Gene detail

Detailed information of OS493_025474-T1 in Lophelia pertusa

Genomic Location: scaffold_125:886940...892001
NR annotation: KAJ7356365.1, DNA-binding transcription factor [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
Q5E9S2	Nuclear transcription factor Y subunit alpha OS=Bos taurus OX=9913 GN=NFYA PE=2 SV=1
P18576	Nuclear transcription factor Y subunit alpha OS=Rattus norvegicus OX=10116 GN=Nfya PE=1 SV=1
P23708	Nuclear transcription factor Y subunit alpha OS=Mus musculus OX=10090 GN=Nfya PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008743 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02045 all species →	CBFB_NFYA	CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001289 all species →	Family	Nuclear transcription factor Y subunit A	Interproscan
IPR018362 all species →	Conserved_site	CCAAT-binding factor, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12632 all species →	TRANSCRIPTION FACTOR NF-Y ALPHA-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	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
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
K08064	NFYA, HAP2; nuclear transcription factor Y, alpha	-	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_025474-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

66.7Max TPM

34.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	30.82	45.32
polyp at pH7 6	18	18	30.88	47.84
coral polyp · control treatment	16	16	42.15	61.66
coral polyp · oil and dispersant treatment	16	16	42.01	66.66
coral polyp · oil treatment	16	16	36.64	55.12
coral polyp · dispersant treatment	16	16	30.50	42.65
Polyp	10	10	27.03	54.99

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.32
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.93
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.14
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.65
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.66
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.48
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.83
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.88
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.82
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.70
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.69
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.19
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.98
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.67
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.32
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.02
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.64
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.91
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.84
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.01
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.51
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.78
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.22
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.46
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.81
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.75
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.03
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.63
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.19
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.82
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.73
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.40
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.90
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.09
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.21
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.46
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.66
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.67
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.55
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.94
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.89
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.83
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.55
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.18
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.87
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.14
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.73
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.92
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.75
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.43
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.41
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.88
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.66
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.37
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.36
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.79
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.38
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.33
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.45
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.03
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.96
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.89
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.94
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.31
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.26
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.65
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.28
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.42
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.12
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.72
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.17
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.43
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.05
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.41
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.73
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.50
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.09
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.83
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.87
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.29
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.80
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.42
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.51
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.34
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.65
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.55
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.31
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.17
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.81
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.92
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.13
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.22
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.46
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.91
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.75
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.99
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.54
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.93
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.32
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.39
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	54.99
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	43.01
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	34.00
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	27.34
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	24.80
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	24.32
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	22.71
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	19.74
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.05
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	8.39

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.