Gene detail

Detailed information of amic_s0054.g2.t1 in Acropora microphthalma

Genomic Location: sc0000054_pilon:37466...52189
NR annotation: XP_029203767.2, phosphoserine aminotransferase-like isoform X2 [Acropora millepora]
Species Acropora microphthalma · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

amic_s0054.g2.t1

TTTGGTTTTTTGGAAAAGTCTGAATCTTGGAATCGGATGATGCCTATTAGCGAAAAGGCTTACTTAATCTCTGTAAGGACCAACTGGAAACATTGCCGTTGAACGGACGGGaagaacttaaaaaagaaaaacgaaagaaaagagaaagTTATTCGTACCATAGAGATCGTACTGGTACATTTTCACTATTTTACTTAATGTAGAAATGAGCCATAGATCAGCACACTTTGCAAAAATTGTAAACGAGGCAGAGAGTGACCTCAGAGAACTTCTTGGTATTCCAGACAACTATAAGGTTCTATTTTTACAAGGAGGCGGGACGGGAGAGTTTGCGGCAGTGCCGTTAAACTTAGCCAGAGAGGGAAAATCCGCAGATTACATTATCACCGGAGCCTGGTCGGCAAAAGCAGCAAAAGAGGCAGAGAAATTCACTAAAGTAAAGCCTGTTTTAAAGAAGCTTGACAAATATGACAGAATTCCTCCACAGAGTGAATGGAATTTAGATCCAAATGCTTCATATGTGTATTACTGTGCCAACGAGACAGTTCATGGTGTGGAGTTTGATTTTGTCCCAGAGACAAATGGCATTCCTCTTGTTTGTGATATGTCTTCAACATTCTTGTCAAGACCTGTCGATGTCAGCAAATTTGGTCTGATATATGCTGGAGCTCAAAAGAATATTGGCTGTGCGGGTGTTACTGTGGTAATTGTGCGTGATGATCTTATCAGCAACCCTTCACCACAATGTCCAATTGTGTTTGACTACAAGGTTCAAGCTGGAAATAATTCTATGTATAATACTCCTCCAACATTCAATATCTACATAATGGGACTTGTTTTCAAATGGATTAAAAAAGTCGGAGGAGTTGAAGAAATGGACCAAAGAAACGACATCAAGTCAAACCTCTTGTACAATCTTATAGACTCATCCAATGGTTTCTACTGCGGAACAGTGGAAAAGAAGAGCCGTTCCAGAATGAATGCTCCTCTTAGGATTGCTAGCCCAAGTGGAGACCAGGAACTTGAGAAAACATTCATTGAAGAGGCTGCTGCCAAAAACATGATTCAGCTGAAAGGCCACAGGTCGGTTGGTGGGATAAGAGTATCGATGTACAACGCTATTAAACCTGAAGATGTCAACACTCTAGTGGATTTCATGAAGGACTTCAGACAAAGACACCAAAAGCAGTGATTCTTGAATCTTGCTGTTTGTGTACAATGTATTAGCAGAGACAATATCATTCCGAAATTAACACATGTGGGCTAATTAATAAAATTGTTGAGAAGGGGACCATTTGATATTTTGAAGGAAGCAACTTCATATGGACGCGTGACAATGGGGGAAATTGTGTAAATCCCTAAAATACTGAGGAAGTCAACTTTTATGAAATATTTCGGCTGTCTTGCGATGCTGCATTAATTTTTCGCAGACTCTCAGTTGGGTTACTATCGCCCTAAGGAACAGTGCAGTAGAGATTGTTAGATGacgataacgtccattatatgattggcttgtgtgaggaaaacttaatggaattcttGCTATAGCGCGTCCGTTAAACTGAACGGTCATAAAcaagagaggatgaggtaaagagacccgatctctatgccccatcaaagattttttttaaatctatttttagtttcgcaaagctattttaagttctcgttcccaatgccaggcatatttaaaaattttattacgtaattggaactggtcaatcaggtgcctctctaaaaatagctgcgtatatattggaagaggcccatgtatgggggatccattctttacctcttcctctcttgTCATAAACTAACAGTTTGCCCTTTGGTGGGAAAGATTTAACTTCACGAATGCATTTCAACGACTAGTGCCTTTTCCTTCCCAGAGCCCATCCTTTCTCTTAGCCGAGCAAGAGAAACTATGGGCTATGCAAACGAGAATGCGACGGGTGTTGAGACCCAACATCCAGCTTTGCTGTTTCATTGCCAAGGCATTTGCCGTTGAGGATCATATAATAATGTGCTTTATATAAATGAATACCGGACCGTGTACGTGCTTGAAATATGTAGAACTAATCCTTTTAATTGACTTTTAATTGGGTATAATGAGCGAAAACATTTTTCCTCGTTACGGTTTCTCACGTGGCTTTTATTACATGAACGATAATTCAAAAAATGCTTACACTGTGAAATTATTAATTTTTCTGCTTATGTTCGCACTGTTTTATTTCGTGTGAATTTCATGATCGCAACTTTTGTTCAGGTTTAGAACTAAATTAAACGAAAATTGTTTAGCTTTCTTGGTGGACTTGAAACAGACCCCTCCCTGCATGGAAATGAAGTACATGGAAGGGCTTTTTGTAGCTTGAGCAGTTTCTCTCTGCATTCTGGGTATGGTTTGGTACTCatgaagaaaatagaagcagaagt

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q99K85	Phosphoserine aminotransferase OS=Mus musculus OX=10090 GN=Psat1 PE=1 SV=1
Q9Y617	Phosphoserine aminotransferase OS=Homo sapiens OX=9606 GN=PSAT1 PE=1 SV=2
P10658	Phosphoserine aminotransferase OS=Oryctolagus cuniculus OX=9986 GN=PSAT1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004732 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00266 all species →	Aminotran_5	Aminotransferase class-V	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR022278 all species →	Family	Phosphoserine aminotransferase	Interproscan
IPR000192 all species →	Domain	Aminotransferase class V domain	Interproscan
IPR020578 all species →	Binding_site	Aminotransferase class-V, pyridoxal-phosphate binding site	Interproscan
IPR015422 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, small domain	Interproscan
IPR015424 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase	Interproscan
IPR015421 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, major domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43247 all species →	PHOSPHOSERINE AMINOTRANSFERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004648 all species →	Molecular Function	O-phospho-L-serine:2-oxoglutarate aminotransferase activity	Interproscan
GO:0006564 all species →	Biological Process	L-serine biosynthetic process	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0030170 all species →	Molecular Function	pyridoxal phosphate binding	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
K00831	serC, PSAT1; phosphoserine aminotransferase	EC:2.6.1.52	Amino acid related enzymes	ko01007	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 Acropora microphthalma 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 Acropora microphthalma, 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.	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 →