Gene detail

Detailed information of BRAKERHOCP00005006657.1 in Haliclystus octoradiatus

Genomic Location: chr3:33788182...33799719
NR annotation: XP_002161201.2, fumarate hydratase, mitochondrial [Hydra vulgaris]
Species Haliclystus octoradiatus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERHOCT00005006657

ATGCATATATGTGCTGTTGCTACGTGTTACTCGCCTAAGGGTAacgattttaaatatttccaCTTCCCAAAAGATGCGAGACGAGAAATTTGGATACAACGTTGCTATAGAAAAGATGAAGTTCCTGCTTCCGCTGAAATGTGTAGCGTACATTTCGATTTGGATTCATTTGAAAGAGATCTGGAACATGAATTACTACAACTTCCAATCCGAAAGCTTTTAAAAAAAGATGCATTACCTACGCTGTTTTTAAAAGATACATACGATGGCTCTAGTATCAACAACAGGGTACAAAGCGACCGGGAAGAAAGAGCTGCAAAAAGAAAGCATAAAGaattaattgatgaaatattaaaGAATGCAGAGATTGAAGCATCTGCTAAGAAGTCGGCTATTGAACTTAATCCTGTTAACAATACACCCACTCCTTGTTCTAATCATTCTACCCATAGCCATACGATGATTGCATCATATAATCAAGATCGGTCTGTTGctgttaaaattattaaagGAGGACTTACAATTATACCTCGAAATAAATTAGCacaaaatgttatcaaaaagaCTCAAAATGAGCTGGAAAACAAGTCTGAATATAGAATTGAGAAAGATACTATGGGAGATATGAAGGTGCCGAAAGGGAAATACTACGGTGCGCAAACTGCAAGATCCATGCAGAATTTTCCAATTGGAGATGAGACGGAACGCATGCCAGAGCCGGTTATTAGAGCGTTTGGTTATTTGAAAAGAGCAGCTGCAGAAGTTAATGTGGAGTTTGGACTTGATTCTAACGTGGCTAAGAATATTATTGCTGCTTGCGATGAGGTGATCAATGGAAAGTTACGTGATCACTTCCCTCTTGTTGTTTGGCAAACAGGATCTGGTACGCAAAGTAATATGAACGTTAACGAAGTGATTAGTAACCGTGCAATTGAAATGATGGGCGGAGAATTAGGTAGCAAAACGCCTGTGCATCCAAATGATCACGTCAACAAAAGTCAGAGCTCGAATGATACCTACCCGACTGCTATGCATGTTGCAGCTGGCCAAGTGGTGTCTGAAATACTTCTGCCTGGATTAAAGAAATTACACAGTGCTCTGCTTGAGAAATCTGAAGCGTTTAAAggaattattaaaattggaagAACTCATACACAGGATGCTACACCATTAACACTCGGACAAGAATTCAGCGGTTATGCTACACAGCTTGAATATGGTATCCAGCGAATTGAAAATACTTTGCCAAGAGTCTATCAATTGGCTATTGGCGGTACTGCTGTTGGGACAGGATTGAATACGCGCATTGGTTTTGCTGAGAAGATGTCAAAAAAGATTGCTGATTTAACCGGATTGCCTTTTATTAGTGCGCCAAACAAGTTCGAAGCATTAGCTGCACACGATGCTATGGTTGAATTAAGTGGTGCCATGAACGTTGTAGCTGGTAGCATCATGAAGATTGCTAATGATGTTCGATTTCTTGGTTCCGGTCCAAGATGTGGTCTTGGTGAACTCTCATTACCTGAGAATGAGCCAGGAAGTAGCATCATGCCAgGTAAGGTGAACCCCACTCAATGCGAGGCAATAACAATGGTTGCAGCACAAGTGATGGGTAATAACGTCGCAGTTACTATTGGAGGAAGcaatggtcattttgaattgaattgttttaaaCCATTAATAATTCGAAACGTTTTACAATCAGCAAGATTACTTGGTGATGCCAGTGTAGCATTTACTGATAATTGTGTGAATGGTATTGTTGCTAACGAAGatagaatatcaaaattattgcACGAATCGTTAATGTTAGTCACATCATTAAATCCACATATTGGTTACGATAAATCTGCACAAATTGCGAAGAAAGCCCACGCTGAACATACAACATTAAAAGAAGCGGCGATTTCATTGGAATATTTAACAGAAGAACAATTTGATCAATGGGTAAAACCAGAAGAAATGTTAGGAcctaaataa

Transcript

BRAKERHOCT00005006657

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P14408	Fumarate hydratase, mitochondrial OS=Rattus norvegicus OX=10116 GN=Fh PE=1 SV=2
P97807	Fumarate hydratase, mitochondrial OS=Mus musculus OX=10090 GN=Fh PE=1 SV=3
Q60HF9	Fumarate hydratase, mitochondrial OS=Macaca fascicularis OX=9541 GN=FH PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003293 (this species only) · gene tree & orthology
Transcription factor family	THAP · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00206 all species →	Lyase_1	Lyase	Domain	Interproscan
PF10415 all species →	FumaraseC_C	Fumarase C C-terminus	Domain	Interproscan
PF05485 all species →	THAP	THAP domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR020557 all species →	Conserved_site	Fumarate lyase, conserved site	Interproscan
IPR005677 all species →	Family	Fumarate hydratase, class II	Interproscan
IPR006612 all species →	Domain	THAP-type zinc finger	Interproscan
IPR022761 all species →	Domain	Fumarate lyase, N-terminal	Interproscan
IPR018951 all species →	Domain	Fumarase C, C-terminal	Interproscan
IPR000362 all species →	Family	Fumarate lyase family	Interproscan
IPR024083 all species →	Homologous_superfamily	Fumarase/histidase, N-terminal	Interproscan
IPR008948 all species →	Homologous_superfamily	L-Aspartase-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11444 all species →	ASPARTATEAMMONIA/ARGININOSUCCINATE/ADENYLOSUCCINATE LYASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0004333 all species →	Molecular Function	fumarate hydratase activity	Interproscan
GO:0006106 all species →	Biological Process	fumarate metabolic process	Interproscan
GO:0006099 all species →	Biological Process	tricarboxylic acid cycle	Interproscan
GO:0016829 all species →	Molecular Function	lyase activity	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0006108 all species →	Biological Process	malate metabolic process	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
K01679	E4.2.1.2B, fumC, FH; fumarate hydratase, class II	EC:4.2.1.2	Cushing syndrome	ko04934	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 Haliclystus octoradiatus 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 Haliclystus octoradiatus, 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 →