Gene detail

Detailed information of PFX35004.1 in Stylophora pistillata

Genomic Location: Spis.scaffold1:573091...581780
NR annotation: no NCBI-NR hit recorded
Species Stylophora pistillata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-Spis44_mrna

cgagacgtgagcttgggacatCTGTGTTGTGATCGTAGATAGTTTCCTCTCGTGTAGGGCTGTTAGTGTTATCCGTCACTGTGCTagatatttctttaaataacAAACAGTAAAGAGGAGTTATATTATTTTTAGGACTATAATGAGTACATGTGGTGATGGTGTTCATCACATTTTGCTTCGCGCCGAGACAAAACCAAATGAGCAGCGGAGAGCTCTAACCCCCGATAAATGCCAGGAGTTAATTGAAAAAGgttttcaagTTTCTGTAGAATATTCTGACCAGTCAGCCTTCAAGAATGAGGAATATCAGTGCATACCAGGAATCAGTATGGTCCAAGCTGGATCTTGGGTCCATGTTCCGAATGATGTTATAATTTTGGGACTAAAAGAGCTTCCTCAGTCTGATGAACCAGTATCTCATAGACACATCTACTTTGCTCATGCTTATAAGAATCAGACAGGTTGGGCAACTTTACTCCATCGTTTTATTAAGGGAGGGGGCAGCATTTTAGACATTGAATTTATGACAGATGTAGAAGgtaGGAGAGTTGTGGCAGAATTTAGTGGAATGGCCGGACTTGTTGGAATGGGACTGGGAATACTTGCTTGGTGCCATCAACAGTTGAGTTCTGATAAGCCAATGGGTGAGGTGAAACCATATGGTAATGAAGCAGCTTTCATTGATCACATAGCACTACAAATCAAACAAGTTGCTGAATTAAAAGGTGTTCAAAAAGTTTTCCCTCTGATAATGGTGATTGGTGCCTTGGGTCGCTGTGGAAGAGGAGCATCAGAGATTGCCCATAAACTGGGTATTCCAAAGTCTTCTATAGCAGAATGGGACATGGAAGAAACAAAGGCTGGAGGGCCATTTGAGGAGATACTAAACTATGATATTCTTATTAGTTGTATTCTCCTAACAGAGAAAATTCCACCATTTCTCACAAAGGAAATGTTAGAGAGAGAAGACAGGAACCTGAGTGTGGTGGTTGATGTGAGCTGTGATCCTAATAATCCATACAACCCTTTGCCTTTCTACCATGCAACAACTTCATTTGATAAGCCCTGTGACAGAATAAGGCTTAGatCTGCTAAGAAACTTGATGTCATAGCTATAGATCACTTGCCTTCTGCTTTACCCCGTGAAAGTAGTCAGAGATTTGCCAATAAGATGACACCTTATTTGCTGAGATTAAGCGATGATCCTGTTTGGAACAGAACCAAGAACATGTTTGATAAAAAAGCTATGGAAGCAATGGCAATTTTGAATTCTGGCTTCCTTCATTGACATTAAGGGAATCTTGACATACTTTCCACTAAATGATTAGAGATTACTTTACAGTTTTAAAACCATTAATATTTAGCAGACTCATGTTAAGACGTGATGTGcacttgcaattttttaaattgaaattgatcctgaaatattttcatttcatgaAGCATCTTTAACCACCCCTGGTGGAGTAAAATGAAAGGGATGAGAAGTTTGTTTTAGGTTGtatcaaattaatttcatcaaTTATATGACTGGTCCATGCAGTTGTCTTCAGGTGAATGTTTGACATTTGATTTGAGCATAAGCTTCAAGCCAATAATATCACTACTCTACTTGAATGTTATTAACATCttatttgaaacaaattgtATTCATCACATATGGAGGACCACTTATCTATTAACTGAATATTTTATATATGTTGGAgtaaattaagttatttttatctgtCACGTTGCTGTGCAAAGAACGCTTTACAACTTTatatgacctttttttttcttaaaatgcaGCTTTGTGTCGTTTTGATTACGTGATtataaaatatccttttttgGCTAGCTGCACAaagagttgtttcagtttagtttccttTACATCATAGAAGTATATTAGGCATTTTTTCACgcaaacattttagttttaaggaGTTGTCCCTGGAGTAAAGAGGAGTTTTATAGGAGTctttcagagtttttttttacaacttggAGTTTTCTCATACCCAGAGTCAAGATCAAACGTAACTCACGATTGTCAGTTGTGTTTTCTGTTGTCAGATTTGTAGTTTAGCTTGTTTCCTTAGCTTAGACAAATCG

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001866 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05222 all species →	AlaDh_PNT_N	Alanine dehydrogenase/PNT, N-terminal domain	Domain	Interproscan
PF01262 all species →	AlaDh_PNT_C	Alanine dehydrogenase/PNT, C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007698 all species →	Domain	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain	Interproscan
IPR007886 all species →	Domain	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal	Interproscan
IPR027281 all species →	Family	Saccharopine dehydrogenase [NAD(+), L-lysine-forming]	Interproscan
IPR051168 all species →	Family	Alpha-aminoadipic semialdehyde synthase	Interproscan
IPR036291 all species →	Homologous_superfamily	NAD(P)-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11133 all species →	SACCHAROPINE DEHYDROGENASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004754 all species →	Molecular Function	saccharopine dehydrogenase (NAD+, L-lysine-forming) activity	Interproscan
GO:0009085 all species →	Biological Process	lysine biosynthetic process	Interproscan
GO:0004753 all species →	Molecular Function	saccharopine dehydrogenase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0019878 all species →	Biological Process	lysine biosynthetic process via aminoadipic acid	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
K00290	LYS1; saccharopine dehydrogenase (NAD+, L-lysine forming)	EC:1.5.1.7	Lysine degradation	ko00310	deepkoala

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

Co-expression network

Genes whose expression across the transcriptome samples of Stylophora pistillata 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.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Stylophora pistillata, 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.

Dataset	Tissue / stage	Cells	Cell types	This gene	Marker of
SPIST_whole_adult	Whole adults · Adult tissues/organs	13,896	25	not in this dataset	–

A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.

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.	no expression matrix	–
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 →