Gene detail

Detailed information of OS493_001422-T1 in Lophelia pertusa

Genomic Location: scaffold_3:1132375...1133418
NR annotation: KAJ7381301.1, rhombomere 2 development [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
Q14549	Homeobox protein GBX-1 OS=Homo sapiens OX=9606 GN=GBX1 PE=1 SV=2
P82976	Homeobox protein GBX-1 OS=Mus musculus OX=10090 GN=Gbx1 PE=2 SV=2
Q91907	Homeobox protein GBX-2 OS=Xenopus laevis OX=8355 GN=gbx2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000082 (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
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan
IPR020479 all species →	Domain	Homeobox domain, metazoa	Interproscan
IPR042982 all species →	Family	Homeobox protein GBX-1/2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24334 all species →	HOMEOBOX PROTEIN GBX	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:0000977 all species →	Molecular Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0051960 all species →	Biological Process	regulation of nervous system development	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
K09321	GBX; homeobox protein GBX	-	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_001422-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

24.4Max TPM

8.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.65	17.14
polyp at pH7 6	18	18	10.91	16.24
coral polyp · control treatment	16	16	9.88	24.39
coral polyp · oil and dispersant treatment	16	16	6.04	10.60
coral polyp · oil treatment	16	16	8.70	14.01
coral polyp · dispersant treatment	16	16	3.77	10.62
Polyp	10	10	5.14	10.26

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.14
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.54
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.25
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.48
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.40
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.10
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.77
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.70
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.62
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.77
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.56
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.67
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.59
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.41
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.47
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.45
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.10
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.72
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.24
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.59
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.08
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.14
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.10
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.86
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.50
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.79
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.36
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.24
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.14
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.56
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.32
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.55
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.93
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.46
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.41
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.18
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.39
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.00
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.76
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.54
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.24
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.01
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.90
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.68
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.49
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.27
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.98
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.85
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.74
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.90
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.83
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.48
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.60
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.24
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.62
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.49
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.42
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.19
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.08
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.77
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.87
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.27
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.39
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.46
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.30
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.89
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.70
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.39
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.01
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.13
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.12
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.58
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.48
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.09
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.97
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.72
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.69
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.57
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.75
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.87
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.64
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.62
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.41
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.62
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.62
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.06
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.89
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.68
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.33
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.25
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.85
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.19
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.13
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.93
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.65
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.29
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.23
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.95
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.90
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.45
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.26
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.87
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.78
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	5.61
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	5.26
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.03
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.72
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.80
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.87
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.18

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.