Gene detail

Detailed information of aint_s0056.g49.t1 in Acropora intermedia

Genomic Location: sc0000056_pilon:647984...652710
NR annotation: XP_029199086.2, LOW QUALITY PROTEIN: mismatch repair endonuclease PMS2-like [Acropora millepora]
Species Acropora intermedia · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

aint_s0056.g49.t1

ATGGCGGGAGCTTCGTCTCCAGTAGTTCAAGCTATTGATAAACGAACTATTCACCAGATATGTTCTGGACAGGTAATATTGAGTATAGCAACGGCTATGAAAGAGCTTGTTGAAAATAGCTTGGACGCTGGAGCAACAAATATCGACATTAAACTCAAAAATCGCGGCGCGGACATCTTGGAAGTGAATGACAATGGCGCCGGAGTCGAACCACATAATTTCGAAGCTTTAACCTTGAAACACCACACGTCTAAACTTAAGGATTTTTCGGATCTAGCAAGTGTGGAAACGTTTGGTTTCAGAGGAGAGGCTCTCAGCTCACTTTGCGCCTTGAGTAAACTATCAATAGTAACTCACCATTCTACACAAGCTGCAGCTACAAGACTTGAGTACGATCACAATGGAAAACTGATCTCAAAGACACTTTGTGCGAGGGATTTGGGTACCTCAGTTTCCTTGGAAAATTTGTTTTCTACTCTGCCTGTAAGACACAGGGAATTTCTACGGAACATCAAGAGAGAATTCACAAAGTTGGTTCACGTTTTACAGGCCTATTGTCTGATTAGTACTGGAGTCAGAATAGCATGCAGTGATCAACTCGAGAAAGGAAAGAAAACCACTGTTGTGTCTACAAATGGTAGCAAACAAGTGAAAGATAACATTACTTGTGTATTTGGACCCAAACAGGTCCAAACATTAATGCCTTTTCAACAACACAAGCCATCCGAGGAAGACTGTAGTGAGCTTGGTATTGACGCATCAAAGCTCAGTGCACAGGAAGACCTCTTCCAAATTACTGGGTACATATCGAAACCAGAGCATGGAATGGGACGAAGCAGTGCTGATCGGCAGTTCTTGTTCATTAACAAACGTCCATGTGATCTAATGAAAGTTTCACGTATTGTCAATGAGGTGTACCATATGTATAACAGGAACCAATACCCTTTTATCATGTTGGACATTTCTCTGGCAAGAGATGGAGTGGATGTAAATGTAACTCCCGACAAGCGTCAAGTTTTTGTCCAAAATGAAAAAGCCCTTCTTGCAACCATTAGAACATCCTTGAAGAGAATGTTTGACCCCAGCACTGCATCCTTTGACATCAACCAGAAACCTTTAATGCAAATAAAACTTCCTGTTGATTCATGTGCACTGAGGACAAGAGCTGACCCCTTTGAAGATGAGAAACACCATCAGTCAAACAATATCTGCACAGAAACCAAAGAGGAAAGCAAAGATGTAAAGCCATGTGCTTCATTAACATCAGTTGTACCTGATGAAGCAAAAACTAAATTCCCGTCACTGAGTGGCTTCAAGAGAAAATTTTCATCCATTGAGGAAAAGTCAACCGGGAAATTCAAAGAACCACGTTCAAAGCAAGCCAAATTAACATCTATTTTTGGCAATGACAAGAAAGCATTTTGTCAAGCAGAGAAAGACTCTGCACGATCAAATGATGGATTTTCCTGTTATGAAAGACCTATTCAAAATTTGGAACCTGGTGTAAAAAAGGGTGGCCAATATGGGAATGATATCGAAGTTATTGATTCAAGAGAGTTCAACAACTCTGATGTTGAAGTTATAAAACCACCAGAGATGGATAAAACTGGTATTGATGTCATTGAATTAAGAGAGACAAAAAATGTAAAGGACATAGACTTTGAGTTTCAAAGTGATGAGTCAGCTGTAAAAACTCCAAAGCAGGTCAAAATTGTGGAATCAAGCAGTGAACTCTCTCAAAACAACAGTATGAAAAATGCTCTGAAAGAGAGAGACAAAGATGGAGAAGCACTCAATGAAACATCCAAGACGTCAGCAGATCTCGGAGGTAACAAGGCCACTGAATTAGTGATGGTTACTCCTAAGATGTGTGAAAAATCTAATCATGTTTTGGACATAGTAAGAAGCAGAAAGGAGAAAAAAGTCAACTTTTGCTTGGAAAAACTCAAAAGAACTGTTAAAAAACCAAACAAGGTGATGATAAGAGAAGCTGAAGCTCGCCTATTTAGAGCAAAAATTGCACCTGATAGCAACTCCAGCGCTGAGAACGAACTGAGAAAGAACATATGCAAAGAAGCATTTGAACGGATGGAAATTCTAGGCCAGTTCAACTTAGGGTTTATCATCACAAAACTGGACAACGATCTGTTCATCATTGATCAGCACGCTTCAGATGAGAAGTTCAATTTTGAGGATCAACAGCGCAACATGACGATTAAATCACAACGTCTTATTATTCCACAGAAACTTGAACTAACAGCTGCTAATGAAGCTATTCTCATGGACAATGTGGAAATATTTCGCATGAATGGATTTGAATTTGAAATTGATCAGAATGCTCAAGCCATGAACAAGATTAAATTAGTTTCTCTTCCAATTAGCAAGAATTGGACATTTGGTGCAGAAGACATAGAAGAGTTGATTTTTATGTTGAGCGATTCCCCTGGTGTGATGTGCAGGCCATCAAGGGTGAGGAAAATGTTTGCAAGTCGTGCATGTCGCATGTCAGTCATGGTCGGAACTGCACTGAATCAGGCTCAAATGAAAAGGATTGTTTCCCACATGGGAGAGATAGAACATCCTTGGAACTGTCCTCATGGCCGCCCCACCATGAGACATTTGATAAATCTTGGAATGCTCCCAAAAGCAGAAACGTAA

Transcript

aint_s0056.g49.t1

GTCCCTTCCGATGAAATCCCTGTTGCTCACTGGCTGGCAAAATGGCGGGAGCTTCGTCTCCAGTAGTTCAAGCTATTGATAAACGAACTATTCACCAGATATGTTCTGGACAGGTAATATTGAGTATAGCAACGGCTATGAAAGAGCTTGTTGAAAATAGCTTGGACGCTGGAGCAACAAATATCGACATTAAACTCAAAAATCGCGGCGCGGACATCTTGGAAGTGAATGACAATGGCGCCGGAGTCGAACCACATAATTTCGAAGCTTTAACCTTGAAACACCACACGTCTAAACTTAAGGATTTTTCGGATCTAGCAAGTGTGGAAACGTTTGGTTTCAGAGGAGAGGCTCTCAGCTCACTTTGCGCCTTGAGTAAACTATCAATAGTAACTCACCATTCTACACAAGCTGCAGCTACAAGACTTGAGTACGATCACAATGGAAAACTGATCTCAAAGACACTTTGTGCGAGGGATTTGGGTACCTCAGTTTCCTTGGAAAATTTGTTTTCTACTCTGCCTGTAAGACACAGGGAATTTCTACGGAACATCAAGAGAGAATTCACAAAGTTGGTTCACGTTTTACAGGCCTATTGTCTGATTAGTACTGGAGTCAGAATAGCATGCAGTGATCAACTCGAGAAAGGAAAGAAAACCACTGTTGTGTCTACAAATGGTAGCAAACAAGTGAAAGATAACATTACTTGTGTATTTGGACCCAAACAGGTCCAAACATTAATGCCTTTTCAACAACACAAGCCATCCGAGGAAGACTGTAGTGAGCTTGGTATTGACGCATCAAAGCTCAGTGCACAGGAAGACCTCTTCCAAATTACTGGGTACATATCGAAACCAGAGCATGGAATGGGACGAAGCAGTGCTGATCGGCAGTTCTTGTTCATTAACAAACGTCCATGTGATCTAATGAAAGTTTCACGTATTGTCAATGAGGTGTACCATATGTATAACAGGAACCAATACCCTTTTATCATGTTGGACATTTCTCTGGCAAGAGATGGAGTGGATGTAAATGTAACTCCCGACAAGCGTCAAGTTTTTGTCCAAAATGAAAAAGCCCTTCTTGCAACCATTAGAACATCCTTGAAGAGAATGTTTGACCCCAGCACTGCATCCTTTGACATCAACCAGAAACCTTTAATGCAAATAAAACTTCCTGTTGATTCATGTGCACTGAGGACAAGAGCTGACCCCTTTGAAGATGAGAAACACCATCAGTCAAACAATATCTGCACAGAAACCAAAGAGGAAAGCAAAGATGTAAAGCCATGTGCTTCATTAACATCAGTTGTACCTGATGAAGCAAAAACTAAATTCCCGTCACTGAGTGGCTTCAAGAGAAAATTTTCATCCATTGAGGAAAAGTCAACCGGGAAATTCAAAGAACCACGTTCAAAGCAAGCCAAATTAACATCTATTTTTGGCAATGACAAGAAAGCATTTTGTCAAGCAGAGAAAGACTCTGCACGATCAAATGATGGATTTTCCTGTTATGAAAGACCTATTCAAAATTTGGAACCTGGTGTAAAAAAGGGTGGCCAATATGGGAATGATATCGAAGTTATTGATTCAAGAGAGTTCAACAACTCTGATGTTGAAGTTATAAAACCACCAGAGATGGATAAAACTGGTATTGATGTCATTGAATTAAGAGAGACAAAAAATGTAAAGGACATAGACTTTGAGTTTCAAAGTGATGAGTCAGCTGTAAAAACTCCAAAGCAGGTCAAAATTGTGGAATCAAGCAGTGAACTCTCTCAAAACAACAGTATGAAAAATGCTCTGAAAGAGAGAGACAAAGATGGAGAAGCACTCAATGAAACATCCAAGACGTCAGCAGATCTCGGAGGTAACAAGGCCACTGAATTAGTGATGGTTACTCCTAAGATGTGTGAAAAATCTAATCATGTTTTGGACATAGTAAGAAGCAGAAAGGAGAAAAAAGTCAACTTTTGCTTGGAAAAACTCAAAAGAACTGTTAAAAAACCAAACAAGGTGATGATAAGAGAAGCTGAAGCTCGCCTATTTAGAGCAAAAATTGCACCTGATAGCAACTCCAGCGCTGAGAACGAACTGAGAAAGAACATATGCAAAGAAGCATTTGAACGGATGGAAATTCTAGGCCAGTTCAACTTAGGGTTTATCATCACAAAACTGGACAACGATCTGTTCATCATTGATCAGCACGCTTCAGATGAGAAGTTCAATTTTGAGGATCAACAGCGCAACATGACGATTAAATCACAACGTCTTATTATTCCACAGAAACTTGAACTAACAGCTGCTAATGAAGCTATTCTCATGGACAATGTGGAAATATTTCGCATGAATGGATTTGAATTTGAAATTGATCAGAATGCTCAAGCCATGAACAAGATTAAATTAGTTTCTCTTCCAATTAGCAAGAATTGGACATTTGGTGCAGAAGACATAGAAGAGTTGATTTTTATGTTGAGCGATTCCCCTGGTGTGATGTGCAGGCCATCAAGGGTGAGGAAAATGTTTGCAAGTCGTGCATGTCGCATGTCAGTCATGGTCGGAACTGCACTGAATCAGGCTCAAATGAAAAGGATTGTTTCCCACATGGGAGAGATAGAACATCCTTGGAACTGTCCTCATGGCCGCCCCACCATGAGACATTTGATAAATCTTGGAATGCTCCCAAAAGCAGAAACGTAACTTCAATGGTGAAGTGCAGAAGTGACTGAGTTTTTTATTGGTGTAGTTTAGTTTTAACTCAACCCACTCAAACATTTAGACTTCAAGTAGCTCCACTTGCAACACCACTTTAAGTTTTTGTAATAGAGACTACTAGCAGTCTAACTCAAGGAAAGATCGGGCCCACAAAAAGTCAATGCATTTATTTCATTTATATTTTGCAATACCGTTTCTTCATAATAGATTTCAAGAGTGCTGACATTGAAAAATCCTTTTTCACAACATGACAGATTTTGAAAAATCTCATCAGTCTGTATTTTTTTAACAAATAATCCCTACTAAGTGTAACGAGTAGTGTTACAGTCGAACCTCGATTATCCGGACCTCGATTATCCGGACTTTTCGATTATCCATACTTTTTCTCTGGTCCCGTTTTTTGCATGAATATTAATAAGCTTTGATCTCAAAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P54278	Mismatch repair endonuclease PMS2 OS=Homo sapiens OX=9606 GN=PMS2 PE=1 SV=2
F1NQJ3	Mismatch repair endonuclease PMS2 OS=Gallus gallus OX=9031 GN=PMS2 PE=2 SV=3
P54279	Mismatch repair endonuclease PMS2 OS=Mus musculus OX=10090 GN=Pms2 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006205 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08676 all species →	MutL_C	MutL C terminal dimerisation domain	Domain	Interproscan
PF01119 all species →	DNA_mis_repair	DNA mismatch repair protein, C-terminal domain	Family	Interproscan
PF13589 all species →	HATPase_c_3	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR020568 all species →	Homologous_superfamily	Ribosomal protein uS5 domain 2-type superfamily	Interproscan
IPR014762 all species →	Conserved_site	DNA mismatch repair, conserved site	Interproscan
IPR014790 all species →	Domain	MutL, C-terminal, dimerisation	Interproscan
IPR013507 all species →	Domain	DNA mismatch repair protein, S5 domain 2-like	Interproscan
IPR038973 all species →	Family	DNA mismatch repair protein MutL/Mlh/Pms-like	Interproscan
IPR036890 all species →	Homologous_superfamily	Histidine kinase/HSP90-like ATPase superfamily	Interproscan
IPR042120 all species →	Homologous_superfamily	MutL, C-terminal domain, dimerisation subdomain	Interproscan
IPR014721 all species →	Homologous_superfamily	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Interproscan
IPR002099 all species →	Family	DNA mismatch repair protein MutL/Mlh/PMS	Interproscan
IPR042121 all species →	Homologous_superfamily	MutL, C-terminal domain, regulatory subdomain	Interproscan
IPR037198 all species →	Homologous_superfamily	MutL, C-terminal domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10073 all species →	DNA MISMATCH REPAIR PROTEIN MLH, PMS, MUTL	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006298 all species →	Biological Process	mismatch repair	Interproscan
GO:0030983 all species →	Molecular Function	mismatched DNA binding	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0032300 all species →	Cellular Component	mismatch repair complex	Interproscan
GO:0032389 all species →	Cellular Component	MutLalpha complex	Interproscan
GO:0140664 all species →	Molecular Function	ATP-dependent DNA damage sensor 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
K10858	PMS2; DNA mismatch repair protein PMS2	-	DNA repair and recombination proteins	ko03400	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 intermedia 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 intermedia, 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 →