Gene detail

Detailed information of OS493_028148-T1 in Lophelia pertusa

Genomic Location: scaffold_159:439170...446659
NR annotation: KAJ7377589.1, High mobility group [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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0010669 (this species only)
Transcription factor family	HMGA · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02178 all species →	AT_hook	AT hook motif	Motif	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017956 all species →	Conserved_site	AT hook, DNA-binding motif	Interproscan
IPR000116 all species →	Family	High mobility group protein HMGA	Interproscan
IPR000637 all species →	Conserved_site	HMG-I/HMG-Y, DNA-binding, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23341 all species →	HIGH MOBILITY GROUP PROTEINS HMG-A AND C	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0000785 all species →	Cellular Component	chromatin	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0003712 all species →	Molecular Function	transcription coregulator activity	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
K09283	HMGA2; high mobility group AT-hook protein 2	-	Chromosome and associated proteins	ko03036	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_028148-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

112.7Max TPM

41.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	44.84	82.42
polyp at pH7 6	18	18	46.85	69.07
coral polyp · control treatment	16	16	46.14	73.40
coral polyp · oil and dispersant treatment	16	16	36.21	83.72
coral polyp · oil treatment	16	16	48.20	112.70
coral polyp · dispersant treatment	16	16	39.52	64.74
Polyp	10	10	24.30	52.04

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	82.42
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	79.44
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	67.28
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.54
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.73
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.74
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.78
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.70
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.40
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.55
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.26
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.26
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.94
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.52
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.42
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.31
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.63
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.12
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	69.07
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.84
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.70
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.52
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.44
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.19
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.06
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.16
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.06
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.24
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.95
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.79
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.78
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.52
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.11
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.81
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.17
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.84
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.40
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.98
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.68
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.17
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.99
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.35
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.23
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.02
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.88
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.71
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.16
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.81
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.83
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.19
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.78
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.99
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	83.72
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.90
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.32
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.33
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.32
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.66
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.42
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.78
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.63
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.84
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.42
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.65
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.45
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.09
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.64
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.21
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	112.70
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	79.87
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.30
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.74
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.51
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.51
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.12
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.83
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.13
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.36
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.93
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.20
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.61
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.21
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.51
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.62
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.74
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.81
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.99
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.26
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.18
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.00
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.42
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.24
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.31
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.43
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.40
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.54
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.93
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.16
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.42
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.43
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	52.04
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	31.82
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	28.64
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	24.59
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	23.62
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	20.34
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	19.79
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	18.51
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.93
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	11.68

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.