Gene detail

Detailed information of OS493_016732-T1 in Lophelia pertusa

Genomic Location: scaffold_52:333258...335040
NR annotation: KAJ7372812.1, HMG box-containing protein 1 [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
Q2KJ34	HMG box-containing protein 1 OS=Bos taurus OX=9913 GN=HBP1 PE=2 SV=1
Q62661	HMG box-containing protein 1 OS=Rattus norvegicus OX=10116 GN=Hbp1 PE=1 SV=2
O60381	HMG box-containing protein 1 OS=Homo sapiens OX=9606 GN=HBP1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008832 (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
IPR009071 all species →	Domain	High mobility group box domain	Interproscan
IPR036910 all species →	Homologous_superfamily	High mobility group box domain superfamily	Interproscan
IPR051356 all species →	Family	SOX/SOX-like transcription factors	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45789 all species →	FI18025P1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific 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

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_016732-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_016732-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

65.6Max TPM

17.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.63	14.64
polyp at pH7 6	18	18	10.10	14.55
coral polyp · control treatment	16	16	23.03	31.04
coral polyp · oil and dispersant treatment	16	16	26.35	44.78
coral polyp · oil treatment	16	16	30.11	65.59
coral polyp · dispersant treatment	16	16	15.56	33.11
Polyp	10	10	6.80	17.90

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	-	14.64
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.93
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.27
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.43
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.92
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.58
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.20
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.70
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.58
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.23
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.07
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.04
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.60
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.49
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.07
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.80
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.99
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.78
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.55
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.03
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.06
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.86
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.49
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.17
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.83
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.46
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.19
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.52
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.35
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.27
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.55
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.31
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.29
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.81
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.77
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.29
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.04
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.74
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.50
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.48
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.09
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.80
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.88
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.73
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.79
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.96
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.81
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.65
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.87
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.73
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.86
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.56
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.78
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.35
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.25
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.37
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.00
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.43
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.48
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.78
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.12
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.39
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.70
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.61
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.18
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.73
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.82
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.65
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.59
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.51
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.98
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.62
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.30
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.01
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.01
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.18
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.04
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.91
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.63
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.47
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.39
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.68
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.57
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.94
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.11
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.48
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.50
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.23
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.00
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.74
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.66
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.44
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.65
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.26
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.50
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.92
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.46
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.25
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.53
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.28
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	17.90
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.45
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.73
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.65
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.03
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	4.37
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.31
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.98
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.56

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.