Gene detail

Detailed information of OS493_011692-T1 in Lophelia pertusa

Genomic Location: scaffold_30:234176...255133
NR annotation: KAJ7336490.1, Nucleolysin TIA-1 isoform [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
Q01085	Nucleolysin TIAR OS=Homo sapiens OX=9606 GN=TIAL1 PE=1 SV=1
P52912	Cytotoxic granule associated RNA binding protein TIA1 OS=Mus musculus OX=10090 GN=Tia1 PE=1 SV=1
P31483	Cytotoxic granule associated RNA binding protein TIA1 OS=Homo sapiens OX=9606 GN=TIA1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003554 (this species only) · gene tree & orthology

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
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR050825 all species →	Family	RNA Recognition Motif and Poly(A) Binding Protein Families	Interproscan
IPR003954 all species →	Domain	RNA recognition motif domain, eukaryote	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR47640 all species →	TRNA SELENOCYSTEINE 1-ASSOCIATED PROTEIN 1-RELATED-RELATED	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

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_011692-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_011692-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

405.9Max TPM

185.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	125.71	192.13
polyp at pH7 6	18	18	118.95	175.79
coral polyp · control treatment	16	16	246.24	394.59
coral polyp · oil and dispersant treatment	16	16	232.41	404.55
coral polyp · oil treatment	16	16	243.23	405.86
coral polyp · dispersant treatment	16	16	171.58	262.11
Polyp	10	10	172.65	258.95

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	-	192.13
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	183.72
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	183.35
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	177.56
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	146.92
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	146.63
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	122.94
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	119.29
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	117.89
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	117.32
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	115.86
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	111.01
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	99.51
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	98.65
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	90.57
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	84.23
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	79.11
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	76.09
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	175.79
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	168.22
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	165.08
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	161.46
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	137.96
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	137.50
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	137.16
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	129.84
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	126.49
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	122.99
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	98.86
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	96.64
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	94.13
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	93.42
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	80.81
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	80.40
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.19
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.15
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	394.59
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	376.96
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	309.37
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	307.95
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	279.24
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	263.52
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	241.94
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	238.65
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	232.27
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	229.36
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	198.36
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	185.93
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	178.08
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	177.70
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	162.99
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	162.88
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	404.55
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	354.43
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	300.57
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	235.37
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	230.11
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	229.93
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	229.48
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	228.92
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	204.37
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	203.61
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	198.48
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	197.04
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	196.44
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	177.74
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	172.90
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	154.65
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	405.86
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	296.64
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	296.12
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	294.45
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	288.07
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	287.98
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	272.93
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	245.20
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	240.98
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	239.10
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	198.29
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	182.44
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	175.22
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	168.12
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	159.89
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	140.31
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	262.11
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	232.14
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	216.80
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	204.99
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	204.84
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	194.80
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	181.91
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	172.51
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	168.63
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	159.87
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	157.09
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	146.36
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	141.04
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	120.49
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	101.95
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	79.74
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	258.95
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	222.24
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	179.63
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	179.38
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	173.63
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	160.53
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	156.47
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	148.63
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	131.27
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	115.73

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.