Gene detail

Detailed information of OS493_001535-T1 in Lophelia pertusa

Genomic Location: scaffold_3:4115561...4117739
NR annotation: KAJ7381401.1, hypothetical protein OS493_001535 [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
O42115	Aristaless-related homeobox protein OS=Danio rerio OX=7955 GN=arx PE=2 SV=1
Q96QS3	Homeobox protein ARX OS=Homo sapiens OX=9606 GN=ARX PE=1 SV=1
O35085	Homeobox protein ARX OS=Mus musculus OX=10090 GN=Arx PE=1 SV=3

Gene family

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

Pfam domain

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

InterPro

InterPro term	Type	Description	Source
IPR050649 all species →	Family	Paired Homeobox Transcription Factors	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR003654 all species →	Domain	OAR domain	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
K09452	ARX; homeobox protein aristaless-related	-	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_001535-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

32.3Max TPM

11.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	16.13	30.62
polyp at pH7 6	18	18	12.46	29.64
coral polyp · control treatment	16	16	14.15	23.67
coral polyp · oil and dispersant treatment	16	16	7.78	13.27
coral polyp · oil treatment	16	16	10.55	20.73
coral polyp · dispersant treatment	16	16	8.99	19.55
Polyp	10	9	12.12	32.32

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.62
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.19
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.98
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.82
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.40
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.11
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.50
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.93
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.91
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.38
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.90
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.71
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.75
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.49
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.90
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.68
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.63
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.52
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.64
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.49
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.38
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.85
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.25
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.83
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.53
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.85
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.81
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.20
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.67
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.49
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.39
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.96
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.72
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.96
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.74
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.45
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.67
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.62
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.58
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.29
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.49
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.79
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.34
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.61
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.07
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.48
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.81
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.32
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.61
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.07
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.04
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.67
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.27
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.30
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.06
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.80
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.02
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.47
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.23
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.18
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.85
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.55
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.34
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.24
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.83
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.62
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.49
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.28
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.73
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.83
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.34
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.29
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.72
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.87
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.13
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.78
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.73
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.69
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.12
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.10
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.41
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.33
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.60
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.11
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.55
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.60
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.24
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.25
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.92
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.23
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.53
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.31
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.25
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.51
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.16
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.76
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.69
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.92
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.73
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.19
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	32.32
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	25.50
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	14.13
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.79
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	11.89
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.07
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.06
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.70
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.76
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.