Gene detail

Detailed information of OS493_023161-T1 in Lophelia pertusa

Genomic Location: scaffold_100:1059176...1062755
NR annotation: KAJ7371820.1, Host cell factor 1 [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
D3ZN95	Host cell factor 1 OS=Rattus norvegicus OX=10116 GN=Hcfc1 PE=1 SV=1
Q61191	Host cell factor 1 OS=Mus musculus OX=10090 GN=Hcfc1 PE=1 SV=2
P51611	Host cell factor 1 OS=Mesocricetus auratus OX=10036 GN=HCFC1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004526 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_023161-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR003961 all species →	Domain	Fibronectin type III	Interproscan
IPR043536 all species →	Family	Host cell factor	Interproscan
IPR036116 all species →	Homologous_superfamily	Fibronectin type III superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46003 all species →	HOST CELL FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003713 all species →	Molecular Function	transcription coactivator activity	Interproscan
GO:0006338 all species →	Biological Process	chromatin remodeling	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0035097 all species →	Cellular Component	histone methyltransferase 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_023161-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_023161-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

56.4Max TPM

19.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	17.60	24.60
polyp at pH7 6	18	18	17.05	21.87
coral polyp · control treatment	16	16	27.62	56.42
coral polyp · oil and dispersant treatment	16	16	22.10	52.63
coral polyp · oil treatment	16	16	22.57	36.70
coral polyp · dispersant treatment	16	16	13.39	26.97
Polyp	10	10	9.57	16.29

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.60
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.96
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.90
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.35
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.14
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.67
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.59
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.21
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.11
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.26
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.03
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.53
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.66
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.96
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.59
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.16
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.05
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.98
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.87
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.40
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.54
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.79
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.40
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.90
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.19
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.65
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.57
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.79
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.50
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.26
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.06
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.95
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.88
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.18
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.70
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.34
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.42
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.66
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.73
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.11
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.64
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.86
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.67
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.54
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.03
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.55
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.61
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.96
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.99
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.04
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.94
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.24
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.63
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.25
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.33
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.29
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.73
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.96
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.68
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.09
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.24
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.20
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.93
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.02
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.22
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.61
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.48
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.01
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.70
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.80
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.52
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.15
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.36
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.62
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.99
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.55
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.25
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.87
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.77
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.53
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.30
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.61
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.03
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.07
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.97
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.91
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.97
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.40
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.65
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.80
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.49
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.66
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.28
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.09
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.54
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.17
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.47
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.83
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.31
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.63
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	16.29
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	14.16
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.87
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	10.05
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.70
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.85
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.43
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	6.95
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.59
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.79

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.