Gene detail

Detailed information of OS493_008746-T1 in Lophelia pertusa

Genomic Location: scaffold_20:3738619...3742664
NR annotation: KAJ7386598.1, R3H domain-containing protein 4 [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
Q96D70	R3H domain-containing protein 4 OS=Homo sapiens OX=9606 GN=R3HDM4 PE=1 SV=3
Q2KIL7	R3H domain-containing protein 4 OS=Bos taurus OX=9913 GN=R3HDM4 PE=2 SV=1
Q4VBF2	R3H domain-containing protein 4 OS=Mus musculus OX=10090 GN=R3hdm4 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006962 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13902 all species →	R3H-assoc	R3H-associated N-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036867 all species →	Homologous_superfamily	R3H domain superfamily	Interproscan
IPR039629 all species →	Family	R3H domain-containing protein 4	Interproscan
IPR025952 all species →	Domain	R3H-associated N-terminal domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR32019 all species →	R3H DOMAIN-CONTAINING PROTEIN 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	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_008746-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_008746-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

36.0Max TPM

18.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	16.49	35.99
polyp at pH7 6	18	18	22.78	33.31
coral polyp · control treatment	16	16	19.66	28.03
coral polyp · oil and dispersant treatment	16	16	15.25	25.96
coral polyp · oil treatment	16	16	16.23	23.38
coral polyp · dispersant treatment	16	16	18.56	30.50
Polyp	10	9	15.71	31.48

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	-	35.99
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.13
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.33
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.10
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.25
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.93
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.83
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.59
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.73
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.47
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.06
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.87
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.04
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.60
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.43
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.37
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.17
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.86
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.31
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.58
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.14
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.74
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.31
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.71
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.56
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.72
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.71
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.18
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.98
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.81
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.34
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.33
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.32
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.85
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.18
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.35
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.03
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.51
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.65
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.14
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.78
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.39
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.67
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.08
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.25
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.85
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.64
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.21
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.08
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.33
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.12
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.80
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.96
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.28
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.73
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.47
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.73
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.85
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.06
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.83
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.93
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.95
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.92
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.70
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.08
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.90
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.59
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.97
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.38
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.61
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.41
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.98
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.18
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.95
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.38
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.51
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.44
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.11
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.23
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.05
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.93
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.21
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.88
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.48
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.50
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.67
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.17
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.14
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.07
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.19
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.87
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.47
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.67
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.63
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.42
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.78
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.90
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.47
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.55
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.49
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	31.48
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	21.90
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	18.75
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	17.69
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	15.57
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	15.25
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	15.21
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	11.83
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.45
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.