Gene detail

Detailed information of OS493_029602-T1 in Lophelia pertusa

Genomic Location: scaffold_181:481763...484875
NR annotation: KAJ7389703.1, hypothetical protein OS493_029602 [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
Q75B82	Non-histone chromosomal protein 6 OS=Eremothecium gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) OX=284811 GN=NHP6 PE=3 SV=1
P07746	High mobility group-T protein OS=Oncorhynchus mykiss OX=8022 PE=2 SV=2
Q6CVH3	Non-histone chromosomal protein 6 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) OX=284590 GN=NHP6 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002244 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00505 all species →	HMG_box	HMG (high mobility group) box	Domain	Interproscan
PF09011 all species →	HMG_box_2	HMG-box domain	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
IPR050342 all species →	Family	High Mobility Group Box (HMGB)	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR48112 all species →	HIGH MOBILITY GROUP PROTEIN DSP1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008301 all species →	Molecular Function	DNA binding, bending	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_029602-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_029602-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

927.3Max TPM

404.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	493.60	587.45
polyp at pH7 6	18	18	481.57	746.59
coral polyp · control treatment	16	16	375.37	725.31
coral polyp · oil and dispersant treatment	16	16	394.33	790.10
coral polyp · oil treatment	16	16	404.90	927.35
coral polyp · dispersant treatment	16	16	348.46	700.49
Polyp	10	10	253.76	523.09

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	587.45
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	578.37
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	562.22
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	549.01
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	544.13
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	544.04
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	541.31
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	537.91
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	515.18
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	514.38
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	502.25
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	496.16
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	468.93
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	448.56
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	398.73
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	381.16
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	360.61
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	354.45
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	746.59
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	735.63
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	619.21
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	598.80
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	559.10
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	552.20
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	521.21
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	507.44
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	475.29
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	470.87
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	425.98
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	424.66
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	420.35
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	412.23
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	405.48
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	405.40
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	194.50
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	193.29
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	725.31
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	677.89
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	491.76
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	469.43
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	440.39
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	428.51
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	364.31
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	334.57
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	332.45
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	329.52
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	326.75
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	315.49
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	284.25
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	180.03
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	179.27
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	126.05
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	790.10
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	640.20
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	611.28
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	603.55
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	504.40
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	418.17
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	401.33
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	397.19
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	384.25
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	348.23
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	327.32
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	240.50
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	190.95
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	161.78
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	146.26
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	143.80
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	927.35
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	670.32
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	623.55
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	603.95
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	538.68
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	415.86
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	376.65
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	374.66
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	339.36
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	332.42
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	297.56
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	283.11
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	259.62
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	205.97
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	183.74
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.64
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	700.49
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	697.48
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	591.69
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	585.33
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	508.42
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	398.40
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	339.79
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	304.39
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	295.21
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	209.99
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	205.35
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	204.08
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	202.26
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	199.86
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	96.96
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.68
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	523.09
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	466.76
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	371.95
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	289.29
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	215.97
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	194.89
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	169.77
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	132.04
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	104.82
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	68.99

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.