Gene detail

Detailed information of OS493_011759-T1 in Lophelia pertusa

Genomic Location: scaffold_30:1188494...1201206
NR annotation: KAJ7336546.1, hypothetical protein OS493_011759 [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
Q9DC33	High mobility group protein 20A OS=Mus musculus OX=10090 GN=Hmg20a PE=1 SV=1
Q9NP66	High mobility group protein 20A OS=Homo sapiens OX=9606 GN=HMG20A PE=1 SV=1
Q32L68	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related OS=Bos taurus OX=9913 GN=HMG20B PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009876 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00505 all species →	HMG_box	HMG (high mobility group) box	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036910 all species →	Homologous_superfamily	High mobility group box domain superfamily	Interproscan
IPR009071 all species →	Domain	High mobility group box domain	Interproscan
IPR036236 all species →	Homologous_superfamily	Zinc finger C2H2 superfamily	Interproscan
IPR051965 all species →	Family	Chromatin Regulation and Neuronal Gene Expression	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46040 all species →	HIGH MOBILITY GROUP PROTEIN 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0010468 all species →	Biological Process	regulation of gene expression	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

No KEGG orthology assignment for OS493_011759-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_011759-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

18.6Max TPM

8.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.30	11.90
polyp at pH7 6	18	18	8.66	17.67
coral polyp · control treatment	16	16	8.87	18.58
coral polyp · oil and dispersant treatment	16	16	7.13	14.93
coral polyp · oil treatment	16	16	9.01	15.14
coral polyp · dispersant treatment	16	16	6.96	11.13
Polyp	10	10	7.52	11.95

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	-	11.90
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.39
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.76
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.74
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.65
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.40
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.03
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.99
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.70
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.51
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.58
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.46
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.34
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.08
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.03
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.73
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.36
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.70
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.67
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.87
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.80
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.73
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.96
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.89
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.43
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.33
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.67
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.56
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.53
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.47
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.07
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.91
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.82
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.51
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.31
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.27
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.58
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.69
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.86
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.85
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.58
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.84
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.73
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.43
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.91
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.04
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.95
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.72
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.72
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.41
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.18
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.48
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.93
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.08
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.65
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.40
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.14
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.85
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.51
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.95
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.77
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.45
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.89
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.60
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.56
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.08
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.06
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.22
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.14
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.74
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.74
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.89
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.06
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.82
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.27
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.20
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.98
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.87
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.81
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.26
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.22
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.30
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.78
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.13
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.89
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.99
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.88
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.64
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.84
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.10
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.96
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.90
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.50
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.17
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.24
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.10
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.91
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.23
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.91
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.95
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	9.64
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.45
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.35
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	8.31
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	8.26
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	5.44
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.18
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.96
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.62

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.