Gene detail

Detailed information of aech_s0054.g119.t1 in Acropora echinata

Genomic Location: sc0000054_pilon:1837234...1843526
NR annotation: XP_029206801.2, uncharacterized protein LOC114970508 [Acropora millepora]
Species Acropora echinata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

aech_s0054.g119.t1

TGATATGTAAATATTTGACGTTGCATAAATAGATGGCTTTTCCCCTGCGCAGCAGCTGTTTCGTTGTCAGGAGAAACAAGGAGAAATGAGATAATACGCCTAAAAGGCTCGTGGAAGGTCGTTGCTTGGATGCGGCCATAGCTCACAGATGATTGGTAAGTATCTTGATTTCTTAGTTGATCCTATTCTTTGCGTGGACAAACTTCTTTGTTTCACCAGACAATAATTTGAAACAGTCACGTTTATTTGTTTACAATATACCTGCCTTTATTTGCAAATTAGTTTTGAGAGTGATGTAGTAAATTGGTCGACACAAATCGACCACAAGGTGAATGGGACTTCTCTCCGCATTGTTCTTTGAGCTCAACGCTATCGCCAGTTTCCGCAACTCAGGGCTCTTTTTTGAAGCAAACGTTTTTGGAAGTTGTATTTAACTGATCCAAGTTGTTGCAATCGAATTTACTAGTTTCAAAATAATTTTTTCAAGTCCTGAAACACGTTTACTAAACGACGAAAATCACGATACATAGCTGTCATAAGAGTTTCAAACCTCATTCGTTCTGCCAGAACCACAAAATATTTTGTTGACAATATTTTGTTATCATCAAAGATTTGAGTCACAATCCTTTCCTGCTCTGCTTCAGCAAGTATTATTAGATCCTAAGCTGTATGAAGAGCTGTATATTCAGTAGCCAAGGTTTTGTAAATGAACCAGTTTGCAACTCCGGAAGAACTAGAAAAACATCACGTCCGCGATGTCTACGATAAAATAGCGCCTCATTTTGCTGGATATAGTCATAAAGCTTGGCCTCGGGTCGAGGAATTTCTTTTATCTCTACCAGCTGGAAGCCTGATTGCTGATGTGGGGTGTGGAACTGGGAAGTACTTGGGTCTTGCACTAGATTCCTTTGTGATTGGATCAGACAGCTGTGTAGAATTTGCAGAGATTGCAATACAGAGAGGTCACAGTGTTGTAGCCTGTGATAACCAAAGCCTTCCTTTTAGGGAAAGTTGCTTTGATGCTGTAATTTCAGTTGGCGTCATTCATCATTTTGCTTCAGGAAAGAGACGGAGCAAAGCCCTTGAAGAACTGTATAGGATACTTAGACCAGGAGGGAGAATGCTGGTCTATGTTTGGGCATTTGAACAAGAACAGAGAAAGTTTGATGGCCAAGATGTGTTAGTTCCCTACAAACATTTCCAAAGAAACAAAGTATTAGCGCGTAGAAGCTTGTCCGCTCCAGTTAGGCCTAGACAACAAGCCCAATTTCACAATGGAAGCACACCCAACATGACGAGTTCCTCATGGCGCTCAGGACGAGCCCGCTCTTCTCATGATTGCTTTGGTGGTCACGTGTACAAGCGGCAGCAAACCCAAACATCTAAAAGAGAAGATAGCTCTAGTAACGATACTGGTTTAGGACGGGTTCAAGTGAACGATACTTCTAAATATGCTGTTTTGCGGAAAATCAGAAATCAAGAGCCTGTTTCTTCTTTAAGACTTGAAAAAAGCGAAGAAGATAATCCAGTGACAAAAATTTCGAAATTTCTGAACTCTGTCCTGAAAAAGGTTTTCAATAACGCAGACGACGGTGGCGGTGAATCCGAAAAATTACCAAGTGCGTCCGCTAACGAAAAGACCCACCAGAGGAACAGGTCTTCAGAAAATGCCAGTTCGGAATTTAGCCCAAAGTTTTCGGCCTTGATGACTTATTTTTCTTCTGAAAAGCGGGAGACGATTTTGAAGACAGACGTTCTCTCTCAGCTTGCGAGAAAATTGTTCGCGTGGAAAGACGACTTGCGACTTGACAATGATTTTGTCAAAACATTAGATTACTGCGATGAGATTGATAAAGAGCAACGCGAGAAAAGTGTTGTCGTGATTGGCTTGAAAAAGGAAAACGTAGGTGTTGATGGTACGTGTGGACATCAGGCTCCAAGTGCCACGACCAGTGTGAGCCTCAACGTGATGGCGAGGCTGGTCGACTCTCTTGTATTGCCAAGCGATGTGTATAACGACAGCTCCAGTTCCAGTGACGCTCTTTCATCGGACGATTCGAGCAGTGCAGAGGGCTGGGATCAAGTTGAACCTTCTCACCCCACTCACAGCAAGAAGACTTTTCAACACACTACTATTAGCTGCCAAGAACCTGCTGAACCTGTTTGTGCAGCGGATAAAGATTCTCAGTATTCATCGTCGTCATCATTTTTTTCAACGACTGCTTCTTCATCGTCACAGTCTTCCCCATTACTTTCATCTTCGTCCTCCTCACCGAGAACAGAAACTTCATCGAAGCTGGCAACGAGAAAGCTTCAACGATACTATCATGTGTTTTGCGAGGGTGAACTGCCGAAGCTAGTTCAAGATGGAATCCCATCTGCTGTTATTTTGAAAGAATATTATGATCATGGAAACTGGGCAGTTATCTTAGAAAAGGCAATCTCAAGGAAGGGTTGTGCAAAAACTCTGAAATTCGTTTGAAGGTTAGGTTGCTCTTTGTCTCTCTCTGGTGCTTCTCGTTTTCCCCAGCAAGGATCTCTCAAGATCCATAAACGAACTGTCGTGCCTTCTTCATCATCCAGGACGTAAAAATTAAGAAAGACAGTATGTTTCTTATGGAGAAAGCCGCTCTCTTACTTTGGTGAGAGGATAGTTGCTGTTCCTGCTTGTAAGGAGATATGTTTCGTAACGAAGGAAAGCTAATGTATAACGCCGAAAAAAAAGCTAAGGAACGGAATTCTTAGTCTTAAAATGAGTGGGGATCCAGTTTCGGATTCATGGATTTTAACCTCGGTTCACTTTAATATTTTCAATTTTAGTTCTTAACACAACGTTACAATATTTTTTTCTTGCGCTATCTTCTTGGAAATGCATTTTCTTGCAAGAATTTTATGCCTTCAATTCTGATAGCTAGTTGCTTTTTGTCGGAGTTGCATTGCGCCGAGAGATTGCTCCTTTAAAGGAACTTGCTATTATAATGGTCTTTTCATAAAAAATTCCCTTACTGGGTTTACTTAAGGAGAATTAATCTGAAATCTTGTTTTTCTTTCTTTTCCGCTTGTTATATAATTGTCGTCGTGGAAATATTTTGCACTTTTAACTTTGTATGTCGTACAATTTTTATCGCACAAGAATAAATTATTTTTTAAGGGTTGTATCTAAGCAGCACTATGCTATTTTATTTCACTAACTTAACAAAACGGGGAAGAAGTGATGAAACTTTGTAATAAAGATTTTGTTGGTAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q08DH3	Probable tRNA methyltransferase 9B OS=Bos taurus OX=9913 GN=TRMT9B PE=2 SV=1
Q80WQ4	Probable tRNA methyltransferase 9B OS=Mus musculus OX=10090 GN=Trmt9b PE=1 SV=1
Q9P272	Probable tRNA methyltransferase 9B OS=Homo sapiens OX=9606 GN=TRMT9B PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001951 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08241 all species →	Methyltransf_11	Methyltransferase domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR013216 all species →	Domain	Methyltransferase type 11	Interproscan
IPR051422 all species →	Family	AlkB Family tRNA Methyltransferase/Dioxygenase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13069 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008757 all species →	Molecular Function	S-adenosylmethionine-dependent methyltransferase activity	Interproscan
GO:0000049 all species →	Molecular Function	tRNA binding	Interproscan
GO:0002098 all species →	Biological Process	tRNA wobble uridine modification	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0030488 all species →	Biological Process	tRNA methylation	Interproscan
GO:0106335 all species →	Molecular Function	tRNA (5-carboxymethyluridine(34)-5-O)-methyltransferase 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

No KEGG orthology assignment for aech_s0054.g119.t1.

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 echinata 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 echinata, 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 →