Gene detail

Detailed information of BRAKERTYJP00000024936.1 in Cladopsammia gracilis

Genomic Location: JAJGOT010000145.1:1133994...1144757
NR annotation: no NCBI-NR hit recorded
Species Cladopsammia gracilis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERTYJT00000024936

ATGATTATTCCGTGTTTATATTTAAAGCAGGGAAGCCTAGTAGACCCAAGCAACGGACAGAATGTTCAAGATGTATCTACATGCCTTGACAAAATTTCATTGTGCCCAGAAATTTCCATCGTGTTCTTGGATACAAAGAAGGAGACCAAAGCATTTGGAAAGAAACTTGTTGAAATTAGCGCTTGCTATGTTCAGTATGAAGCTGAAAATGAAGACGAGTTGCTCGATTTTTTGGATGTTGGTGCAAATCGTGTTGTTCTTGGCAAAGATCTTTTAAAAGATTTTGGTCAATCTATACCTAAAGAAAGAATAACGTACAAATTAAGTTATGCAAATTCCTCCATTGAAGAGTTGACCAAGGAGATCAGTGACACGAAGGACAGAATTTCCAGTTTTCTTTTGCCTCAGAAGGTTTCCCAAGTGGATGAAGCGGCACTTGTTGAGTTTGTAAAGAAACTCAAGAACTCTGTTTGTGATGATGATTTCAGACTTATCCTCTCTTTGAATGAGGTGATTTCATGCTCAACCATTTCACAGCTCCACACTCTTGGAATTGATGTGCAGCTAAGTGCAACATATCTGTTAAACGAGCTCAGTCTTGGACAGGTCATTGCATCATGCCTTAAAGGAGACCGCCCCGATGGTCTGTTTCCTACCTTAGTGACAGACGAGCACAGTGTGGCTCTTGGACTTTGTTACTCCAGTGCTCAAAGCATCCAAGAAGCAGTTAACACCAAGAAAGGTGTTTACTTTTCACGAACAAGAGGATTATGGAGGAAGGGACAAACTTCGGGAAATGAACAGgaTTTGTTGAAAGTTTATTTGGATTGTGACTCTGACACCTTGAAATTTGTTGTTCGACAACAAGGTCAGGGATTCTGCCATTTAAACACCTGGACTTGTTTTGGACCAAGCAATGGTCTACCATCACTCATGAACACCTTGAGATCAAGGAAACAGTCAGCACCTCCAGGCTCCTACACTGAACGTCTTTACAAGGACAGCAAGCTGCTGCATGCAAAGATATGTGAAGAAGCAGAGGAACTGTGTGAAGCAGAGAGCAAAGAGGAGATCGCTTGGGAAGCAGCTGATGTGTTATATTTCACATTAGTGAAATGTGCAAAGGAAGGaatatctttggctgaaattgaAAAGGTGCTTGATCAAAGGTCACTCAAGGTCAGACGTCGCCCTGGTAATGCAAAACCTGACAAATTGCCTTGCTGTAATGGTGATTCAATTACTATAGCAACCAAACCCATTGCTTCACAATCAACCACACAGGTCAACATGCCTAACTCTGCATTAAAGAGCTATGATTTTCAATTACTTAGTGAAAAGGAATTGCAAGATCTTTGCAAACGCCCAGCTGTGATAGATACAGTAAAGCTAGAGGCTATTGTGCGACCTATTATTGCCAATGTACGAACCAGTGGGGACAAAACATTGTTAGAATTGACAGAGAAGTTTGATAAAGCAAAGCTATCCAGTCCTGTGATTGATGTGTCATCAATAGCTGAACCAGTCCTGGACAAAGAAGTGACAGATGCAATTGATCTGGCTTATGACAACATTTATAAATTTCACAAGGCTCAGTTGAATCTGAAGCCACTTGTGGTAGAAACTTGTAAGGGCGTGGTTTGTTCTCGGCATGTTAGAGCTATTGAAAAAGTGGGTCTTTATGTGCCTGGTGGCAGTGCAGTGTTGCCGTCAACAGCTCTCATGCTTGGTATTCCAGCTCAGGTCGCAGGATGCAAGGAGATTATCTTGGCCACGCCCCCCAAACAAGATGGCTTAGTTTCTGCTGAAATACTTTATATTGCAAAGAAAACTGGAGTTTCCAAAATATTACTTGCAGGAGGAGCCCAGGCAATTGCAGCAATGGCTTACGGAACTGAAAGTGTACCCAAGGTGGACAAGCTGTGTGGCCCAGGAAACTcctttgttaccatggcaaaaATGTTGGTGCAAAATGACAGTACAGCAGGTGTAAGCATTGATATGCCAGCAGGACCATCAGAGGTTATGGTCATTGCTGATGACACTGCAGAACCCTCATATGTTGCTGCTGATCTGTTATCGCAAGCAGAACATGGCACAGATAGTCAAGTGGTTTTAGTTGCTGTTAATTTGACCGATCAGCAACTTGAGAATATTCAGaatcaagtGGATTCTCAAGCGAAGAGACTGCCTCGGGAAAAGATTCTGAGAGAAGCTCTCTCAAAAAGCTTTGTGATGAAAGTTCCAACGATGAGTGAAGCCTTGTACTTCAGTAATAAATATGCTCCAGAACATCTCATCATCAACACACAGAATGCTGAAGACTGTTTGGATGATGTACAAAATGCAGGTTCTGTGTTCCTTGGCCCTTATTCTGCTGAGAGCTGTGGAGACTATGCCAGCGGCACAAACCACACCCTCCCAACATATGGTTATGCACGTATGTATAGTGGTGTGTCCACTGCATCATTCCAGAAACATATAACAGCCCAATGCGTTTCTAAGGAGGGTTTGGCCAACATTGGCCCAGCAGTGGCAACACTTGCAGCTGTGGAGAAGTTGGATGCTCATCGCAATGCAGTGTTAATAAGACAGGGACAATTAAACTGCTAA

Transcript

BRAKERTYJT00000024936

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
PF01503 all species →	PRA-PH	Phosphoribosyl-ATP pyrophosphohydrolase	Family	Interproscan
PF01502 all species →	PRA-CH	Phosphoribosyl-AMP cyclohydrolase	Family	Interproscan
PF00815 all species →	Histidinol_dh	Histidinol dehydrogenase	Family	Interproscan

InterPro

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

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
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:0000105 all species →	Biological Process	L-histidine biosynthetic process	Interproscan
GO:0004635 all species →	Molecular Function	phosphoribosyl-AMP cyclohydrolase activity	Interproscan
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0004636 all species →	Molecular Function	phosphoribosyl-ATP diphosphatase activity	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

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.

Co-expression network

Genes whose expression across the transcriptome samples of Cladopsammia gracilis 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 Cladopsammia gracilis, 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 →