Gene detail

Detailed information of XP_068749983.1 in Montipora capricornis

Genomic Location: chr4:46714857...46728697
NR annotation: XP_020613680.1, pyridoxal 5'-phosphate synthase subunit SNZERR-like [Orbicella faveolata]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068893882.1

ATTTGAAGCTCTCATGACACGTGCGTAGTGAGTACAAACAGAGTAAGGAAAATTGTTGTGGCTCAGGGAGAGACAAGTGGAATTTCACAGCCATGTCTAGTATTGTTCCAGCACCGATAATAAACGGCATAGGTAACGGTGTAGAGTTGGAAGTGAGTAATCTATCTTTAGAAGGCAGGAAAGTAGAACAAGCCATCAAAGATGTTGCATCATCACACAAAACAGGAACTTTCAAGGTGAAAGCAGGACTGGCTCAAATGGCAAAAGGTGGAATTATAATGGATGTCACAACTGCAGAACAAGCGCGGGTGGCTGAGAAGGCTGGGGCCTGTGCTGTGATGTCATTGGAGAGAGTTCCCGCGGATATCCGTAAACAAGGAGGTGTAGCAAGAATGACAGATCCCAAGagaacaaaagagatcatGAATGCTGTCACTATACCTGTGATGGCAAAGGCCAGAATTGGTCATTTTGCCGAGGCACAGATCCTTGAGGCGATTGGTGTGGACATGATTGATGAATCAGAAGTGTTGACTCCAGCTGATGAGGCAAACCACATTGATAAACACAAGTTTACAGTTCCCTTTGTTTGTGGAGCAAGAGATCTTGGAGAAGCTCTAAGAAGAATTGCGGAAGGAGCAGCAATGATAAGAACAAAAGGACAGGCAGGGACAGgtgatgttgcTGAAGCCGTTCGGCATGCAAGAACAATACGCAATCAGATTCGCCATGCTCAATCACTGGACAAGGCCGAACTGTATACTTATGCCAAGGAGTTAAGAGTGCCCTTTGAGCTCCTTCAGAGGACAGCTGAGATGGGTAGATTGCCTGTTGTTAACTTTGCTGCTGGAGGTCTTGCCACCCCTGCTGATGTGGCACTTCTGATGCAGCTTGGCGTAGATGGTGTCTTTGTGGGATCAGGAATTTTTAAGAGTGACAATCCTGAGAAGAGGGCTTGGGCAATGGCACAAGCTGTGACTCATTGCAACAATCCCAAGAAACTTGCCGAACTTAGTGAGGACTTGGGGGAAGCTATGTTTGGAACAccagttagtgatgtcagatgCAAGTGATGCAGTGCACTAGACTCAACTAAGTACTACTTTGAAATTGAAAGATGACCGTTTCTCTCATAAACTGTCACAATATTGCTTAACACATGGGTCATCAACAATCCATCTACACTAGTATTTACTTAGAACTGCATCAATTTTATACTTTCAATTCGTCTAGAAATGTTTGTTGTGTAACTGTAGAGGGGAAATTCAATGTAAAAGTAGAAATTTTTCCAGGAAGAATTGGGGAACAATTTGGGTCCAAGAAGGTATCCCTtgtgaaatattgtttttttgcaattttaataCCAAGTCTGTGTGCAAATCTGTCTTTGGACACTTCAGTATGAATTTAAACACAAAATGGGTTGAAAAGGTTGTGATTTATAGACTGCTGGCAGCCCTTTTCTGGATAGTTGAGAAGGAGTGAAAAAATCTGAAAGTGCACAGCACAGCAAGACTGGAGCAAtaggagaaaaagaaagagaagagactGGAACAAAGCCCCCTGTGCttgtttttggctttttcaTTCACTTATCATTTATCCAGAAGCTGAAGTATTTGCGGTTCATAGTACTTAGCCTTAAAAGGTATACTGTGAGAATCATCGACATTGGCTGGTGTAAGtttaccttattacatgaaattttggcGACACGTTAATTTAGCGATTTTGAAAAATCAGGATTTAGCGACACCTTCATTTAGCGATTTTTCGTAAATTTTGGAACATAAGTCACTTAATTTTTGCGATTTTGTAAGCTGAAACTTTCTGGCGAATTAAGGTATTCAAAACTTTTGCGACGACAATAGaacattaaaattattaatCGTTTGTGTCATGATGTAGTTACTTGGCGATTCatatcacaagtgaccacatcgtgagacaaacgataataccttgattattattattgtactttaccACGATGAACAAACACAATTTTTCTTACgaaatagaaaatttatttGATAAAATCATAAACGTCAATgggttcattaaaaaaaaaatcgtaaaaaaaatcatacaacGTTATAAAacttaacaaaacaaataaaactgcAACTATAATGTCATATCTTCAGCTTCATGCTGTCCTCACTCATATTTACATTATCACACAGAGTCAATGCTCCTTTTACGAGTACCTAGCCATTAACTTTCTAAAAACACCGATCAAGACAGGTCGATTTCTTCAAATCGATCAACAGGTGGTAGTGGTTTGTCGCTGTTGGCAATTTCCTTGACTCCCGCTTTCTCCCATCCCTTGAGGATACATCTCCTTCCTGGAGACTGGTGTAAGCCGACTAACAGTTTCTCTTATTGCAGCAACTGCGTACCAGTCGTGCGGATTATTTTCCTGGTGAATTGTGTCAAGCTTTTCATTTAGTCTAGGATTCCACAGCTCTTTTTAAACGTGGAAACCCCCTAGTCCACATGGGAAAGCGAGATTTAATGCGAGCGAAGAATCCATTTCAGTTGTGAAGCTGAAATGTATTCAGTAGACATCCGATACAAGTCAAAATCGACCGTAAATAGCGTGATCTTGTGAAACGGACCAGATGGCGGAATTTCCCATTGGAGTCACTTTAATTTAGCGACGATTTAAAGTTAGCGACACttaattttggtacattttAATTTAGCGATATTTTGTGTCgccaaaatttcatgtaataaggtacctTGCACCGTAAATTATCTGTTAAATGAATATAACAGTCATGACATAACCTCTCtcatagataaataaataatgaactttgtttaa

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8WPW2	Pyridoxal 5'-phosphate synthase subunit SNZERR OS=Suberites domuncula OX=55567 GN=SNZERR PE=2 SV=2
O14027	Probable pyridoxal 5'-phosphate synthase subunit PDX1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=snz1 PE=1 SV=1
Q54J47	Probable pyridoxal 5'-phosphate synthase subunit pdx1 OS=Dictyostelium discoideum OX=44689 GN=pdx1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006294 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01680 all species →	SOR_SNZ	SOR/SNZ family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001852 all species →	Family	Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ	Interproscan
IPR011060 all species →	Homologous_superfamily	Ribulose-phosphate binding barrel	Interproscan
IPR033755 all species →	Domain	PdxS/SNZ N-terminal domain	Interproscan
IPR013785 all species →	Homologous_superfamily	Aldolase-type TIM barrel	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR31829 all species →	PYRIDOXAL 5'-PHOSPHATE SYNTHASE SUBUNIT SNZ1-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0042819 all species →	Biological Process	vitamin B6 biosynthetic process	Interproscan
GO:0042823 all species →	Biological Process	pyridoxal phosphate biosynthetic process	Interproscan
GO:0006520 all species →	Biological Process	amino acid metabolic process	Interproscan
GO:0008615 all species →	Biological Process	pyridoxine biosynthetic process	Interproscan
GO:0016843 all species →	Molecular Function	amine-lyase 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
K06215	pdxS, pdx1; pyridoxal 5'-phosphate synthase pdxS 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_068749983.1 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

30TPM > 0

1Conditions

63.6Max TPM

30.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	30	30.06	63.58

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	63.58
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	60.82
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	59.34
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	58.45
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	52.31
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	51.93
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	48.80
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	47.18
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	46.17
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	44.68
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	43.86
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	40.64
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	40.46
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	40.18
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	40.13
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	39.00
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	37.61
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	27.25
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	26.04
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	25.33
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	24.74
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	23.46
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	23.42
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	22.27
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	20.08
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	19.79
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	19.08
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	12.97
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	11.52
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	10.92
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
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.

Co-expression network

Genes whose expression across the transcriptome samples of Montipora capricornis tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

Direction	Partners	Most correlated partner	PCC
Positively correlated	24	XP_068717719.1	0.943435856457727
Negatively correlated	3	XP_068724527.1	-0.463595266198177

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Montipora capricornis, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	ready	open →
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →