Gene detail

Detailed information of OS493_020178-T1 in Lophelia pertusa

Genomic Location: scaffold_73:1528125...1528649
NR annotation: KAJ7391148.1, Homeobox protein tgif1 [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
Q90655	Homeobox protein AKR OS=Gallus gallus OX=9031 PE=2 SV=1
P70284	Homeobox protein TGIF1 OS=Mus musculus OX=10090 GN=Tgif1 PE=1 SV=2
Q9GZN2	Homeobox protein TGIF2 OS=Homo sapiens OX=9606 GN=TGIF2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0010026 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05920 all species →	Homeobox_KN	Homeobox KN domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR008422 all species →	Domain	Homeobox KN domain	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR050224 all species →	Family	Three Amino acid Loop Extension (TALE) homeobox	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11850 all species →	HOMEOBOX PROTEIN TRANSCRIPTION FACTORS	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	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_020178-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_020178-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

37.2Max TPM

11.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	21.34	28.77
polyp at pH7 6	18	18	18.50	28.69
coral polyp · control treatment	16	16	9.51	12.97
coral polyp · oil and dispersant treatment	16	15	4.90	8.37
coral polyp · oil treatment	16	16	9.10	15.97
coral polyp · dispersant treatment	16	16	4.00	9.19
Polyp	10	10	13.01	37.17

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	-	28.77
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.75
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.06
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.11
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.77
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.50
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.74
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.01
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.07
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.76
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.52
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.22
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.15
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.91
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.90
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.27
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.28
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.34
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.69
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.57
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.04
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.69
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.29
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.19
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.18
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.16
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.79
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.64
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.52
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.44
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.13
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.87
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.64
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.46
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.44
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.33
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.97
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.68
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.37
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.10
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.42
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.99
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.87
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.50
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.31
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.34
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.28
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.26
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.69
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.32
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.40
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.71
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.37
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.13
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.09
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.67
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.37
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.38
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.08
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.89
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.82
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.78
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.71
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.05
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.84
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.02
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.15
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.97
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.40
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.04
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.01
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.69
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.25
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.84
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.24
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.96
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.80
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.18
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.05
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.52
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.50
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.92
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.19
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.19
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.35
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.85
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.81
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.35
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.23
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.50
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.46
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.23
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.10
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.05
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.55
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.50
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.17
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.97
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.64
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	37.17
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	17.65
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	14.75
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	14.26
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	13.49
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	11.55
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.95
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.06
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.90
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.36

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.