16	4.52	8.54
coral polyp · dispersant treatment	16	16	3.75	10.35
Polyp	10	10	11.20	22.53

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.84
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.29
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.16
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.10
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.81
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.51
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.38
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.87
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.76
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.22
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.00
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.76
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.75
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.71
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.68
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.55
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.89
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.72
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.62
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.06
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.80
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.61
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.37
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.12
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.01
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.32
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.44
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.26
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.01
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.89
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.72
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.51
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.22
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.77
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.49
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.91
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.31
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.29
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.43
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.38
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.66
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.44
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.24
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.42
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.32
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.24
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.18
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.23
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.84
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.46
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.67
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.45
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.80
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.90
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.75
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.70
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.52
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.45
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.42
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.33
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.26
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.08
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.93
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.52
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.11
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.72
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.86
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.54
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.05
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.25
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.21
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.05
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.45
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.35
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.51
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.42
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.76
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.66
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.63
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.28
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.82
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.79
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.64
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.35
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.32
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.33
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.15
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.08
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.79
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.74
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.91
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.91
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.75
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.55
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.39
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.25
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.56
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.46
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.46
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	22.53
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	21.13
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	17.17
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	12.02
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	9.35
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.15
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	8.01
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.87
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.85
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.94

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.