Gene detail

Detailed information of scaffold103.g19.t1 in Morbakka virulenta

Genomic Location: scaffold103:929648...941694
NR annotation: XP_029193635.2, yrdC domain-containing protein, mitochondrial-like [Acropora millepora]
Species Morbakka virulenta · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

scaffold103.g19.t1

GAGAGGAAATGTTTGTGGCCATGGAGTACCTTGGAAAGTCACTTGTAGTTACTTCTTAAAGCGATTAAAAGTAGATGTAAAACTGTACTGTTTTCACGAAAGCGTTTTATATGTGGATTGTTCTTGTATCAACGCATACAGGAACGTTTGCACTGGACAAGCAATAAAGCAAAATTGAAAAGCACAACGACAATATAAAGCCATGAAAGTTGTGCGTTTACATCAGAAGACAGATTATGATAGTGACTACTGCCCAGAAGTAATTCAGCTGGGAGTGAAATCATTGTGCTCTGGTAACATAGTTGGTGTGCCAACAGATACTATATATGGGATTGCCTCACTTGCACAGTCATTGGAAGCAGTTGAAAAGCTATATGAACTAAAACAAAGACACAGAGAGAAACCAATTGCTATTTGTGTTGGCAGTATTGATGATATTTACAGATGGTGTGAAGTAACAGTGTCCAGAGATTTACTTAATGATCTACTTCCAGGGCCAGTCACTCTAATATTCAAAAGGACTCAATTATTGAACAATAGGCTCAACCCATCAACGTCAAATGTTGGTGTCCGTATTCCAAAATTTAAGTTTATTCAGGACTTAGCAAGAGCGTGTGGTGAACCTCTGGCCTTAACAAGCGCAAATCTGAGCAACGAGAAAAGCTGCTTGGATGTTGAGGAATTCAAGCATCTTTGGGGCCAGTTGGACATTGTCTTTGATGGCGGTCGTTTGGGCCAGAGTGAGGAATCGCGGTCAGGATCAACAGTGATCAATCTTTCAGAGCACGGCTGTTACAGCATTGTAAGAGACGGTTGTGCATTAAGTCATGTAGAGACTGTATTAAACCAAAAGTATGGATTGATTCCGTTAAACAAATGACACATTACTACTCCGCTTCAATTTACCAGTTGCATTTCAGTAGTCATACAGAGTCATGGTCACGGAAATGCCTTTCCTGTGGTGTAATAATGGCTTATATGGGTAAATTCACTGTTGGTTTTTCTATGCCTATGGTAGTATCGTAAATTTCGAGCTTTTTGATTCGCCATCTTAAGAACTATGCCAAGTTACTCGGTTTTTACACGTATTGTGATTCCGTCAAGCCATCAACATATACGACACGATGACCTCAGAATGGTACTGGTAGCACCGGAGACTCGCGTTCACAGGAATAGTAGCACTGAATGAGATAACTACATTTTGTCTAAGGACGGAACGATGCAGTCGTCGGGTTGTGACGTCATTTTCCCATGGTTTCGTCATATATCTATGGACTGGGGCATGGTATATAAAAAGATAATATTTTGCAGACTAATGGATTTAACGAAAGGACCCTCTTCATTGTTAAGCAGTATGGAATAAGCTGGAAAATAATAAAAGGCTAAAAAGCAAATCAAATAGATTAGTTTTTTTAAATTAGATTTTCTATGGAAATGGCGCTTGTCTTGTATTTTATCGGAAAGAAACTGAGCAACGTCTGGAAAAATCTATTTAAAAATCGTAATTTCAAGGATGAAAGCATTCTGAAAATTAAGAAACTTGTATAAGTAACCCTAAATGGACTAAACGTCTTTTGAGAAACGTATGATATCACCTTGTTCCTTGGGAATTTAAAGACAGGCAGGGATAGTTTATCGATGTAATCAAATGAGTACTTGATTTGAAAAAAGTTTTTATTTAATGTATTCTGGCAGCAGTGTGGGTATAAGTATTGAATATTATTAGCTATTTATTCGTAACGGCAATTAAATGCTTGCTTTTTTATTATACATTTTTGTTTAATGGTATTTTGCCAACCACTGTTAGTTTAGGTCATGTGACAACGAAAGTGGATCTCAATGACGGCCTATAATGAAGTATAATATGGCATTCAAGATGCTTCTGATTTTTTTCTGCTCCATTTTTCATTTTCATACCGAAAATACTATATCATAGGGGTTCCGTTTGGTGTCTTGCACCTCCATTAACTTTACAATAGTGTTTCTACGTACCAGATTTTTTAAATATTCGCATGCGAAGCGTGGAGTTTTATTAAATGATTTTGTTGAAAAGACTAACTATGCCAGAAGCTTGGCTTAAAAATGGTGACTATGAAATAACTAACTTGTTTTATACATTTAAATTATTGGTAATCGTTAATATCATCAATCAGGCATTTATCTATTGTTTGGGGTTTTCCATTCTAAGCTTTTTATGATATGTGAGCATATCCTGTTTTTAATAAATCTTAAATATAGTAACACAAGAAATCTTGCGGGAATACCGAAGCTATTATATCTGGTCGAAGAGGTCAGTGTAGGGTAGAATATTTGTTATACACATACTCTGGTGCAACAATATAGATACGTATTTAGATAACGAAGGAATATAAGTTTGATATATTAACCTAAAGAAAAGTGGAAAGGGACTATAGTAGCTCAGGATAATTCTAGCAAATATCTATCCCTTAACGTACATATTTTGATCTCAGTTAATTCAACTAAATCATGATCTTGAAAGTGAAGCGTATTTCAATAACCAAATTTGTGTCCTCGAAAGGGAGCTCTTGTTTATTCTGATAAGAAAGGATCGAGTTCAATTCAATATTGACTTCTATTTTTAGTTTTTAGATCCTCGTGACCCTTGTATGTATCTATTGTGTAAATGACGTATGGTATAATGTTTTGCTCCAAAAACTTTAGCTTTAACTGGTAATCATCAATATTTTTACCACTGATATACCTTAATCATGTTCGATTTCCATTATCCCGTGTAAAGTACTCCGATAAGAGAAGATCCACATTGGCGTAAATTGCAATTAATTTGTAGTTACCATCCGTGTCTTTTGGTAATTATGTATTGCATATTTCCCGAAAGCTCTGTCTCTTAAAAGTTCATAAATAACGCAACACAAATTTTTGTTTCGCATGGTTTTGTTGGGTTTAATTGGGTTTTCAATAATTTTCTGTTTGTATATGGTAACAAACAGGAATTTTACTACTCTTAGCCTTACATGTACAGAGAAGCTGCAAGTACTTGTTTTATTTATGGTTCCACTGTTTTTACATGAAATGTACATACAGCAATAGCAATATATTACATATGATGTC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3U5F4	Threonylcarbamoyl-AMP synthase OS=Mus musculus OX=10090 GN=Yrdc PE=1 SV=1
Q86U90	Threonylcarbamoyl-AMP synthase OS=Homo sapiens OX=9606 GN=YRDC PE=1 SV=1
Q499R4	Threonylcarbamoyl-AMP synthase OS=Rattus norvegicus OX=10116 GN=Yrdc PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005983 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01300 all species →	Sua5_yciO_yrdC	Telomere recombination	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017945 all species →	Homologous_superfamily	DHBP synthase RibB-like alpha/beta domain superfamily	Interproscan
IPR006070 all species →	Domain	Threonylcarbamoyl-AMP synthase-like domain	Interproscan
IPR050156 all species →	Family	Threonylcarbamoyl-AMP synthase, SUA5	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR17490 all species →	SUA5	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003725 all species →	Molecular Function	double-stranded RNA binding	Interproscan
GO:0000049 all species →	Molecular Function	tRNA binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006450 all species →	Biological Process	regulation of translational fidelity	Interproscan
GO:0016779 all species →	Molecular Function	nucleotidyltransferase activity	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
K07566	tsaC, rimN, SUA5, YRDC; L-threonylcarbamoyladenylate synthase	EC:2.7.7.87	Transfer RNA biogenesis	ko03016	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 Morbakka virulenta 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 Morbakka virulenta, 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 →