Gene detail

Detailed information of OS493_027326-T1 in Lophelia pertusa

Genomic Location: scaffold_148:284903...291546
NR annotation: KAJ7371212.1, embryonic hindlimb morphogenesis [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
P51826	AF4/FMR2 family member 3 OS=Homo sapiens OX=9606 GN=AFF3 PE=1 SV=3
P51827	AF4/FMR2 family member 3 OS=Mus musculus OX=10090 GN=Aff3 PE=1 SV=2
Q9UHB7	AF4/FMR2 family member 4 OS=Homo sapiens OX=9606 GN=AFF4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004121 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18876 all species →	AFF4_CHD	AFF4, C-terminal homology domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007797 all species →	Family	AF4/FMR2 family	Interproscan
IPR043640 all species →	Domain	AF4/FMR2, C-terminal homology domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10528 all species →	AF4/FMR2 FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0010468 all species →	Biological Process	regulation of gene expression	Interproscan
GO:0032783 all species →	Cellular Component	super elongation complex	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	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
K15185	AFF4; AF4/FMR2 family member 4	-	Transcription machinery	ko03021	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_027326-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

91.0Max TPM

40.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	28.18	44.40
polyp at pH7 6	18	18	29.16	43.88
coral polyp · control treatment	16	16	46.69	75.19
coral polyp · oil and dispersant treatment	16	16	52.67	86.56
coral polyp · oil treatment	16	16	47.60	83.49
coral polyp · dispersant treatment	16	16	58.46	90.96
Polyp	10	10	12.73	19.82

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	-	44.40
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.44
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.64
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.27
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.87
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.30
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.85
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.18
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.73
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.70
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.69
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.45
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.34
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.05
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.24
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.13
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.99
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.98
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.88
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.18
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.32
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.55
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.49
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.69
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.37
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.07
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.36
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.74
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.65
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.57
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.95
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.20
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.23
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.76
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.50
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.31
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	75.19
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.53
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.67
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.19
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.03
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.41
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.36
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.29
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.86
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.51
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.95
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.49
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.20
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.93
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.66
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.71
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	86.56
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.80
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.42
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	65.48
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.56
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.80
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.93
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.60
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.90
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.76
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.37
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.38
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.06
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.41
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.32
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.35
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.49
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	60.91
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	60.42
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.76
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.69
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.19
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.51
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.96
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.69
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.55
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.35
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.24
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.16
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.13
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.68
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.93
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	90.96
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	77.54
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.87
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.50
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.46
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.76
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.06
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.37
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.70
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.86
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.94
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.86
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.45
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.86
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.30
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.87
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	19.82
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	17.18
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	16.94
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	16.85
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	13.08
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.97
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	11.06
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.17
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	6.68
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.53

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.