Gene detail

Detailed information of OS493_001161-T1 in Lophelia pertusa

Genomic Location: scaffold_2:5848730...5865639
NR annotation: KAJ7387815.1, Chromatin assembly complex, subunit 3 [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
Q61474	RNA-binding protein Musashi homolog 1 OS=Mus musculus OX=10090 GN=Msi1 PE=1 SV=1
Q8K3P4	RNA-binding protein Musashi homolog 1 OS=Rattus norvegicus OX=10116 GN=Msi1 PE=1 SV=1
O43347	RNA-binding protein Musashi homolog 1 OS=Homo sapiens OX=9606 GN=MSI1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000504 (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
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR48032 all species →	RNA-BINDING PROTEIN MUSASHI HOMOLOG RBP6	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005844 all species →	Cellular Component	obsolete polysome	Interproscan
GO:0006417 all species →	Biological Process	regulation of translation	Interproscan
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_001161-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_001161-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

123.9Max TPM

54.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	58.94	105.24
polyp at pH7 6	18	18	52.49	82.20
coral polyp · control treatment	16	16	66.48	112.27
coral polyp · oil and dispersant treatment	16	16	50.06	122.97
coral polyp · oil treatment	16	16	65.78	123.87
coral polyp · dispersant treatment	16	16	55.28	111.15
Polyp	10	9	18.93	46.14

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	105.24
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	97.44
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	91.95
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	85.66
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	70.78
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	70.72
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	65.36
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	65.20
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	61.17
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.71
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.16
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.76
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.29
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.07
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.38
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.14
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.30
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.59
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	82.20
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	78.96
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	77.27
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	76.91
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.03
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.95
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.55
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.92
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.22
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.46
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.10
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.70
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.46
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.61
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.64
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.46
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.70
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.73
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	112.27
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.00
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	100.68
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	99.38
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.95
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	75.85
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.84
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.53
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.77
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.37
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.25
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.68
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.12
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.85
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.97
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.24
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	122.97
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	96.34
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	70.50
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.71
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.69
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.16
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.07
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.78
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.43
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.06
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.81
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.65
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.43
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.70
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.98
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.60
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	123.87
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	116.48
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	86.70
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.24
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	77.87
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	74.87
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.07
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.47
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.47
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.27
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.56
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.76
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.88
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.38
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.38
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.28
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	111.15
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	104.28
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	87.31
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	83.76
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.99
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.52
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.91
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.85
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.05
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.77
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.65
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.30
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.06
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.65
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.93
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.29
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	46.14
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	30.11
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	26.97
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	20.46
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	20.23
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	15.84
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	11.60
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	10.73
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.23
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.