Gene detail

Detailed information of amic_s0145.g5.t1 in Acropora microphthalma

Genomic Location: sc0000145_pilon:42606...52504
NR annotation: XP_015752236.1, PREDICTED: LOW QUALITY PROTEIN: tRNA wybutosine-synthesizing protein 4-like [Acropora digitifera]
Species Acropora microphthalma · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

amic_s0145.g5.t1

ATGGCGGCTGATAATATCGTTTTTGATGAAAGGAAGGCATATGAAGAGAAGACAGACGTTCAGGTTCAAGGGACAAACGACCATGCTACGCTCAGCAAACTTTCCACTGTTAGAATGGGTTACTTTGAAGACAGGTTTCTGCCATATTTTGTATCCAAGAGGTCCAGAAGAGCACCAGTTATTCATAGGTCATATTACATAAGGACAAAGGCAATTCATTTTGTGGTAAAAGGATTTCTGCAAAGTCTGAAGTTTAGAGGATCAAAAAAGCAGATAGTTTCCCTTGGAGCAGGATATGACACACTTTTCTTTTCCCTTGCTAATCAAGGACTCTTGAAAGAAACCAAATATTTTGAGGTTGATTTTCCAGAGGTTGTTCAAAAGAAGACAAATTTGATTTTAAAAAACCAAGAACTGGCTCAAGTGCTTGGAACAGTCAGTTCCCAGAATGAGCATTGGCTCGGAGGAGGAATTAACAGTGAAAAGTATTCTTTGTTGGGCTGCAACTTGAAGAACTGTTCAGCGCTGGAGAGGTGTCTTTTGAAATGCGGTTTGAACACCTCATCTGTCACACTTTTGTTATCTGAAGTGGTACTTACATACCTTAATCCACCTAAAAGTGCCACAGACATTATTGGATGGGCAGCACTTTTCTTTACATCTGCAACGTTTGTCATGTTTGAGCAGGTTCACCCAAGTGACCCGTTTGGAATCAAGATGATGAATCATTTTCAGCATACAGTGGGCGCCCCCCTCTATGGCACGGAAGCTTTCCCCACCCAGCAAAGTCAAATTCAACGTTTTATGAAAGAGGGCTGGGCTCTTGTTAACTGTCCAACGTTAGACTTCATTTACTACGAGACACTCTCGATTGAAGAAAAAGCTCGCGTTGAAGGAATTGAACCTTTCGATGAATTTGAGGAGTGGCACCTGATGTGTTCACATTATGTCATCTTAACAGCCTTCAAAGGATCCTGTCAAAATATTCAAGAGGAATTGTTTTGTCCGCAAAATGAAAACAAGCAGTTAACCGATCAGCCGCGTCTTGTTGATAATAAGCAGTGTATTATTCAACCCTTGAGTGTTCTACCTTCATCGGATGGAGTAAAAAGGTTTGGACACACAGCCACTTCTTTGTCGGCTGACACGGTTCTTCTTGTTGGAGGGTTTGGTCCTCGCAATAAAAAACACACGCGACTTGATGGAGCACAGCTGTTACACTTTGTACAAGATAAGTGGCATTGTGTGGACATCACAACAACTTCGGACATTGCACTTGGCAGCCGGATGTTTCACACTGCAACCAGACTAAGTAATGAAGATGTCTTTATTTACGGTGGCCGAACGTCGCCATCCAAGCCTTGCAAAGAAGCTATTTCACTATCTTTAACGACAAGCATTGTATCGCAAGCAACTTCTTCACACACAAAAGACGACAGTTCCAGTCGCTCAGAGACTGATTATGAAGGAAGCAAATGTTTAGCAAACGCTGTTATTTCTGAGAAGAGTTATACGCATTCTGTTGTACGTTGTCATGGAGACATTCCTGAGCCGAGATGGCGGCACACCGCGTCGTGTGTTGTCCTTCCTGATGGTAGTGAGAATATATTAGTGTTTGGAGGTCGCAGTTCTACCCAAGTCGCAATGGGGGATTGTTGCTTGCTTCATATCAAGTCACAAACGTGGCGAAAGGTGTTCGTCGGTGGAGATACCGCTGTGCCGCGCCATTCCCATACTGCGTGCGTCTGGAAGGACAAAGTGATACTAGCGGGGGGTCTGGATGCTAATCTTCTTGCTCTCAACATCATCCAGATATTAGACACTCAGGTTAGTCCAATGATGTTGCAAACGTTGAACATTGATCCACAGTTGATGCCAAGATACTCTCATACAGCACATGTGGTAGATGACAAACTTATACTTGTCGGCGGAGTCACGACCAATTCATCGCATACTCCTGGAATAGTGATTCTTAATCTTGAGTCATTGACGTGGAACTCGTTTACTCTACCGGCCATGTCAGCTCCCAATACACCTTTGATGCTTCACAATCACGACAGTGTCTACTGGGAAGATGTGCAAGGTATTATGGTCCTTGGTGGTGGAGGGAATTGTTTTTCATTCGGAACTCATTTTAATGAGGGACCAATCATGATCAAACTTCTGCAGAACTGA

Transcript

amic_s0145.g5.t1

AGTTACGCCGTGGCAGGATAGAAGCTTCTCATATTAGGTAGAGGGGCTGGAGTTCTATAGCTCTCTCCCATTGCCTGGTGTGGGACAGGATAAAATTTGATAACGCGTCTAGCAACGCTACAGGTTTGAATCCTTGATTGCCTGCCTGATGAACTTCATTGAATATTCCACAATTCTGTGCCGCTGCTGGTCAGCGGGTACTGCTTTCTAGTTCCAGACCTCTCTAGGCTAGAAAGAAAGATGGCGGCTGATAATATCGTTTTTGATGAAAGGAAGGCATATGAAGAGAAGACAGACGTTCAGGTTCAAGGGACAAACGACCATGCTACGCTCAGCAAACTTTCCACTGTTAGAATGGGTTACTTTGAAGACAGGTTTCTGCCATATTTTGTATCCAAGAGGTCCAGAAGAGCACCAGTTATTCATAGGTCATATTACATAAGGACAAAGGCAATTCATTTTGTGGTAAAAGGATTTCTGCAAAGTCTGAAGTTTAGAGGATCAAAAAAGCAGATAGTTTCCCTTGGAGCAGGATATGACACACTTTTCTTTTCCCTTGCTAATCAAGGACTCTTGAAAGAAACCAAATATTTTGAGGTTGATTTTCCAGAGGTTGTTCAAAAGAAGACAAATTTGATTTTAAAAAACCAAGAACTGGCTCAAGTGCTTGGAACAGTCAGTTCCCAGAATGAGCATTGGCTCGGAGGAGGAATTAACAGTGAAAAGTATTCTTTGTTGGGCTGCAACTTGAAGAACTGTTCAGCGCTGGAGAGGTGTCTTTTGAAATGCGGTTTGAACACCTCATCTGTCACACTTTTGTTATCTGAAGTGGTACTTACATACCTTAATCCACCTAAAAGTGCCACAGACATTATTGGATGGGCAGCACTTTTCTTTACATCTGCAACGTTTGTCATGTTTGAGCAGGTTCACCCAAGTGACCCGTTTGGAATCAAGATGATGAATCATTTTCAGCATACAGTGGGCGCCCCCCTCTATGGCACGGAAGCTTTCCCCACCCAGCAAAGTCAAATTCAACGTTTTATGAAAGAGGGCTGGGCTCTTGTTAACTGTCCAACGTTAGACTTCATTTACTACGAGACACTCTCGATTGAAGAAAAAGCTCGCGTTGAAGGAATTGAACCTTTCGATGAATTTGAGGAGTGGCACCTGATGTGTTCACATTATGTCATCTTAACAGCCTTCAAAGGATCCTGTCAAAATATTCAAGAGGAATTGTTTTGTCCGCAAAATGAAAACAAGCAGTTAACCGATCAGCCGCGTCTTGTTGATAATAAGCAGTGTATTATTCAACCCTTGAGTGTTCTACCTTCATCGGATGGAGTAAAAAGGTTTGGACACACAGCCACTTCTTTGTCGGCTGACACGGTTCTTCTTGTTGGAGGGTTTGGTCCTCGCAATAAAAAACACACGCGACTTGATGGAGCACAGCTGTTACACTTTGTACAAGATAAGTGGCATTGTGTGGACATCACAACAACTTCGGACATTGCACTTGGCAGCCGGATGTTTCACACTGCAACCAGACTAAGTAATGAAGATGTCTTTATTTACGGTGGCCGAACGTCGCCATCCAAGCCTTGCAAAGAAGCTATTTCACTATCTTTAACGACAAGCATTGTATCGCAAGCAACTTCTTCACACACAAAAGACGACAGTTCCAGTCGCTCAGAGACTGATTATGAAGGAAGCAAATGTTTAGCAAACGCTGTTATTTCTGAGAAGAGTTATACGCATTCTGTTGTACGTTGTCATGGAGACATTCCTGAGCCGAGATGGCGGCACACCGCGTCGTGTGTTGTCCTTCCTGATGGTAGTGAGAATATATTAGTGTTTGGAGGTCGCAGTTCTACCCAAGTCGCAATGGGGGATTGTTGCTTGCTTCATATCAAGTCACAAACGTGGCGAAAGGTGTTCGTCGGTGGAGATACCGCTGTGCCGCGCCATTCCCATACTGCGTGCGTCTGGAAGGACAAAGTGATACTAGCGGGGGGTCTGGATGCTAATCTTCTTGCTCTCAACATCATCCAGATATTAGACACTCAGGTTAGTCCAATGATGTTGCAAACGTTGAACATTGATCCACAGTTGATGCCAAGATACTCTCATACAGCACATGTGGTAGATGACAAACTTATACTTGTCGGCGGAGTCACGACCAATTCATCGCATACTCCTGGAATAGTGATTCTTAATCTTGAGTCATTGACGTGGAACTCGTTTACTCTACCGGCCATGTCAGCTCCCAATACACCTTTGATGCTTCACAATCACGACAGTGTCTACTGGGAAGATGTGCAAGGTATTATGGTCCTTGGTGGTGGAGGGAATTGTTTTTCATTCGGAACTCATTTTAATGAGGGACCAATCATGATCAAACTTCTGCAGAACTGACTTGTTTCTATTCGTACGTCAATGTAACCAGCCTTGTGTGATGTTGGCTATTATGAAAGAAATCCTTGTAAACAAGAGGTTTGATATTATTGTAAATAAACAACGCCGGAATCTATGGACCACATTCATGTTTTGTGCCTGGGCCATCCGGAAAGAGCAAGGGAGCCGAATCTGGGTAGATCTAACAAGCAACTTTGTGAACTGGATTAAAACAATAATGGAACAAGGATTGTATTTTCCTTATGTTTCGTTTGGTCTTACCGGGCCTCTTCAAGGAGTTAAATGATTTGCCGTGACATTCTTTTAAAATAAAAATATACTCCATTG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O60294	tRNA wybutosine-synthesizing protein 4 OS=Homo sapiens OX=9606 GN=LCMT2 PE=1 SV=3
Q8BYR1	tRNA wybutosine-synthesizing protein 4 OS=Mus musculus OX=10090 GN=Lcmt2 PE=2 SV=4
Q5XIA3	tRNA wybutosine-synthesizing protein 4 OS=Rattus norvegicus OX=10116 GN=Lcmt2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001702 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04072 all species →	LCM	Leucine carboxyl methyltransferase	Family	Interproscan
PF13418 all species →	Kelch_4	Galactose oxidase, central domain	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007213 all species →	Family	Methyltransferase Ppm1/Ppm2/Tcmp	Interproscan
IPR015915 all species →	Homologous_superfamily	Kelch-type beta propeller	Interproscan
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46529 all species →	TRNA WYBUTOSINE-SYNTHESIZING PROTEIN 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008175 all species →	Molecular Function	tRNA methyltransferase activity	Interproscan
GO:0030488 all species →	Biological Process	tRNA methylation	Interproscan
GO:0031591 all species →	Biological Process	wybutosine biosynthetic process	Interproscan
GO:0008168 all species →	Molecular Function	methyltransferase activity	Interproscan
GO:0032259 all species →	Biological Process	methylation	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	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
K15451	PPM2, LCMT2, TYW4; tRNA wybutosine-synthesizing protein 4	EC:2.1.1.290 EC:2.3.1.231	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 Acropora microphthalma 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 microphthalma, 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 →