Gene detail

Detailed information of FUN_003846-T1 in Acropora pulchra

Genomic Location: ntLink_8:16003740...16015908
NR annotation: XP_029197551.2, YTH domain-containing protein 1-like isoform X2 [Acropora millepora]
Species Acropora pulchra · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

FUN_003846-T1

ATGGCAGAGGAAGGAGAACTTTCATCGCCCGATGAATTGGAAACAAGCAATGATGGTGTTGAGCTGAACGTCCTTGATAACATTCTTGGTGAACAAGTCAACGATGAGTTTGCCGATGAACTTGATACTGCCACAGTGAAAGCAAGTGCACCCAGCAGAAAGCGAAAGATAAGTACAGATGTCAGGAGTGTTTCACCCAAAAAGAAGAACATAGAAAAGGCTTCAAGTCCAAAAATTCAATCAAAAGAAAAGACAGCTACAAGTGGACAGTACTCAAAGAACTCAAACCAGGCTCCAAGCAAACCAAAGAGTGCAAAGACAAGCGATGTAGAGATCACCAGCACGGTAGCTGAAGAGGAAAAGGAGAAAGAAGAACAACATAGCAGAGATGGAAGTAAAGAAAGCAAAGTTAAAAGTAAAGACAAAGAGAAAGGTTCTAGTTTGAGTGAGAGTGCAAGTAAGGAAAAAGACAAGGAGAAGGAAACACGGAGGAACAAGCAGAAGGAGACAAAAACAGTTGACAATGAGACAGAGAGAAAGACTGTGGAGAAGATGTCAAAGAAAAAACAAGAGCAGACTTCAGAGGATAGTGGAATGAAAGAGGCTGTGGACAAGAAGAAAGAATCTGTGAAGAAACTTGGTAGTGCTTCCAAAAAGACTGTTAATCTCAAAAGGAAAGAACCTGTTAAAGTTGTTAAGAAAGAGGTGAAAAAGGATGTTTCTTCAAAGAATGATGCTGTAAAGAAGGAAGTGAAGAAGGAGGTTGTCAAGAAAAGTCCTGTAGCCAGCAAAGGGCAAGTAAAGGCAAAAGTTGTAGTAGAAGAGAAGAAGAAGGCCACAGGACAACCAGTTAAAAAAGTGGCAAAGACCACGGAGCACAGTACTCGCACTGAGGCTAAAACTAGCGACACAACAGCAGAGGCAGAAGTCAGCACTGTTAGGGCTAAAGAGATGCCTTGTCAAGATGTTGAAGAAGATTCAGTGAAAAGCCAACCAGCTGAAAAAAAACTTGAGAAAAAGAGTGTGAGAAAGATCAGTGGAAAGGAGAGCAAGAAAACTGGCAAAACTGAAAGCAAGCAAGTAACAGTAGTGGCAAGACAGCGTAAAGTACAGAAGGTCAAAGAGACTGCTGCTGAATCAAAGGAGAAAACTAAGGAAAAAGCAGTCAAAAAAGATGATGTCGTGGAGTCAGTCATAGAAAATGAAGTTTCTCACTCAAGAGAAACGGAAGCAGCAAGCAAAGATAATGGTGCTGAGGATGAAGACATGGAAGTGATTGATGATTTAGAGGAGGGGAGTCTTGGGGGAAGTACTGCTGCAAGTGGAGACATAGATTTCAGTGAAGAAGAAGAAGAAGAGGATGATGATGATGAGCCGTCAGGGTCTGTCACACCATCATCTTCAGTGTCATCCAAAACAGAATCAGAAATTGCAAGCGATGACGATGAGAAAGAGGACGAAGAACCTAGAGAAAGGAGACCGAAACGGAAAGCTTCATCGGCTACTGAAGAACAGCAATCCAGTGCGGAGAGCGATAACTCGGATTCAACGGAAAGTGTTCATGTTAAGAGTAAAGTGGCAAAAGCATCAAAGCAGAAAATTAATATGGATGAGTTCTTTGAGGAAGCGCGATACTTCGTTATGAAGAGCAATAATCACGAGAATGTTGCGCTGTCAAAGGCAAAGGGTGTGTGGTCAACACCAAAAGCGAATGAGAAGAAACTCAATGTTTCCTTCAAGAGATACAAGAATGTTATCTTGATATTCTCTGTCAAAGAGAGCGGGAAATTTCAAGGTTTTGCGCGGCTGGCATCCGAGGCAAAGCACGGGGGTCCAATGATCCCCTGGGTACTCCCACCGGGGATGAGTGCCAAGGCTCTGGGAGGAGTGTTTAAACTGGAATGGCTCAACAGGAGGGAGCTGTGGTTTAGCAAGTGTCTGCATTTAAGGAACCCATGGAATGAGAACAAAGAGGTGAAGATATGCCGCGATGGACAGGAAGTAGAGCCTGCAGTTGGTGAAGCTCTTTGTCGCCTTTTCCCAGAGGACGAGACAGTTGACATTAGCTCATCGCACCAGGCATCAGAACGACGCCACAGGAAGGATAGGGAATCATCTAGGTTAGCACCAATCATCATAACCTGCTGCTGGATACAAGTCACATAG

Transcript

FUN_003846-T1

TAGTACCCATTGCCCAGGTGAATTGTTGTCCGATGGAGATCTGGAAACAGATATTCCATAATAATTTCCAACACGAGGAAGGAAGCAAGAGCTTTGAAAATTCTCGTTCTACTTGTGGCCGTATTTTGCGGACAAATAAAGACAGCTTCGTCAATTTTAGTTATTCTTAGATGGCAGAGGAAGGAGAACTTTCATCGCCCGATGAATTGGAAACAAGCAATGATGGTGTTGAGCTGAACGTCCTTGATAACATTCTTGGTGAACAAGTCAACGATGAGTTTGCCGATGAACTTGATACTGCCACAGTGAAAGCAAGTGCACCCAGCAGAAAGCGAAAGATAAGTACAGATGTCAGGAGTGTTTCACCCAAAAAGAAGAACATAGAAAAGGCTTCAAGTCCAAAAATTCAATCAAAAGAAAAGACAGCTACAAGTGGACAGTACTCAAAGAACTCAAACCAGGCTCCAAGCAAACCAAAGAGTGCAAAGACAAGCGATGTAGAGATCACCAGCACGGTAGCTGAAGAGGAAAAGGAGAAAGAAGAACAACATAGCAGAGATGGAAGTAAAGAAAGCAAAGTTAAAAGTAAAGACAAAGAGAAAGGTTCTAGTTTGAGTGAGAGTGCAAGTAAGGAAAAAGACAAGGAGAAGGAAACACGGAGGAACAAGCAGAAGGAGACAAAAACAGTTGACAATGAGACAGAGAGAAAGACTGTGGAGAAGATGTCAAAGAAAAAACAAGAGCAGACTTCAGAGGATAGTGGAATGAAAGAGGCTGTGGACAAGAAGAAAGAATCTGTGAAGAAACTTGGTAGTGCTTCCAAAAAGACTGTTAATCTCAAAAGGAAAGAACCTGTTAAAGTTGTTAAGAAAGAGGTGAAAAAGGATGTTTCTTCAAAGAATGATGCTGTAAAGAAGGAAGTGAAGAAGGAGGTTGTCAAGAAAAGTCCTGTAGCCAGCAAAGGGCAAGTAAAGGCAAAAGTTGTAGTAGAAGAGAAGAAGAAGGCCACAGGACAACCAGTTAAAAAAGTGGCAAAGACCACGGAGCACAGTACTCGCACTGAGGCTAAAACTAGCGACACAACAGCAGAGGCAGAAGTCAGCACTGTTAGGGCTAAAGAGATGCCTTGTCAAGATGTTGAAGAAGATTCAGTGAAAAGCCAACCAGCTGAAAAAAAACTTGAGAAAAAGAGTGTGAGAAAGATCAGTGGAAAGGAGAGCAAGAAAACTGGCAAAACTGAAAGCAAGCAAGTAACAGTAGTGGCAAGACAGCGTAAAGTACAGAAGGTCAAAGAGACTGCTGCTGAATCAAAGGAGAAAACTAAGGAAAAAGCAGTCAAAAAAGATGATGTCGTGGAGTCAGTCATAGAAAATGAAGTTTCTCACTCAAGAGAAACGGAAGCAGCAAGCAAAGATAATGGTGCTGAGGATGAAGACATGGAAGTGATTGATGATTTAGAGGAGGGGAGTCTTGGGGGAAGTACTGCTGCAAGTGGAGACATAGATTTCAGTGAAGAAGAAGAAGAAGAGGATGATGATGATGAGCCGTCAGGGTCTGTCACACCATCATCTTCAGTGTCATCCAAAACAGAATCAGAAATTGCAAGCGATGACGATGAGAAAGAGGACGAAGAACCTAGAGAAAGGAGACCGAAACGGAAAGCTTCATCGGCTACTGAAGAACAGCAATCCAGTGCGGAGAGCGATAACTCGGATTCAACGGAAAGTGTTCATGTTAAGAGTAAAGTGGCAAAAGCATCAAAGCAGAAAATTAATATGGATGAGTTCTTTGAGGAAGCGCGATACTTCGTTATGAAGAGCAATAATCACGAGAATGTTGCGCTGTCAAAGGCAAAGGGTGTGTGGTCAACACCAAAAGCGAATGAGAAGAAACTCAATGTTTCCTTCAAGAGATACAAGAATGTTATCTTGATATTCTCTGTCAAAGAGAGCGGGAAATTTCAAGGTTTTGCGCGGCTGGCATCCGAGGCAAAGCACGGGGGTCCAATGATCCCCTGGGTACTCCCACCGGGGATGAGTGCCAAGGCTCTGGGAGGAGTGTTTAAACTGGAATGGCTCAACAGGAGGGAGCTGTGGTTTAGCAAGTGTCTGCATTTAAGGAACCCATGGAATGAGAACAAAGAGGTGAAGATATGCCGCGATGGACAGGAAGTAGAGCCTGCAGTTGGTGAAGCTCTTTGTCGCCTTTTCCCAGAGGACGAGACAGTTGACATTAGCTCATCGCACCAGGCATCAGAACGACGCCACAGGAAGGATAGGGAATCATCTAGGTTAGCACCAATCATCATAACCTGCTGCTGGATACAAGTCACATAGAGAGATAAGATTTTCAGTGCTTCACAGGGATGTGTGATTATCGCTGGCTATAGCTGCAGTCAGGACCTTAATCCATTGTTATTCCACAGCAGTTCCAGACCTGTGGATTTAAACCTCTTCGGGCTTTTGTCACCCGCTGGATTTGCCCGCGGGTGCCTCACTTTGATGTTCTTCTATTATGAGGTCACAGGAATGCCGAAGTCATTGCAGAGCGTGGTTCTTCACATCATCGAAGGCTCTCTTTGGAGTCAATTGATGTTTTATTCTCACTTGCTCTATTTTGCTGTGCTTTTGTAGGGTGTGTGATTAGAGAATTGTGATCCAGCATTATCTCCACTCACAAATGGACCTAAGGCCATTCATGCCACTAAGACTTTCAAGAATTCGAGAATTCCTCAATGGACTTTCATCAAAAAAAAGAACTTTTTTTCTGTTTGCTTATCAAGATCATTTGTTGAAAATGGCGGACAATACTGACCACGAGACGAAAAAGAGGCCGAGGGCTCGGGCCCTCTGGCAACAGATTCTTAGCTGAAGGCGGAGAAACCAAAATTACGGATGCTTTCCAAAATCCTTTCGATGTAGGACCCACAAAGAAATTCTGTTATTCACACAATTTCTCTTGCGGTGTGCGCATTTTTTCGGAAGACGATCTTTGCTAAACGTGTCGGCATTCGAAGTGTTTTTTGATAAGCTCTCCATTCGACAAGCCTGTGCGTGCGGGCATCTGCTGATAACGGAAAAATGTATTGCTCGCCTTGAGGTGGTTCTCGCTCGGGTGTTAGATTAATGAATGGTTTGGGGAAACGAGGAAGGACATGTTTGTAAAACTGGGACTTACGGGATTTGAATGGACAATAATGTTTTGCAACGATGCACAATTTCTTGGGGTCTTTTGCACTGGTTATTGCCCTCAGTATTGACGTCAAGAATAGCGCACACTTATTTCTTTTCACTTACAAGTGCATGATTTAAAAAAAAAATGAAGGTTTTGTTCAAAAGCCTAACATGTCAACACAGCCTGGATGGGGAGTAAGGCTTGTCAAAGAATCGCAGTTTGGACTTGAATGAAACGCATACTCTTTGACTGTTTACGCAAGTCAGGAAAGGACTTAGATAGGATGTGATCATCATCTAGGACATTACTATGCGTGGTTCGTGTCTTTTGACAACAGAATTCACCAACTCAAGGAGAGTGCAAGCGGGTTTGCTGTCTGGAGGTGACACGATTGTGCATCCATAAAACTTAAAACTGATGCTAATCTATTCCTACCTTGACAGGTTATAGTTAATGTTTTATTGCGGTAGTTGCCCATTATGGTTGTCATACCGTTGTCTTGTGTTACATTCCACATGCAGCCCCTAGGGATTTTGCCCTGTGGAATGTGCCGTTAACATGAGAATGTGTTTTGTCGTTTAGGCGTCATGCGAGACATTCCGACGATTTGCGCAAATTGAAAAGAAAGCGGCGAGGTAAAGAGTGGCTCTTTGTTGTCCTTGCTGTGCAGACAAGCTGCCTGGATAGCAATGATACTGATCTAAAGAATACTGCAACTTAAGGGCGCTCAGCATTTGTCAGACCTTGTTGGCGGGGTCAGCTCATATTGAATTCTGCTTAGCTGAGGGAGCTTCTTTTGTAGAGCAACGTCAGTTTGGCCAGAAACTGCTTCCATATAAGCAGCACTATTGCGTCGCAATAGCGAACTAGGCCCGGTTGTTCTAAAGCCGATTAACGCTAATCCCAGATTAAAAGTAAACCAAGGAGTTTATTTCTCTTTTCTAAGGTCTTGTTCAACGTTGATGTTCGCCAAAACTTTACCTTAGATGAAGGCAATTTTGTAAAACATAAAATAAGCAAAGAAACTTTCGTCAAAAAGTTGAAAATGTGAGATAAAAGTTCGCGCTAATCCTGGATTAAGTTAATAGGCTTTCGAACAACGAGGCCCTGGCTGGTCCGGCGCGCCAGTCCTGATGAATGCTAAGCGTCGCAAAGTAATATTTTTAAAGTGATTAGTGTCCAGGCGTGCGTTTCTCAAAAGACCCGAAAACTTTTCAGGCCCGAAAAGCCATTTGTAAAACTCCGACCCGCTTATTCTGTAAAGCTGGTCTTTTTATATTTTGTAAAGGGAATAAGTTAAGATAACTGGGAAATTTCGAGGCACGGAACACCTTCGTTTTCAAGATA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q96MU7	YTH domain-containing protein 1 OS=Homo sapiens OX=9606 GN=YTHDC1 PE=1 SV=3
E9Q5K9	YTH domain-containing protein 1 OS=Mus musculus OX=10090 GN=Ythdc1 PE=1 SV=2
Q9QY02	YTH domain-containing protein 1 OS=Rattus norvegicus OX=10116 GN=Ythdc1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003105 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04146 all species →	YTH	YT521-B-like domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007275 all species →	Domain	YTH domain	Interproscan
IPR045168 all species →	Family	YTH domain containing protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12357 all species →	YTH YT521-B HOMOLOGY DOMAIN-CONTAINING	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0000381 all species →	Biological Process	regulation of alternative mRNA splicing, via spliceosome	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005654 all species →	Cellular Component	nucleoplasm	Interproscan
GO:0048024 all species →	Biological Process	regulation of mRNA splicing, via spliceosome	Interproscan
GO:1990247 all species →	Molecular Function	N6-methyladenosine-containing RNA reader 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 FUN_003846-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 pulchra 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 pulchra, 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 →