Detailed information of ANN36348-RA in Montipora grisea

Genomic Location: Scaffold_6129__1_contigs__length_27727:4237...7183
NR annotation: MBK9568689.1, tryptophan synthase subunit beta [Chitinophagaceae bacterium]
Species Montipora grisea · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q5LBZ8Tryptophan synthase beta chain OS=Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2) OX=272559 GN=trpB PE=3 SV=1
Q64SX9Tryptophan synthase beta chain OS=Bacteroides fragilis (strain YCH46) OX=295405 GN=trpB PE=3 SV=1
A6L9K4Tryptophan synthase beta chain OS=Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152) OX=435591 GN=trpB PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0013114 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF10988
all species →
DUF2807Putative auto-transporter adhesin, head GIN domainRepeatInterproscan
PF00291
all species →
PALPPyridoxal-phosphate dependent enzymeFamilyInterproscan
PF00290
all species →
Trp_syntATryptophan synthase alpha chainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR002028
all species →
FamilyTryptophan synthase, alpha chainInterproscan
IPR021255
all species →
DomainPutative auto-transporter adhesin, head GIN domainInterproscan
IPR001926
all species →
DomainTryptophan synthase beta chain-like, PALP domainInterproscan
IPR023026
all species →
FamilyTryptophan synthase beta chain/beta chain-likeInterproscan
IPR013785
all species →
Homologous_superfamilyAldolase-type TIM barrelInterproscan
IPR006654
all species →
FamilyTryptophan synthase, beta chainInterproscan
IPR011060
all species →
Homologous_superfamilyRibulose-phosphate binding barrelInterproscan
IPR036052
all species →
Homologous_superfamilyTryptophan synthase beta chain-like, PALP domain superfamilyInterproscan
IPR006653
all species →
Conserved_siteTryptophan synthase, beta chain, conserved siteInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR48077
all species →
TRYPTOPHAN SYNTHASE-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0004834
all species →
Molecular Functiontryptophan synthase activityInterproscan
GO:0006568
all species →
Biological Processtryptophan metabolic processInterproscan
GO:0000162
all species →
Biological Processtryptophan biosynthetic processInterproscan
GO:0005737
all species →
Cellular ComponentcytoplasmInterproscan

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
No KEGG orthology assignment for ANN36348-RA.

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 Montipora grisea 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 Montipora grisea, 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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch 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 foundopen →
Expression heatmapDraw 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 / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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