Gene detail

Detailed information of FUN_035034-T1 in Siderastrea siderea

Genomic Location: contig_39:170602...179391
NR annotation: no NCBI-NR hit recorded
Species Siderastrea siderea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

FUN_035034-T1

Transcript

FUN_035034-T1

ATGATCATTCCCTGTTTGTATTTAAAACAGGGAAGCCTTGTAGACCCAAGCAATGGACAAAGCGTCAAAGATGTGCCTTCATACCTTGAGAAAGTCTCACTGTGCCCAGAATTTGCCATGGTGTTCTTGGATACGGAGAAAGAGACCAAAGAATTTGGAAGGAAACTTGTCGATATCGGGTCCTGTTGTGTTGAATGTGAAGCTGGGAATGAAGACGAGCTGATCAATTTGTTGGACAGCGGTGTAAATCGTGTTATCATTCGCAAAGATCGTCTAACTGGTTTTTCCGAATTTATATCTAAAGAGAGAATAACTTGCCAATTGTCAGGGGCAGAAAACCCCATTGAAGAGTTGACAAGGGAGATCAGCAGCATAAGAGAGAGAACCTCCTGTTTTCTGTTGCCCATGGACATTTCTAAAGTAGATGAACAGTCACTTGTTGAGTTtgcaaaggaaataaaaaacatatgCGGTGATGCCAGACTCATATTGTCTGTTAATTTGTGTGAGGTGATTTCATACACTTCAATTTCAAAGCTCCACAGTCTTGGAATTGACGTGCAGATAAGTGCAAAGCGTCTATCAAATGAGCTTAGCCTTGGACAGATCATTTCATCATGTCTCAAAAGTGACCGCCCTGATGGACTGTTTCCCACCCTAGTGACTGATGAGCACAATGTGGCTTTAGGCCTGTGTTACTCCAGCATTGAAAGCATTCAAGAAGCAGTAAACACCAAAAAGGGTGTTTATTTCTCTAGAACAAGAGGATTGTGGAGGAAGGGGCTGACGTCAGGAAATGAACAGGATTTGTTGAAGGTTTATTTAGACTGCGATTCTGACACACTAAAGTTTGTAGTGCGACAACAAGGTCAAGGCTTCTGCCATCTAGACACTTGGACTTGCTTTGGAGAAAGTGGCAGATTACCCTCACTCATGAGAACGTTAATATCACGGAAACAGTCGGCACCTCCTGGATCCTACACTGATCGCCTTTACAAAGACAGTAAGCTGCTGCATGCGAAGATTCGTGAGGAGGCAGAGGAACTGTGTGAAGCAGAAAGTAAAGAACACATTGCAACAGAAGCAGCTGATGTGCTGTATTTTAGTTTAGTAAAGTGTGCAAAAGCAGgagtTTCTTTGACTGATATTGAGAAAGTGCTTGATCAAAGGTCACTCAAAGTCAGACGTCGTCCTGGCAATGCAAAGCCTGGCAAACTCTCTCACTGCAATGGTGATTCAGTTAACATAGCAAACAAACCTGCCACTCCTCAAACCCACCCTCAGGATGCCATCTCCGACTCAATTTTGAAGAGCTATGATTTTCAGACACTTGGTGAAAAAGAATTACAAGGTCTTTGCAAACGTCCAGCAGTGGTTGATTCAGCAAAGCTGGAGTCTATTGTGAGACCTATCTTGGCAAATGTGCAAACCAATGGAGACAAGGCTTTGTTGGAATTGACAGAAAAATTTgataaagccaaactggacaGTCCTGTCATTGATGTTTCAGAAATAAATGAACCAGTTCTGGACAATGAAGTGCAGAATGCAATTGACTTGGCTTACAACAACATCTACAAGTTTCACAAAGCACAGTTGAACCCAGAACCTCTTGTTGTGGAAACTTGTAAGGGTGTGGTTTGTTCACGTCATGTTAGAGCTATTGAGAAAGTGGGCCTTTATGTACCTGGAGGAAGTGCAGTGTTACCGTCCACAGCTCTGATGCTTGGTATTCCAGCTCAGGTTGCAGAATGTGCAGAGATCATCCTGGCCACACCTCCTAAACAAGATGGCTCAGTTTCTCCAGAAATACTTTACATTGCAAAGAAAGTTGGAGTGTCCAAAATATTACTTGCAGGTGGAGCTCAGGCAGTTGCAGCAATGGCATATGGAACTGAAAGCGTACCCAAGGTGGACAAGCTGTGTGGCCCTGGAAACTCATTTGTTACCATGGCAAAAATGTTGGTACAAAATGACAGTTCAGCATGTGTCAGTATTGATATGCCAGCAGGACCATCAGAAGTTATGGTAATAGCTGATGACAGTGCAGATCCTTCATATGTTGCAGCTGATTTGTTATCCCAAGCAGAACATGGTCCTGACAGTCAAGTGGTTTTAGTTGCTGTAAATTTGACTGACAAACAACTTGAGAATATTCAGAGTGAAGTGGAAAGTCAAGTAGAGAGACTTCCTCGTGAAAAGATTGCTAGAGAAGCTTTGTCAAAAAGCTTTGTGATCAAAGTACCATCCATGAGGGAGGCATTGTACTTCAGCAACAAGTATGCTCCAGAACATCTAATCATTAACACACAGAATGCTGAAGATTGTTTGAAAGATGTACATCATGCAGGTTCAGTGTTCCTTGGTCCTTATTCTTCAGAGAGCTGTGGAGATTATGCCAGTGGCACAAACCACACCCTCCCGACATATGGCTATGCGCGCATGTATAGTGGCGTATCCACAGCAACATTCCAGAAACACATTACAGCCCAGCGCATTTCCAAGGAGGGATTGGCCAACATTGGCCCAGCAGTGGCAACACTTGCCGCTGTAGAAGAGTTAGATGCTCATCGCAATGCAGTATTAATTAGGCAGGGACAATTAAACTGATGTAATTCGTGGGTAGTTGAGGAAGGAAGGCTTTAACTCAGCCTAGGAAATAATTAATACGAATTGAGAAATGCTTTAGTTAGATTTGCATCAAATAATTTGGTGAATTTCTGTGACCTTAACCGATTTGCAAAGCAATTATGAATTTCTATCGTTTTCACAAAAAAACAGTATTATTTGCATAAAATGCTAGCCACGTTACTCTTATATGTGATGCTTTCCAAAGTAAAGCACATTTGGATATAATTGAAAATTAATATGAGGTTTCATATTAAGGTATTCATATCTGGAGATAATGTATACAAAACCACCAGCATGTACGCATGGCCACAATAAGAAAATAATGTCGTAATTTAGTTTCAAACATTACATGTTTTGTCATAGAACATTTGAAGATTAGCTGGGCATTACGTGAAATTAGCTGTTTGTTATGAAGTTTAGATGACAGTGTGCTTAACTGTAGTTAAGTTTAAATCTTGTTAGTGTTTGAATAAATGTAACCCAATGGAAAACGTGTCTGAAAGCAAACTCGTTTCTGATCAACACTCAACGTTTGCGAAAGTTCGCCTAAATTCAAACTTCAAATGTTCGATGACAAAACATGCCATTTTTTTGGTGAAGTGGACGTGCTCGGATAAAAACGATACATGCACTTAGTGTAAATCTAATTATTAATAGTCTCCTGCCAGAATTAAATGAGACAATTTCGGTGGGGTGCTTTGGTCatattttcaaacaataatAAACGGAAAATAACGACCTCAAAAGTAACTTGACCTTTCTATTCGAAAAGCCCTGTATAGCTGCTTCTGTGAGTACATTTGTAGAACGGTCAAAGAGTGGTTTCTTTAAGGGAACCTTGCAGAAGAGGTAGAAGCGTAGAGCTCTTTGAAAACTTCTACGCATgtgttagcctgttccaggctctgaGATAGTtgggaaagcgtgaattgagaaaacgagAGCGAAAAACGCGTGGAGGCTGCCCCCATTgtccagatcccgcgcgtcttattttcgcgttccctttctaattttcgtgccgttccaactatctgagagcctcgAACAGGCTACGCATATGTTTGACTTTCTCGCGTCGCCTTCATAAGAAAGTGCGAGACACTAAAGTCTGCGCGTGTACGAGCGCGCGAGAAAAGggtctggcacccagggtacaTTTGGTACTGTTCGAATCAAATGAATTGGCCCAAATATGGTACACCTTTTTTAACCAAACGAGCGAGCCCCTGAAAGTAACAATACAAAGAGGTTGTTAATTCTAAAAGCAATGAGAATTGTTACCGTCGGTCTTAAATTTTAAAACGGAGTTAACTTAAATATCTCCTAACTCTTGCTTACACACGAAATGAAAGTTATATTTCATATTCTTGTAGCTCCAAGTTGAGAGATTTTTAGTGTTAACTCTGtgtattcttattttaaaataaagtaaatcTCGC

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0012135 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00815 all species →	Histidinol_dh	Histidinol dehydrogenase	Family	Interproscan
PF01502 all species →	PRA-CH	Phosphoribosyl-AMP cyclohydrolase	Family	Interproscan
PF01503 all species →	PRA-PH	Phosphoribosyl-ATP pyrophosphohydrolase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012131 all species →	Family	Histidinol dehydrogenase	Interproscan
IPR008179 all species →	Family	Phosphoribosyl-ATP pyrophosphohydrolase	Interproscan
IPR038019 all species →	Homologous_superfamily	Phosphoribosyl-AMP cyclohydrolase domain superfamily	Interproscan
IPR016161 all species →	Homologous_superfamily	Aldehyde/histidinol dehydrogenase	Interproscan
IPR002496 all species →	Domain	Phosphoribosyl-AMP cyclohydrolase domain	Interproscan
IPR016298 all species →	Family	Histidine biosynthesis trifunctional-protein	Interproscan
IPR001692 all species →	Conserved_site	Histidinol dehydrogenase, conserved site	Interproscan
IPR021130 all species →	Family	Phosphoribosyl-ATP pyrophosphohydrolase-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21256 all species →	HISTIDINOL DEHYDROGENASE HDH	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000105 all species →	Biological Process	L-histidine biosynthetic process	Interproscan
GO:0004399 all species →	Molecular Function	histidinol dehydrogenase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0016616 all species →	Molecular Function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Interproscan
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0051287 all species →	Molecular Function	NAD binding	Interproscan
GO:0004636 all species →	Molecular Function	phosphoribosyl-ATP diphosphatase activity	Interproscan
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0004635 all species →	Molecular Function	phosphoribosyl-AMP cyclohydrolase activity	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
K14152	HIS4; phosphoribosyl-ATP pyrophosphohydrolase / phosphoribosyl-AMP cyclohydrolase / histidinol dehydrogenase	EC:3.6.1.31 EC:3.5.4.19 EC:1.1.1.23	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 FUN_035034-T1 across 85 RNA-seq samples of Siderastrea siderea. 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.

85Samples

71TPM > 0

7Conditions

606.5Max TPM

214.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	18	287.62	541.02
holobiont · low.pH Control.temp	20	16	197.71	606.49
holobiont · control.pH_high.temp	20	17	239.93	578.25
holobiont · control.pH Control.temp	19	14	193.36	553.02
Whole organism	4	4	14.12	15.56
unannotated	1	1	11.46	11.46
live coral tissue/skeleton	1	1	13.56	13.56

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	541.02
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	418.16
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	415.97
SRR22214403	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	413.18
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	408.34
SRR22214416	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	405.98
SRR22214418	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	352.34
SRR22214421	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	346.88
SRR22214419	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	340.85
SRR22214414	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	327.65
SRR22214417	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	297.33
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	286.71
SRR22214405	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	274.62
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	261.32
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	191.00
SRR22214406	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	176.42
SRR22214415	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	149.66
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	145.05
SRR22214409	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214420	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214439	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	606.49
SRR22214430	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	549.99
SRR22214435	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	439.17
SRR22214429	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	312.09
SRR22214438	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	296.86
SRR22214428	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	229.52
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	222.91
SRR22214440	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	219.76
SRR22214441	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	213.19
SRR22214443	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	186.78
SRR22214427	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	186.03
SRR22214425	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	134.50
SRR22214434	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	105.62
SRR22214437	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	101.52
SRR22214424	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	94.66
SRR22214426	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	55.14
SRR22214431	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214432	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214445	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	578.25
SRR22214457	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	569.66
SRR22214456	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	367.88
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	345.60
SRR22214447	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	327.18
SRR22214461	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	306.82
SRR22214453	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	270.26
SRR22214452	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	269.83
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	244.84
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	240.63
SRR22214448	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	227.01
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	223.86
SRR22214467	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	210.02
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	181.31
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	166.52
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	146.74
SRR22214450	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	122.09
SRR22214449	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214451	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	553.02
SRR22214444	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	405.94
SRR22214547	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	334.15
SRR22214469	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	321.31
SRR22214492	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	315.00
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	274.71
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	262.60
SRR22214481	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	245.73
SRR22214422	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	195.01
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	190.48
SRR22214548	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	188.59
SRR22214470	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	175.08
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	169.27
SRR22214455	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	42.85
SRR22214433	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214466	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214524	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214535	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214546	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	15.56
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	15.12
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	14.09
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	11.72
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	11.46
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	13.56

Source: CnidoSite RNA-seq expression matrices (SSIDE_TPM, StringTie quantification over 85 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.