Gene detail

Detailed information of OS493_032088-T1 in Lophelia pertusa

Genomic Location: scaffold_233:66924...72269
NR annotation: KAJ7353814.1, hypothetical protein OS493_032088 [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
P25207	Nuclear transcription factor Y subunit beta OS=Gallus gallus OX=9031 GN=NFYB PE=2 SV=2
Q32KW0	Nuclear transcription factor Y subunit beta OS=Bos taurus OX=9913 GN=NFYB PE=2 SV=1
Q6RG77	Nuclear transcription factor Y subunit beta OS=Equus caballus OX=9796 GN=NFYB PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005295 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00808 all species →	CBFD_NFYB_HMF	Histone-like transcription factor (CBF/NF-Y) and archaeal histone	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009072 all species →	Homologous_superfamily	Histone-fold	Interproscan
IPR027113 all species →	Family	Transcription factor NFYB/HAP3	Interproscan
IPR003958 all species →	Domain	Transcription factor CBF/NF-Y/archaeal histone domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11064 all species →	CCAAT-BINDING TRANSCRIPTION FACTOR-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0046982 all species →	Molecular Function	protein heterodimerization activity	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0001228 all species →	Molecular Function	DNA-binding transcription activator activity, RNA polymerase II-specific	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0016602 all species →	Cellular Component	CCAAT-binding factor 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_032088-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_032088-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

83.0Max TPM

36.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	44.85	55.59
polyp at pH7 6	18	18	41.54	53.82
coral polyp · control treatment	16	16	44.35	82.97
coral polyp · oil and dispersant treatment	16	16	33.40	55.86
coral polyp · oil treatment	16	16	34.26	57.82
coral polyp · dispersant treatment	16	16	26.13	54.38
Polyp	10	10	25.72	49.38

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	-	55.59
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.51
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.38
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.24
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.62
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.28
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.85
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.38
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.01
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.86
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.20
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.39
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.36
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.85
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.27
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.73
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.15
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.58
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.82
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.48
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.33
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.69
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.39
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.18
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.61
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.51
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.28
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.48
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.51
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.72
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.96
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.72
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.48
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.14
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.89
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.55
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	82.97
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.63
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.84
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.00
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.23
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.82
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.29
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.13
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.39
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.22
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.57
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.39
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.08
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.57
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.21
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.32
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.86
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.06
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.23
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.95
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.84
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.20
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.88
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.64
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.82
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.01
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.69
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.04
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.67
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.64
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.47
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.37
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.82
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.02
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.73
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.43
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.87
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.96
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.78
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.85
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.47
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.66
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.42
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.57
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.00
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.87
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.13
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.57
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.38
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.79
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.23
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.84
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.37
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.94
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.46
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.14
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.97
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.58
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.41
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.13
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.17
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.62
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.47
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.61
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	49.38
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	34.52
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	33.77
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	27.93
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	26.43
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	22.24
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	17.40
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	17.30
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	17.06
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	11.19

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.