Gene detail

Detailed information of OS493_007268-T1 in Lophelia pertusa

Genomic Location: scaffold_16:170889...178644
NR annotation: KAJ7374195.1, hypothetical protein OS493_007268 [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
Q8VE92	RNA-binding protein 4B OS=Mus musculus OX=10090 GN=Rbm4b PE=1 SV=1
Q64LC9	RNA-binding protein 4B OS=Rattus norvegicus OX=10116 GN=Rbm4b PE=2 SV=2
Q9BQ04	RNA-binding protein 4B OS=Homo sapiens OX=9606 GN=RBM4B PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002199 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00098 all species →	zf-CCHC	Zinc knuckle	Domain	Interproscan
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR050502 all species →	Family	Eukaryotic RNA-binding	Interproscan
IPR001878 all species →	Domain	Zinc finger, CCHC-type	Interproscan
IPR036875 all species →	Homologous_superfamily	Zinc finger, CCHC-type superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR48025 all species →	OS02G0815200 PROTEIN	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:0008270 all species →	Molecular Function	zinc ion 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K13187	RBM4; RNA-binding protein 4	-	Spliceosome	ko03041	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_007268-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

360.0Max TPM

167.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	106.91	161.52
polyp at pH7 6	18	18	111.39	191.25
coral polyp · control treatment	16	16	230.74	360.01
coral polyp · oil and dispersant treatment	16	16	210.90	298.16
coral polyp · oil treatment	16	16	212.96	301.72
coral polyp · dispersant treatment	16	16	195.62	297.55
Polyp	10	10	94.11	161.30

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	-	161.52
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	155.10
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	129.86
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	126.20
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	120.38
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	112.36
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	111.54
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	108.53
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	107.05
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	106.43
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	103.90
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	102.41
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	98.28
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	95.04
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	87.11
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	86.72
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.98
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.01
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	191.25
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	163.74
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	127.79
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	123.67
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	118.19
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	116.33
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	114.42
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	110.05
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	109.34
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	104.64
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	102.50
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	99.78
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	99.61
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	99.43
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	95.65
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	95.51
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.71
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.44
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	360.01
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	337.75
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	311.00
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	296.98
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	283.37
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	254.35
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	252.74
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	252.29
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	242.63
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	233.22
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	219.25
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	141.61
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	141.01
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	134.57
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	129.68
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.44
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	298.16
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	275.58
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	261.64
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	253.96
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	252.12
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	242.05
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	228.03
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	218.29
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	216.01
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	215.71
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	210.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	184.16
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	151.27
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	139.10
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	126.84
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	101.43
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	301.72
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	284.77
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	277.04
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	270.39
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	262.30
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	248.68
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	243.49
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	235.60
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	222.08
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	221.88
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	211.05
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	162.36
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	159.24
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	126.16
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	92.75
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	87.86
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	297.55
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	269.58
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	228.72
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	221.90
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	220.95
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	211.92
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	205.61
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	202.19
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	196.98
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	178.47
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	172.72
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	169.45
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	168.03
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	153.32
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	129.52
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	102.99
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	161.30
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	156.22
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	129.32
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	102.03
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	73.84
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	72.90
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	70.83
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	65.66
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	57.76
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	51.30

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.