Gene detail

Detailed information of OS493_034780-T1 in Lophelia pertusa

Genomic Location: scaffold_299:143399...148624
NR annotation: KAJ7351875.1, Enzyme that catalyzes the fourth step in the histidine pathway [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
Q6C2U0	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase OS=Yarrowia lipolytica (strain CLIB 122 / E 150) OX=284591 GN=HIS6 PE=3 SV=1
Q10184	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=SPAC3F10.09 PE=3 SV=1
Q7RXQ8	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) OX=367110 GN=his-7 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0013199 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00977 all species →	His_biosynth	Histidine biosynthesis protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013785 all species →	Homologous_superfamily	Aldolase-type TIM barrel	Interproscan
IPR006062 all species →	Family	Histidine biosynthesis protein	Interproscan
IPR044524 all species →	Family	Histidine biosynthesis, HisA-like	Interproscan
IPR011858 all species →	Family	His6-like, eukaryotic-type	Interproscan
IPR011060 all species →	Homologous_superfamily	Ribulose-phosphate binding barrel	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43090 all species →	1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO)METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000105 all species →	Biological Process	L-histidine biosynthetic process	Interproscan
GO:0000162 all species →	Biological Process	tryptophan biosynthetic process	Interproscan
GO:0003949 all species →	Molecular Function	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	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
K01814	hisA; phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase	EC:5.3.1.16	Histidine metabolism	ko00340	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_034780-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

19.8Max TPM

7.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.13	19.76
polyp at pH7 6	18	17	9.16	16.80
coral polyp · control treatment	16	16	9.11	13.23
coral polyp · oil and dispersant treatment	16	16	5.31	8.06
coral polyp · oil treatment	16	16	8.38	12.24
coral polyp · dispersant treatment	16	16	5.47	10.14
Polyp	10	10	10.11	19.72

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.76
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.24
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.85
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.51
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.50
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.69
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.64
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.87
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.66
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.60
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.60
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.57
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.51
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.49
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.94
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.86
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.61
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.38
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.80
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.68
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.79
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.70
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.16
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.57
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.21
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.16
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.07
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.55
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.28
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.19
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.18
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.94
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.93
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.76
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.89
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.23
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.67
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.90
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.77
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.51
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.22
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.14
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.83
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.48
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.31
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.16
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.75
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.38
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.76
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.74
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.96
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.06
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.40
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.33
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.19
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.90
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.86
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.74
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.55
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.37
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.15
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.69
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.57
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.19
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.05
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.25
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.60
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.24
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.06
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.30
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.28
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.23
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.18
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.01
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.34
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.04
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.37
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.85
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.78
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.52
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.64
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.29
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.97
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.14
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.04
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.99
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.27
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.68
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.32
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.94
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.54
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.50
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.61
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.57
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.56
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.57
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.78
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.83
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.13
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	19.72
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	16.34
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	14.83
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	10.11
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.99
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.97
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	7.59
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	5.96
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.14
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.48

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.