Gene detail

Detailed information of XP_068749987.1 in Montipora capricornis

Genomic Location: chr4:46728941...46732656
NR annotation: XP_029195178.2, probable pyridoxal 5'-phosphate synthase subunit PDX2 [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068893886.1

TTATGCAACATTACCACTGTTTGCAACATCCAACATGGAGGAGCCTCGAGCGAAATTGAGAATTGGTGTTTTGGCAATTCAAGGTGCCTTCTTTGAGCATAGAGCAGCGCTTACCAAAGCTCTGAACAACTCATCATTAAGCAAAGATTTTGATCTTGAAGTCAGGGATGTCAAAGAATCTTATCAACTGAACGATTTGAACGGACTTATTTTGCCTGGAGGGGAAAGTACAACGATGAGTTTGTTTCTTCAATCTAGTAAATTTGAGGACGTTTTGAAAAAATGGATAACTTCCAAAGAAAACCCTAAAGTTGTGTGGGGGACATGTGCAGGCCTTATTTTGCTGTCTAACAACATTGAAGGTCAAAAACAGGGAGGACAATCAAAGATTGGTGGCATTGATGTCACAACTTCCCGGAATTTTTTTGGGAGACAGGTAAACAGCTTTGAGGCCAAAGTCAAACTTCACAAGAAACTTCTCAATAACAGCAgtgcaataaataaatgcacAGACAGTCCTGATTCTATTGCTAGTTATCATGGAGTCTTCATTAGAGCTCCTGCAGTGGTATCTGTTGACAATCCCAAAGTTGAAATTCTTGCAACCATTGATTGGCTTGAAAGGGAAGAACCTGTCGTTGTAGGAGTCTCTCAGGACAACTTGATTGGAACTGCTTTTCATCCAGAGTTAACAGAGGATACAAGATGGCATGAGTATTTCTTGAGACAAATTGTAGAGAGGACCAACTGGGGAAATAATACTGGTGTTCCAAGGACATAATAATTATGAGATAACTTTCCTGGTGGTCTGACAAAGAGGTGGAGCTCTTTGACAGGCATTGACAATCACTAGGTAGAGAAAGACCAGCATTGATACTTTCtgtgctagcagaggtctcttgcAGAGAGAAGAAATTGTGTGAACCCAGACTCTGCTAACTGGGAAGCATAAATGCAAGCAGCATGCACAGACACATTAGGGAGTTAATGAAACAATCCGGgctacagcaacaacaacaccaaataGCAGTGATATTGTttgttaaaagaagaaaaatggtCATGATGCAGATGCGACatgcatttttgtacatttctctcccgtactcgtggAAGCAACAACTTAAAATTACCAATGTAATGGTTTTGATAACAACATAGGCATACAACAGTGAATTTTCGTACCAATTTAGttataggatacttcgcccaatgTAAACAACAGGGAATGATCACGAAATACTTAAGAGTATATTCTGAAGTCATGTTTTTGTCGATGTAGCCGTCATGGTTTCCTAATCTCCCTGTTAACTTGTTGACAGTGTTTTTTCTAAACAAACACTACTAATAATCAAGAAACTTTTGAGTTTGCATACGTTGTTTGTGCTTTTTAAGCTTTTGTTGCCATTGAAGAAACAATGCTAAGTTGTAGAGTGACCAAAGGCAATGGATTGGTTTAAATCTAGCCACGTTTTAAATGCAGCTATGCCCAGATGTTTGCTACAAATTCTTTTAAAATCAGCTTACATTGACAACATAGGTCAATCTAATAAAAGAGCTCTTAACCCAAGAGTGATTGATATATTACAAATTTTCCCCTCACAAGTTCAATACATCATTAAGCAGATTGGTGAcaagaagaaacaagtttaTCACCTGGgattttttaaatataataCAATGTATATAATCAAATCCCCATAACTGACGTAagaaataacttgtattgtggGCAGTAAGGAGAATTAGCATTCAAATCTTGGGAGTGAGAGGGTTATTGAGGAGTCCTAGGTCTGTTATGAATGCTGTTGGAACCATGGACAAGCCCGTAAACAATAAACCACCTGAACTTTGCTTGTGATACAGCTTCACAGGTTTCAAAGGACTTATTGCAAAGTGGTAAGCATTTTAATATGGAATGTTTGATTTTATATTCTGCATTATTTCTAAAATGTTTGCAATCATAACAGCCAATAACACTTTATTGATTCTGAAGCTGTGAAATCATTATTTCAGCTCGTGTGAGACATGGAGGGCTCAATTTTAAAAAGCCAGTTATTAACCATCAAAAACTGATCTGGGTGGAAAAGTGTTGATGattccatacattctttgtaaaatttcgaattttcaaagcatcatttctcagagattatctgggaTATCGCATTCGAATTTTCAGACATAGCTCATTATGCGAATTATGCACTTTCAacattcagtactttattcttggctgactgattagaacaTGATAGCCTAGTGCTAataaggcaaaaaatgtaacaaagatTGCACTATACCATAACTGGCATTCTGGAGTTGTCCAGTGTACTTGGTGGGAGTTTCAAAGTCCTTGTGAGAATATGTGGATAAGATTAAAATACTGCAAGAGAAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q54J48	Probable pyridoxal 5'-phosphate synthase subunit pdx2 OS=Dictyostelium discoideum OX=44689 GN=pdx2 PE=1 SV=1
Q8LAD0	Probable pyridoxal 5'-phosphate synthase subunit PDX2 OS=Arabidopsis thaliana OX=3702 GN=PDX2 PE=1 SV=1
Q8TH23	Pyridoxal 5'-phosphate synthase subunit PdxT OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) OX=186497 GN=pdxT PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009006 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01174 all species →	SNO	SNO glutamine amidotransferase family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002161 all species →	Family	Pyridoxal 5'-phosphate synthase subunit PdxT/SNO	Interproscan
IPR029062 all species →	Homologous_superfamily	Class I glutamine amidotransferase-like	Interproscan
IPR021196 all species →	Conserved_site	PdxT/SNO family, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR31559 all species →	PYRIDOXAL 5'-PHOSPHATE SYNTHASE SUBUNIT SNO	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004359 all species →	Molecular Function	glutaminase activity	Interproscan
GO:0042819 all species →	Biological Process	vitamin B6 biosynthetic process	Interproscan
GO:0042823 all species →	Biological Process	pyridoxal phosphate biosynthetic process	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0008614 all species →	Biological Process	pyridoxine metabolic process	Interproscan
GO:1903600 all species →	Cellular Component	glutaminase 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K08681	pdxT, pdx2; pyridoxal 5'-phosphate synthase pdxT subunit	EC:4.3.3.6	Vitamin B6 metabolism	ko00750	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of XP_068749987.1 across 36 RNA-seq samples of Montipora capricornis. 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.

36Samples

29TPM > 0

1Conditions

41.3Max TPM

23.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	29	23.04	41.25

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	41.25
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	36.15
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	34.99
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	34.07
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	33.74
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	32.16
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	31.33
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	31.18
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	31.15
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	30.71
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	30.55
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	30.37
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	30.32
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	30.20
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	30.19
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	29.07
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	29.03
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	27.84
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	26.96
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	26.71
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	26.12
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	25.00
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	24.91
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	24.57
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	22.06
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	21.26
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	20.88
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	20.12
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	16.67
SRR12807381	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12849113	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12927880	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR12963484	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9129316	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9613519	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00

Source: CnidoSite RNA-seq expression matrices (MCAPR_TPM, StringTie quantification over 36 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.