Gene detail

Detailed information of amic_s0128.g31.t1 in Acropora microphthalma

Genomic Location: sc0000128_pilon:362763...395565
NR annotation: XP_044184244.1, DNA polymerase delta catalytic subunit-like [Acropora millepora]
Species Acropora microphthalma · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

amic_s0128.g31.t1

ATGGACGGAACGCAAAAGCGCAAGGGGAGCCCAGATCAGAGCAGCTCTGCAAAACGCTCTCGAAGCGAAAACGATAGTTCTAGCGATGGTGGAAGCTTTGAGAAGGAGCTTGCAGCGTTTCGCGAAGATACAGTAGCTTACAGAAATCCAACTGCGAATTGGCCACGACCTCCCGTGCCCAACTTGAACCCTTCAACTGATAAAATCGTGTTTCAGCAGCTGGAATTGGATCATTACGTCGGGAAACATTTAGATGGAATGCCAGGATCAAAAGTTGGCCCAGGGCCAATAATTCAGATGTATGGTGTTACAATGGAAGGGAACAGTGTCCTGTGTCACATACATGGCTTTGTACCATATTTTTATGTCCCTGCACCTCCTGGATTTGATCACAGCCACTGCAGTGAATTTCTGGATGGACTTGACAAGACTGTGTTGAGTGACATGAGATCTAACAAGGATAACATATCTCATGCTGTCTTGGCTGTTGAATGCGAGATGAAGGAGAGCATCTATGGTTTCCATGGTAACAGAAAGATACCATTCCTTCGCATCACAATGGCACTGCCAAGGCTCATTGCACCAGCAAAACGAATTTTGGAGACAGGATTCAAGTTTGCATCATTTCCTGAAAGAGGTTATTCCACTTATGAAAGTAACATTGATTATGAGGTTCGATTCATGGTAGACACTGAAGTCGTGGGTTGCAACTGGATTGAGCTTCCTGCTGGGAAATATAAAGTGCGCTCCCCTGCTACCATTGACGACAGTTACAAGACAGGGGTACAGCCTAAATCATACTGCCAAATTGAAGTGGATATTGCATATGATGAGTTCATTAGCCATACCCCTGAAGGTGAATGGTCAAAAGTAGCACCTCTACGAATTTTGAGCTTTGACATTGAGTGCGCTGGCAGGAAAGGTGTCTTTCCTGAACCAGAAAAGGACCCAGTGATTCAGATAGCTAACATGGTTATTAACCAGGGTGACAGAGACCCCTTCATCAGAAATGTTTTTACATTGAATTCTTGTGCACCCATTGTTGGATCTCATGTGCTGTCATTTCCGCAAGAAGGAAATATGCTGCAGAAATGGAGTGAGTTTGTCAAGAGAGTGGATCCAGACATCATAACTGGTTACAATATTGTGAATTTTGATCTCCCATATCTGCTCAACAGGGCAGCTGCCCTCAAAGTTCAAACATTTCCCTTTCTTGGAAGAGTAAGAGATGAAAAAAGCACCATATCTAACACTACGTTTCAATCTCGTGCTTACGGAAAGCGAGAAAACAAAGTCATAAACATTGCTGGTAGAGCGCAGTTTGATTTGCTGCATGCTTTGTTAAGAGATTACAAACTAAGGTCCTACACACTGAATGCTGTCAGTTTTCATTTTCTGCAAGAACAAAAAGAGGACGTACAACATAGCATCATCACAGACTTACAGAATGGAAATGACCAGACGCGCCGTAGACTTGCGATTTACTGCATGAAAGATGCGATTTTACCATTGAGATTGCTTGAGAAACTGATGTGCATTATAAACTACATGGAGATGGCCCGTGTTACTGGAGTGCCATTGAGTTACCTGTTATCCAGAGGGCAACAAATCAAAGTTGTCTCACAGCTGCTCAGAATGTCCAGAAAGCAAGACTTGTTACTCCCTGCACACAAAGCTGAAGCGGGAGAAGAATACGCTGGAGCTACCGTCATTGAGCCATCGAAAGGGTACTATGATATTCCTGTGGCAACTCTTGACTTTGCTTCTCTATATCCTTCCATCATGATGGCCCATAACCTGTGCTATACATCTCTCCTTCACCAAAGTGACCTAAAGAGTTTGAAACCAGATGAATTCATCAAGACACCTTCTGGTGATCATTTTATTAAAGCCTCAATCAGGAAAGGACTGCTGCCTGAAATCCTGGAGAACTTGTTGTCTGCAAGGAAGAAGGCCAAAGATGATCTGAAGAAAGAAACAGATCCTTTCAAGAAAAAGGTGCTTGATGGTCGACAGTTGGCTTTGAAGCTCAGTGCCAACTCGGTGTATGGTTTTACTGGGGCTCAAGTCGGTAAACTACCTTGTTTACCAATCTCACAGAGTGTGACGGCATTTGGCCGTATGATGATAGAGAGGACTAAAGAGCTTGTGGAATTGAAGTACACAGTGGAAAATGGCTACAAGACAAATGCAAAAGTCATTTATGGCGACACTGACTCTGTGATGGTAAAATTTGGTGTGGAATCTGTTGCGGAGAGCATGGAACTTGGTAGAGAAGCTGCATCGTATGTCTCAGGACATTTTGTGAAACCCATCAAGCTAGAATTTGAAAAGGTATATTTTCCTTATCTTCTGATAAGCAAGAAACGTTATGCTGGCTTGTACTTCACTAAACCTGACAAGCATGACAAGATGGATTGCAAAGGAATTGAAACTGTAAGGAGAGACAACTGTCCTCTGGTTGCCAATCTTATCAATTCATGCTTACAGAAGATCCTCATTGAAAGGGATCCCATGGGAGCAGTGGAATACACTAAACAAGTCATATCAGACTTGCTGTGCAATAGAATAGATATCTCACAGCTTGTCATTACAAAAGAATTGACCAAGACAGGAGATGAATATGCTGGAAAGCAGGCACACTCAGAGCTGGCAGAAAGAATGCGGAAGCGAGATGCAGGATCTGCTCCAAAGCTGGGTGACAGAGTTCCTTATGTCATAATAGCTGGTGCCAAGGGTGAAAAGGCATATGAAAAAGCTGAGGATCCTATCTATGTGTTGGAAAATAACATCCCCATTGACACCAAGTACTACCTTGAAAACCAATTGTCAAATCCACTGCTCAGAATATTTGAACCAATTCTTGGAGAGGCAAAAGCAACGTCTGTGTTGCTAAAGGGTCAACATACTTTGACAAAGACCATAGTCACGTCAAAAGTAGGCAAATTAGCAATGTTCACCAAAAAGAGAAGCACTTGTATTGGCTGCAAATCAGTCTTGGATAATGATGGTGCAGCTGTCTGCAAGCATTGCAAGCCAAAAGAGTCAGCACTTTTCCAAAAGGAGATCTCACACCTGAATGCACTGGAGGAGAAGTTTGCCAGGTTATGGACACAGTGTCAGAACTGTCAAGGAAGCTTGCATGCCGATGTTCTGTGCACAAGTCGTGATTGCCCCATATTCTACATGAGAAAGAAAGTTCAGAAGGATCTCTCTGACCAGGACAAACTCATCCAAAGATTTGGTGACTTCACTTGGTGA

Transcript

amic_s0128.g31.t1

GTAGTCATCACAAAGGCGAGATTTTTCCAGTTAGTCTTGACCAGCTTTTCAGAAGGTTAGTCGCCATGGACGGAACGCAAAAGCGCAAGGGGAGCCCAGATCAGAGCAGCTCTGCAAAACGCTCTCGAAGCGAAAACGATAGTTCTAGCGATGGTGGAAGCTTTGAGAAGGAGCTTGCAGCGTTTCGCGAAGATACAGTAGCTTACAGAAATCCAACTGCGAATTGGCCACGACCTCCCGTGCCCAACTTGAACCCTTCAACTGATAAAATCGTGTTTCAGCAGCTGGAATTGGATCATTACGTCGGGAAACATTTAGATGGAATGCCAGGATCAAAAGTTGGCCCAGGGCCAATAATTCAGATGTATGGTGTTACAATGGAAGGGAACAGTGTCCTGTGTCACATACATGGCTTTGTACCATATTTTTATGTCCCTGCACCTCCTGGATTTGATCACAGCCACTGCAGTGAATTTCTGGATGGACTTGACAAGACTGTGTTGAGTGACATGAGATCTAACAAGGATAACATATCTCATGCTGTCTTGGCTGTTGAATGCGAGATGAAGGAGAGCATCTATGGTTTCCATGGTAACAGAAAGATACCATTCCTTCGCATCACAATGGCACTGCCAAGGCTCATTGCACCAGCAAAACGAATTTTGGAGACAGGATTCAAGTTTGCATCATTTCCTGAAAGAGGTTATTCCACTTATGAAAGTAACATTGATTATGAGGTTCGATTCATGGTAGACACTGAAGTCGTGGGTTGCAACTGGATTGAGCTTCCTGCTGGGAAATATAAAGTGCGCTCCCCTGCTACCATTGACGACAGTTACAAGACAGGGGTACAGCCTAAATCATACTGCCAAATTGAAGTGGATATTGCATATGATGAGTTCATTAGCCATACCCCTGAAGGTGAATGGTCAAAAGTAGCACCTCTACGAATTTTGAGCTTTGACATTGAGTGCGCTGGCAGGAAAGGTGTCTTTCCTGAACCAGAAAAGGACCCAGTGATTCAGATAGCTAACATGGTTATTAACCAGGGTGACAGAGACCCCTTCATCAGAAATGTTTTTACATTGAATTCTTGTGCACCCATTGTTGGATCTCATGTGCTGTCATTTCCGCAAGAAGGAAATATGCTGCAGAAATGGAGTGAGTTTGTCAAGAGAGTGGATCCAGACATCATAACTGGTTACAATATTGTGAATTTTGATCTCCCATATCTGCTCAACAGGGCAGCTGCCCTCAAAGTTCAAACATTTCCCTTTCTTGGAAGAGTAAGAGATGAAAAAAGCACCATATCTAACACTACGTTTCAATCTCGTGCTTACGGAAAGCGAGAAAACAAAGTCATAAACATTGCTGGTAGAGCGCAGTTTGATTTGCTGCATGCTTTGTTAAGAGATTACAAACTAAGGTCCTACACACTGAATGCTGTCAGTTTTCATTTTCTGCAAGAACAAAAAGAGGACGTACAACATAGCATCATCACAGACTTACAGAATGGAAATGACCAGACGCGCCGTAGACTTGCGATTTACTGCATGAAAGATGCGATTTTACCATTGAGATTGCTTGAGAAACTGATGTGCATTATAAACTACATGGAGATGGCCCGTGTTACTGGAGTGCCATTGAGTTACCTGTTATCCAGAGGGCAACAAATCAAAGTTGTCTCACAGCTGCTCAGAATGTCCAGAAAGCAAGACTTGTTACTCCCTGCACACAAAGCTGAAGCGGGAGAAGAATACGCTGGAGCTACCGTCATTGAGCCATCGAAAGGGTACTATGATATTCCTGTGGCAACTCTTGACTTTGCTTCTCTATATCCTTCCATCATGATGGCCCATAACCTGTGCTATACATCTCTCCTTCACCAAAGTGACCTAAAGAGTTTGAAACCAGATGAATTCATCAAGACACCTTCTGGTGATCATTTTATTAAAGCCTCAATCAGGAAAGGACTGCTGCCTGAAATCCTGGAGAACTTGTTGTCTGCAAGGAAGAAGGCCAAAGATGATCTGAAGAAAGAAACAGATCCTTTCAAGAAAAAGGTGCTTGATGGTCGACAGTTGGCTTTGAAGCTCAGTGCCAACTCGGTGTATGGTTTTACTGGGGCTCAAGTCGGTAAACTACCTTGTTTACCAATCTCACAGAGTGTGACGGCATTTGGCCGTATGATGATAGAGAGGACTAAAGAGCTTGTGGAATTGAAGTACACAGTGGAAAATGGCTACAAGACAAATGCAAAAGTCATTTATGGCGACACTGACTCTGTGATGGTAAAATTTGGTGTGGAATCTGTTGCGGAGAGCATGGAACTTGGTAGAGAAGCTGCATCGTATGTCTCAGGACATTTTGTGAAACCCATCAAGCTAGAATTTGAAAAGGTATATTTTCCTTATCTTCTGATAAGCAAGAAACGTTATGCTGGCTTGTACTTCACTAAACCTGACAAGCATGACAAGATGGATTGCAAAGGAATTGAAACTGTAAGGAGAGACAACTGTCCTCTGGTTGCCAATCTTATCAATTCATGCTTACAGAAGATCCTCATTGAAAGGGATCCCATGGGAGCAGTGGAATACACTAAACAAGTCATATCAGACTTGCTGTGCAATAGAATAGATATCTCACAGCTTGTCATTACAAAAGAATTGACCAAGACAGGAGATGAATATGCTGGAAAGCAGGCACACTCAGAGCTGGCAGAAAGAATGCGGAAGCGAGATGCAGGATCTGCTCCAAAGCTGGGTGACAGAGTTCCTTATGTCATAATAGCTGGTGCCAAGGGTGAAAAGGCATATGAAAAAGCTGAGGATCCTATCTATGTGTTGGAAAATAACATCCCCATTGACACCAAGTACTACCTTGAAAACCAATTGTCAAATCCACTGCTCAGAATATTTGAACCAATTCTTGGAGAGGCAAAAGCAACGTCTGTGTTGCTAAAGGGTCAACATACTTTGACAAAGACCATAGTCACGTCAAAAGTAGGCAAATTAGCAATGTTCACCAAAAAGAGAAGCACTTGTATTGGCTGCAAATCAGTCTTGGATAATGATGGTGCAGCTGTCTGCAAGCATTGCAAGCCAAAAGAGTCAGCACTTTTCCAAAAGGAGATCTCACACCTGAATGCACTGGAGGAGAAGTTTGCCAGGTTATGGACACAGTGTCAGAACTGTCAAGGAAGCTTGCATGCCGATGTTCTGTGCACAAGTCGTGATTGCCCCATATTCTACATGAGAAAGAAAGTTCAGAAGGATCTCTCTGACCAGGACAAACTCATCCAAAGATTTGGTGACTTCACTTGGTGACTTTGTTTACAGTGACTTCATGAAACTCCAAATCTTCTTAGCAATGGACTAAAGAGTTTTCTTTCACTTGTAAAATAATGAGTGCAGAACTAT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P52431	DNA polymerase delta catalytic subunit OS=Mus musculus OX=10090 GN=Pold1 PE=1 SV=2
O54747	DNA polymerase delta catalytic subunit OS=Rattus norvegicus OX=10116 GN=Pold1 PE=2 SV=1
P28339	DNA polymerase delta catalytic subunit OS=Bos taurus OX=9913 GN=POLD1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003830 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00136 all species →	DNA_pol_B	DNA polymerase family B	Family	Interproscan
PF14260 all species →	zf-C4pol	C4-type zinc-finger of DNA polymerase delta	Domain	Interproscan
PF03104 all species →	DNA_pol_B_exo1	DNA polymerase family B, exonuclease domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006172 all species →	Family	DNA-directed DNA polymerase, family B	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR017964 all species →	Conserved_site	DNA-directed DNA polymerase, family B, conserved site	Interproscan
IPR050240 all species →	Family	DNA polymerase type-B	Interproscan
IPR006134 all species →	Domain	DNA-directed DNA polymerase, family B, multifunctional domain	Interproscan
IPR025687 all species →	Domain	C4-type zinc-finger of DNA polymerase delta	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR042087 all species →	Homologous_superfamily	DNA polymerase family B, thumb domain	Interproscan
IPR023211 all species →	Homologous_superfamily	DNA polymerase, palm domain superfamily	Interproscan
IPR006133 all species →	Domain	DNA-directed DNA polymerase, family B, exonuclease domain	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10322 all species →	DNA POLYMERASE CATALYTIC SUBUNIT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003887 all species →	Molecular Function	DNA-directed DNA polymerase activity	Interproscan
GO:0006261 all species →	Biological Process	DNA-templated DNA replication	Interproscan
GO:0006287 all species →	Biological Process	base-excision repair, gap-filling	Interproscan
GO:0006297 all species →	Biological Process	nucleotide-excision repair, DNA gap filling	Interproscan
GO:0008296 all species →	Molecular Function	3'-5'-DNA exonuclease activity	Interproscan
GO:0043625 all species →	Cellular Component	delta DNA polymerase complex	Interproscan
GO:0045004 all species →	Biological Process	DNA replication proofreading	Interproscan
GO:0003677 all species →	Molecular Function	DNA 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
K02327	POLD1; DNA polymerase delta subunit 1	EC:2.7.7.7	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 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 →