Gene detail

Detailed information of OS493_013745-T1 in Lophelia pertusa

Genomic Location: scaffold_38:787296...790413
NR annotation: KAJ7385714.1, hypothetical protein OS493_013745 [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
O43390	Heterogeneous nuclear ribonucleoprotein R OS=Homo sapiens OX=9606 GN=HNRNPR PE=1 SV=1
Q7TMK9	Heterogeneous nuclear ribonucleoprotein Q OS=Mus musculus OX=10090 GN=Syncrip PE=1 SV=2
O60506	Heterogeneous nuclear ribonucleoprotein Q OS=Homo sapiens OX=9606 GN=SYNCRIP PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001390 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan
PF18360 all species →	hnRNP_Q_AcD	Heterogeneous nuclear ribonucleoprotein Q acidic domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006535 all species →	Family	HnRNP R/Q splicing factor	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR041337 all species →	Domain	Heterogeneous nuclear ribonucleoprotein Q acidic domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21245 all species →	HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:1990904 all species →	Cellular Component	ribonucleoprotein complex	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_013745-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_013745-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

134.6Max TPM

50.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	25.33	41.67
polyp at pH7 6	18	18	27.00	44.66
coral polyp · control treatment	16	16	70.57	97.95
coral polyp · oil and dispersant treatment	16	16	72.72	105.16
coral polyp · oil treatment	16	16	54.21	83.57
coral polyp · dispersant treatment	16	16	78.62	134.61
Polyp	10	10	24.14	44.54

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.67
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.18
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.94
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.76
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.71
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.40
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.93
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.77
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.76
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.20
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.52
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.35
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.73
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.23
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.81
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.53
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.20
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.21
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.66
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.14
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.32
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.17
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.12
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.52
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.74
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.75
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.47
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.92
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.58
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.43
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.10
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.38
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.59
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.20
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.89
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	97.95
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	96.42
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.45
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	86.82
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	83.26
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.24
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.09
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.89
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	68.40
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.84
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.57
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.30
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.92
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.14
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.65
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.09
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	105.16
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	94.84
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	93.47
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	88.36
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.62
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.62
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	77.48
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.63
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.67
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.91
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	65.00
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.51
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.22
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.75
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.36
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.87
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.57
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	67.30
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.06
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.29
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.23
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.70
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.85
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.51
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.48
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.14
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.93
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.70
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.60
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.02
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.37
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.67
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	134.61
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	108.22
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	100.72
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	98.98
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	94.53
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	92.49
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	91.34
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	76.63
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	76.39
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	75.09
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.45
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.52
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.50
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	56.42
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.00
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	44.54
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	44.28
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	29.54
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	27.75
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	21.08
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	16.94
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	15.54
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	14.43
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	14.40
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	12.88

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.