Gene detail

Detailed information of OS493_029255-T1 in Lophelia pertusa

Genomic Location: scaffold_176:236308...243283
NR annotation: KAJ7383290.1, High mobility group protein 20A [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
Q5ZKF4	High mobility group protein 20A OS=Gallus gallus OX=9031 GN=HMG20A PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002175 (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
IPR051965 all species →	Family	Chromatin Regulation and Neuronal Gene Expression	Interproscan
IPR009071 all species →	Domain	High mobility group box domain	Interproscan
IPR036236 all species →	Homologous_superfamily	Zinc finger C2H2 superfamily	Interproscan
IPR036910 all species →	Homologous_superfamily	High mobility group box domain superfamily	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K24660	HMG20A; high mobility group protein 20A	-	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_029255-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

109TPM > 0

7Conditions

23.1Max TPM

11.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	13.34	19.05
polyp at pH7 6	18	18	14.20	19.19
coral polyp · control treatment	16	16	13.56	20.75
coral polyp · oil and dispersant treatment	16	16	10.98	16.84
coral polyp · oil treatment	16	16	12.14	23.13
coral polyp · dispersant treatment	16	16	7.38	14.29
Polyp	10	9	8.38	17.53

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	-	19.05
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.89
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.06
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.85
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.76
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.05
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.90
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.34
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.30
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.73
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.35
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.16
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.83
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.80
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.63
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.69
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.28
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.40
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.19
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.86
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.37
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.71
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.07
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.90
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.00
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.43
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.15
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.71
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.18
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.95
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.75
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.45
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.27
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.10
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.75
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.91
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.57
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.20
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.75
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.30
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.03
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.60
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.08
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.36
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.93
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.19
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.03
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.69
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.70
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.86
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.84
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.17
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.81
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.46
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.72
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.19
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.16
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.86
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.96
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.39
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.33
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.31
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.19
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.14
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.99
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.12
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.13
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.19
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.75
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.07
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.30
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.81
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.61
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.73
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.96
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.68
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.36
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.87
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.58
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.96
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.63
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.59
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.29
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.93
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.57
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.10
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.49
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.45
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.75
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.43
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.75
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.61
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.50
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.79
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.72
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.32
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.54
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.88
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	17.53
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.45
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	12.15
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.10
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.41
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	8.86
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.60
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.18
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.54
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.