Gene detail

Detailed information of OS493_029459-T1 in Lophelia pertusa

Genomic Location: scaffold_179:623118...630015
NR annotation: KAJ7354900.1, 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
O60381	HMG box-containing protein 1 OS=Homo sapiens OX=9606 GN=HBP1 PE=1 SV=2
Q8R316	HMG box-containing protein 1 OS=Mus musculus OX=10090 GN=Hbp1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002458 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00505 all species →	HMG_box	HMG (high mobility group) box	Domain	Interproscan
PF08517 all species →	AXH	Ataxin-1 and HBP1 module (AXH)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009071 all species →	Domain	High mobility group box domain	Interproscan
IPR003652 all species →	Domain	Ataxin, AXH domain	Interproscan
IPR036096 all species →	Homologous_superfamily	Ataxin, AXH domain superfamily	Interproscan
IPR036910 all species →	Homologous_superfamily	High mobility group box domain superfamily	Interproscan
IPR039655 all species →	Family	HMG box-containing protein 1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15499 all species →	HMG BOX-CONTAINING PROTEIN 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
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:0006355 all species →	Biological Process	regulation of DNA-templated transcription	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_029459-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_029459-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

226.1Max TPM

69.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	55.95	92.11
polyp at pH7 6	18	18	70.78	139.50
coral polyp · control treatment	16	16	71.86	118.90
coral polyp · oil and dispersant treatment	16	16	80.18	226.10
coral polyp · oil treatment	16	16	59.59	134.76
coral polyp · dispersant treatment	16	16	86.21	157.37
Polyp	10	10	63.71	94.24

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	92.11
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	89.88
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	87.38
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	87.37
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	81.30
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	78.75
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.80
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.06
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.99
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.70
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.07
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.94
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.79
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.52
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.28
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.21
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.77
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.19
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	139.50
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	102.77
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	97.95
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	95.65
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	94.61
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	92.61
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	92.57
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	88.32
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.90
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.77
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.85
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.25
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.42
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.78
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.67
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.03
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.98
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.35
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	118.90
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	117.21
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	97.21
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	80.32
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	80.16
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	75.25
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.54
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.66
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.77
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.00
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.26
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.94
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.27
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.92
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.04
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.40
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	226.10
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	124.93
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	89.20
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	88.18
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	86.86
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	83.25
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.81
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	80.64
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.77
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.14
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.37
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.65
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.92
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.16
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.29
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.65
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	134.76
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	91.53
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.60
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	70.17
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.86
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.76
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.61
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.51
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.32
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.08
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.22
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.02
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.35
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.27
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.08
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.33
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	157.37
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	122.26
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	108.85
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	103.47
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	101.05
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	96.58
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	94.37
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.71
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	71.69
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	71.69
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.60
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.52
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.85
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.68
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.81
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.80
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	94.24
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	74.33
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	73.10
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	69.12
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	64.77
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	64.48
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	64.37
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	54.51
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	52.05
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	26.13

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.