Gene detail

Detailed information of OS493_008938-T1 in Lophelia pertusa

Genomic Location: scaffold_21:1831372...1833194
NR annotation: KAJ7380477.1, Hypoxia-inducible factor 1-alpha [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
Q0PGG7	Hypoxia-inducible factor 1-alpha OS=Bos mutus grunniens OX=30521 GN=HIF1A PE=2 SV=1
Q9XTA5	Hypoxia-inducible factor 1-alpha OS=Bos taurus OX=9913 GN=HIF1A PE=2 SV=1
Q61221	Hypoxia-inducible factor 1-alpha OS=Mus musculus OX=10090 GN=Hif1a PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004064 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14598 all species →	PAS_11	PAS domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000014 all species →	Domain	PAS domain	Interproscan
IPR035965 all species →	Homologous_superfamily	PAS domain superfamily	Interproscan
IPR001610 all species →	Repeat	PAC motif	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23043 all species →	HYPOXIA-INDUCIBLE FACTOR 1 ALPHA	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000977 all species →	Molecular Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	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_008938-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_008938-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

1,830.1Max TPM

378.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	103.94	206.69
polyp at pH7 6	18	18	123.54	204.81
coral polyp · control treatment	16	16	310.47	562.34
coral polyp · oil and dispersant treatment	16	16	600.81	1,093.96
coral polyp · oil treatment	16	16	375.06	587.34
coral polyp · dispersant treatment	16	16	1,015.59	1,830.08
Polyp	10	10	68.73	161.84

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	-	206.69
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	196.08
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	175.51
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	170.07
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	127.56
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	106.13
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	105.00
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	99.57
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	94.76
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	94.21
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	72.78
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	72.28
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	65.42
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.77
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.40
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.45
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.90
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.29
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	204.81
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	190.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	185.52
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	175.42
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	156.43
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	149.87
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	145.64
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	141.23
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	116.14
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	113.94
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	95.79
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	91.84
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	91.11
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	88.80
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	74.65
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.72
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	69.67
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.16
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	562.34
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	552.30
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	487.58
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	435.88
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	368.01
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	338.39
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	330.45
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	304.23
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	271.62
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	252.07
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	250.21
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	224.28
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	192.93
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	185.84
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	114.85
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	96.48
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,093.96
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	888.49
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	827.72
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	782.55
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	753.53
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	753.34
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	698.65
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	603.75
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	563.51
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	500.62
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	479.02
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	457.35
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	410.59
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	339.72
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	262.79
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	197.44
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	587.34
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	528.59
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	528.43
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	507.71
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	487.63
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	431.85
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	398.42
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	372.25
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	352.48
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	347.33
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	325.15
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	314.20
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	283.08
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	262.49
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	237.01
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.00
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,830.08
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,725.11
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,470.95
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,219.23
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,173.63
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,120.73
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,091.11
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,069.47
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,060.02
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,044.64
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,000.45
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	840.50
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	690.56
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	654.07
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	156.09
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	102.74
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	161.84
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	87.37
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	86.20
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	72.29
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	67.80
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	57.62
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	49.09
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	39.59
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	36.21
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	29.25

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.