Gene detail

Detailed information of OS493_000941-T1 in Lophelia pertusa

Genomic Location: scaffold_2:2105274...2110255
NR annotation: KAJ7387606.1, hypothetical protein OS493_000941, partial [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
Q5E9X1	Nuclear transcription factor Y subunit gamma OS=Bos taurus OX=9913 GN=NFYC PE=2 SV=1
Q62725	Nuclear transcription factor Y subunit gamma OS=Rattus norvegicus OX=10116 GN=Nfyc PE=2 SV=1
P70353	Nuclear transcription factor Y subunit gamma OS=Mus musculus OX=10090 GN=Nfyc PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006628 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00125 all species →	Histone	Core histone H2A/H2B/H3/H4	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR050568 all species →	Family	Transcription and DNA Replication Regulators	Interproscan
IPR009072 all species →	Homologous_superfamily	Histone-fold	Interproscan
IPR007125 all species →	Domain	Histone H2A/H2B/H3	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10252 all species →	HISTONE-LIKE TRANSCRIPTION FACTOR CCAAT-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
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:0005634 all species →	Cellular Component	nucleus	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
GO:0046982 all species →	Molecular Function	protein heterodimerization activity	Interproscan
GO:0003677 all species →	Molecular Function	DNA 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
K08066	NFYC, HAP5; nuclear transcription factor Y, gamma	-	Transcription factors	ko03000	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_000941-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

58.8Max TPM

19.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.07	16.22
polyp at pH7 6	18	18	13.18	21.73
coral polyp · control treatment	16	16	26.83	47.95
coral polyp · oil and dispersant treatment	16	16	26.49	58.78
coral polyp · oil treatment	16	16	23.77	43.04
coral polyp · dispersant treatment	16	16	26.14	58.84
Polyp	10	9	10.07	20.04

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.22
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.84
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.82
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.72
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.37
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.11
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.34
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.96
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.80
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.61
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.11
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.95
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.94
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.60
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.98
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.50
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.72
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.72
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.73
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.13
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.91
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.38
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.93
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.13
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.70
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.38
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.91
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.80
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.30
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.74
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.68
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.44
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.05
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.79
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.18
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.11
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.95
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.91
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.96
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.73
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.53
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.53
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.15
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.65
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.21
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.11
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.57
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.79
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.18
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.68
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.66
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.61
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.78
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.58
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.68
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.74
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.86
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.21
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.63
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.35
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.53
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.46
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.26
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.89
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.69
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.44
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.19
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.60
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.04
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.82
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.73
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.77
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.73
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.06
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.11
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.37
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.60
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.99
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.63
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.20
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.76
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.20
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.79
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.47
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.84
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.72
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.17
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.67
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.72
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.89
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.06
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.31
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.11
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.50
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.66
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.59
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.52
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.49
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.86
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.19
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	20.04
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	18.09
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	16.16
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.50
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.48
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	8.28
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	5.60
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.60
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.98
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.