Gene detail

Detailed information of OS493_003051-T1 in Lophelia pertusa

Genomic Location: scaffold_6:4314444...4330196
NR annotation: KAJ7340316.1, U2 small nuclear RNA auxiliary factor 2 [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
P26368	Splicing factor U2AF 65 kDa subunit OS=Homo sapiens OX=9606 GN=U2AF2 PE=1 SV=4
P26369	Splicing factor U2AF 65 kDa subunit OS=Mus musculus OX=10090 GN=U2af2 PE=1 SV=3
Q24562	Splicing factor U2AF 50 kDa subunit OS=Drosophila melanogaster OX=7227 GN=U2af50 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003692 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR006529 all species →	Family	U2 snRNP auxilliary factor, large subunit, splicing factor	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23139 all species →	RNA-BINDING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000243 all species →	Cellular Component	commitment complex	Interproscan
GO:0008187 all species →	Molecular Function	poly-pyrimidine tract binding	Interproscan
GO:0016607 all species →	Cellular Component	nuclear speck	Interproscan
GO:0030628 all species →	Molecular Function	pre-mRNA 3'-splice site binding	Interproscan
GO:0071004 all species →	Cellular Component	U2-type prespliceosome	Interproscan
GO:0089701 all species →	Cellular Component	U2AF complex	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006397 all species →	Biological Process	mRNA processing	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
K12837	U2AF2; splicing factor U2AF 65 kDa subunit	-	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_003051-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

313.2Max TPM

174.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	165.27	234.70
polyp at pH7 6	18	18	166.19	205.49
coral polyp · control treatment	16	16	210.44	313.21
coral polyp · oil and dispersant treatment	16	16	200.08	238.71
coral polyp · oil treatment	16	16	207.08	244.96
coral polyp · dispersant treatment	16	16	129.37	207.06
Polyp	10	10	130.94	239.24

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	-	234.70
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	219.74
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	213.03
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	212.30
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	194.76
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	192.78
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	162.85
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	162.81
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	160.43
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	159.86
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	156.63
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	153.78
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	133.48
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	133.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	129.33
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	122.98
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	116.25
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	116.10
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	205.49
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	204.20
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	188.77
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	188.21
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	186.63
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	183.69
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	180.52
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	172.21
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	170.73
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	164.90
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	164.60
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	164.06
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	149.59
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	147.05
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	141.69
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	133.98
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	123.66
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	121.46
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	313.21
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	293.05
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	248.65
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	230.45
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	221.59
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	221.51
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	218.81
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	209.59
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	199.37
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	197.79
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	187.76
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	183.21
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	182.02
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	177.08
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	143.60
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	139.40
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	238.71
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	223.46
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	220.62
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	220.21
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	213.86
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	203.71
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	203.57
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	202.67
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	202.29
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	199.81
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	188.52
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	186.75
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	181.46
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	181.33
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	169.61
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	164.79
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	244.96
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	241.82
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	234.48
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	232.78
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	219.09
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	215.69
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	209.41
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	206.01
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	204.59
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	204.46
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	191.41
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	188.53
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	188.30
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	188.14
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	178.51
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	165.08
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	207.06
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	178.08
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	165.93
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	152.97
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	151.29
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	150.48
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	147.28
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	131.06
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	124.65
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	123.79
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	119.98
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	105.22
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	101.27
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	94.72
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.48
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.68
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	239.24
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	229.92
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	169.05
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	167.88
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	155.17
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	114.01
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	62.76
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	61.06
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	59.91
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	50.37

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.