Gene detail

Detailed information of OS493_031853-T1 in Lophelia pertusa

Genomic Location: scaffold_228:49701...52762
NR annotation: KAJ7323378.1, hypothetical protein OS493_031853 [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
O35750	Short stature homeobox protein 2 (Fragment) OS=Rattus norvegicus OX=10116 GN=Shox2 PE=2 SV=2
O15266	Short stature homeobox protein OS=Homo sapiens OX=9606 GN=SHOX PE=1 SV=1
O60902	Short stature homeobox protein 2 OS=Homo sapiens OX=9606 GN=SHOX2 PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000263 (this species only) · gene tree & orthology

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
IPR052631 all species →	Family	Paired homeobox Bicoid subfamily	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46255 all species →	SHORT STATURE HOMEOBOX	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:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:1990837 all species →	Molecular Function	sequence-specific double-stranded DNA binding	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
K24896	DUX; double 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_031853-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

88TPM > 0

7Conditions

7.4Max TPM

1.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	15	2.19	4.60
polyp at pH7 6	18	10	1.27	4.31
coral polyp · control treatment	16	15	1.76	5.25
coral polyp · oil and dispersant treatment	16	14	0.79	2.67
coral polyp · oil treatment	16	13	0.90	1.79
coral polyp · dispersant treatment	16	13	1.91	7.39
Polyp	10	8	1.76	4.24

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.60
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.42
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.35
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.33
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.05
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.78
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.61
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.60
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.60
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.47
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.32
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.99
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.90
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.53
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.90
SRR11359494	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
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.31
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.66
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.11
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.01
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.01
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.88
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.56
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.81
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.79
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.72
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
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
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.25
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.66
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.06
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.94
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.74
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.01
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.64
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.37
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.30
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.02
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.00
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.92
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.55
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.44
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.19
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.67
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.85
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.04
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.90
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.90
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.89
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.87
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.87
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.72
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.59
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.51
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.26
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.26
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.24
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705994	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	1.79
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.57
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.48
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.41
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.36
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.20
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.19
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.12
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.11
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.73
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.66
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.50
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.26
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.39
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.35
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.16
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.93
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.65
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.39
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.20
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.73
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.50
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.47
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.37
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.36
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.24
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.68
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.01
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.39
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.54
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.48
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.07
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.17
SRR23025712	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.