Gene detail

Detailed information of PcrG019185.mRNA1 in Podabacia crustacea

Genomic Location: scaffold_24:271123...315436
NR annotation: no NCBI-NR hit recorded
Species Podabacia crustacea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PcrG019185.mRNA1

ATGGCGCCAACTTCTACAGAAGACGATGCGACAGGAACGTCTCAAGATGATTCTCAATCAACGAGGCGATCAAAGAGATCCGTAAAACGAAATGCAGGAGCAACCTCGGCGCTAGACAAAATAAGGAAATATCGGCAAACTGGTGAGAGATCGAAGTTTGAGGTTGGTGACGTTGCAGACGTTTACCAAGTGGTAAATGAAGATGAATACTCTGATATTGTTAGGAAACGCCAGGAGGAAGACTGGGTTGTTGACGATGATGGCACTGGATACGTGGATGACGGAAGAGAGATATTTGATGATGATCTTGAGGAAGAACCAACCGGAAAGAATGTTCCCAAATTCAAGCCCAAGAAACCAAATGTTAAGAAGCCAACAGTCAAGCCAAAGTCAATAAACAAAATGTTTTTAGCGGCAAGCGCTAAAGCAAAGAAACCAAAGAATGACGTTACCTCACTTGGCGAAGATGACTTGTTAAATGACCTTCTGAAAGAAGTTGAGCAACCAAAACCAGCTCCAGTGAAAATGTCCAAGGGCAAGGGGCAAGCTTTGAGAACCCCTACAGGAGTTTCTTCAAGTCGTCACACGCCAAGACGGCTCCAGGAATCATCTGGCCCTAGACAGAATATTTTCAAAGTTGAACCTAAATCTCCACCTAAATCCAGCCACACTGCAAGTCTGTCGGCAAAGAGAAAGATGGTTGTCAAAACTGAGCCATCAGAAAGAAGAGAGGGAAGGTACAGTGGCATGGTAGGGGTTCCTGAGGGGGGAGGACAGGAGGAGGATTTTGGAGATGCCATGGATATGGATTCAGGAATGCATGATGACCCTGCAGTTGACATGGCAGAACTTGATACAGGATGCGACAATTTTGATGACGATGATGATCTTGGTGACGCAGAAGCAATTCAAGCATTAACAAATGCCGAGAATAGTCATGATGAGAAACCTCAAGTGCAAATCAAGGTTGAAGCAAAAGAGAGGCAGACTGACAGAAAATGTGCTTTTCCAAGAAAATCAATGGAAATTCCTGAGGACTCTGCCTGGGAAACAATCTTAGAAAATGAAGAATCGCGGCAACAAGAGGTTCTAACAGATGTGAACGTGGATTCTTCATCCCTCCCACTTCAGGAAGTCAATGGAGAGAAGGTTCTTAAGTTTTACTGGTTTGACGCTTATGAGGATAGATTCAAACAACCAGGTACTGTATACCTGTTTGGCAAAGTGTGGATCGAATCTGCCAAAGCATTTGTAAGTTGTTCAGTGGCAGTCAAGAACATTGAGAGACAAATATTTATTCTTCCAAGAGAAAAGAAAAGGGATGTCGATGGTTCTGAGACTAATGAACCTGTTGGATTCATTGATGTTTATCAGGAATTCAACGAGAAGATTGCAACAAAACACAAAATCATGAAGTTCATCTCCAGGAAAGTTCAAAAGGCTTATGCTTTTGAGATTCAAAATGTTCCTGTCATGTCAGAGTACCTGGAAGTCAGATATTCAGCAGATTGTCCCCAGTTGCCATCTGACCTGTCTGGAGAAACCTTTAGCCATGTGTTTGGAACCAACACATCCAGTCTTGAACTTCTTCTCCTCAGTCGGAAAATGAAAGGTCCTTGTTGGCTCAACATCAAGTTGCCTCAGCTTCCCCAACAACAAGTCAGTTGGTGTAAGGTTGAGGCTGTAGTCTCAAAGCCTGATCTAATTGAAGTATCAAGTGAGCAAGACCCTCCACCACCCATAGTTGTTATGAGCCTCAGTTTTAGAACAATGTTAAACACCAAAACCCACACCCATGAGGTCTTGGCTGTGTCAGCCCTCGTTCATCATGAGGTGTCCTTAGACAAGGCTGCCCCAAAACAGAAGTTTCAATATCATTTTTGTGCTGTGAGCAAACCAAGTGATCAGATGTACCCTTATGACTTCAAAGATGCTGTCAAGAAAAAGCAAATTAAAATGGAGATTACAACATCAGAGAGAGCTCTTCTGGGATTATTCATGGCCAAGATTCACAGAATTGACCCAGATGTCCTTGTGGGACATGACATTTATGGTTTTGATCTTGATCTTCTGTTGCACAGAATCAATGCATGTAAGATTCCTCATTGGTCTCGTCTTGGACGGCTCAAAAGAACTATCATGCCAAAGTTGTCCAGCGGGGGTCCTGGTAAAGGAGGAAGTCTTCTCGATCGCTCTATCACGTGTGGTCGAATGGTGTGTGATGTTAAAATCTCTTCCAAGGAGCTCATTAGATGCAAGAGTTACGATTTGACAGCGTTATCTTGGGCAGTTCTTCAGTCTAGAAGAGAAGAGATTGACCAAGACGAAATTCCCAACAAGTTTAATTCCACGCGTGAACTACTTCACATGTTCGAGCTTACCTCAATGGATGCTTTACTGGCCTTAAGGATCATGTATGATCTGAACGTTTTGCCGCTGGCTTTACAGATAACAACTATCGCTGGAAATGTTATGGCTCGAACACTTCTTGGCGGACGATCGGAGAGGAATGAATTTCTGTTACTTCACGCCTTCAACGAAAAGAATTTTATCTGCCCCGACAAAAGCTATGGCAAGAAGCAAGTGGCTGAGGTTGAACGCGATGATGACGAACAGCCCAAAAGTTCAAAGAAAGGAAGAAGAAAGCCGGCTTACGCTGGAGGACTGGTGCTGGAACCGAAAAAAGGTTTCTACGACAAGCACATTCTTTTGCTGGATTTCAACAGTTTGTACCCGTCAATCATCCAGGAGTACAACATTTGTTTTACCACAATCAGCAGAACAAGTTTGCCGTCCAACGGACCCGCGGACGAAGAGGAAGTGGTAGAATTGCCTGATCCTGACTTGGAGCCTGGAATCTTGCCGACTGAGATCAGAAAGCTGGTGGAACGAAGAAAACAGGTGAAAGCTTTGATGAAGAACCATGGTCGTGATTCAGATCAGTATCTACAGTATGATATCAGGCAGAAGGCTTTGAAGCTCACAGCGAACAGTATGTACGGATGCTTGGGATTTTCTCACTCCCGGTTCTATGCTAAGCCACTGGCTGCTCTGGTGACGAGCAAGGGCCGCGAGATTTTGCTGAAAACGAAGGAACTAGTTCAAAACCTGGGCCTTGATGTGATTTACGGCGACACAGATTCCATTATGATTAATACGAACACCACAGACCTGGCAGAAGTCCGCAAGATTGGAAACAAGGTGAAGAATGAAGTTAACAAGCTTTACCGATTACTGGAGATCGACATTGATGGCATTTTCAAGTCCATGCTTTTGCTAAAGAAGAAGAAGTACGCTGCCATTAGTATTTCTGAGAACGAAGACGGAACACTGAATGAAGTGAAGGAAATGAAAGGGTTAGACATCGTGAGAAGGGACTGGTGCGACCTCGCAAAGGATTCAGGGAACTACGTCCTGGCTCAAATTTTGTCGTCGCAGCCACGTGAAACAATCGTGGAGAATATTCATGAGTATCTTATATCAGTTGGAGAAAACGTTGCAGACGGAAAAGTTGACATTCAGAAGTTTGTTATAAACAAGCAATTGACCAAATCTCCCCATGACTACCCCGACAAGAAGTCGTTGGCTCACGTGAACGTGGCTCTGCGCATGCTTAGTAAAGGGAGGAAAGTGAACACCGGTGACACCATCCCCTACGTCATCTGTGACGACGGTTCTACACTGGCAGCCACTCAACGCGCTTATCACCCTGAAGAGTTCTGCAAATCTGAGACGCTGAAGATTGACGTGAAGTATTACCTGGCTAATCAGGTTCATCCGGTTGTATCACGTTTGTGTGATCCTATTGACGGTACGGACGCCGCTCATATTGCACAATGTCTTGGTTTGGATCCGTCTGGTTACCGTGGTAACACAGCTATGCATGATGACGAAAGTGACGCACTGCTTGGTGGCCAGGCCCAGATGACGGACGAGGAGAGATTTAAGGATTGTCAGCGATTCACAGTGAAATGCAAGCGTCCAGGTTGTGGACTAGAGACCACAGTTGAAGTACTGTTTAAAAACACTTCACATCCATTTGGCCTCAATGACACCTGTCCCGGATGTAAGAACCAGTACAGCGCGGGCGCTGTTTCAAATCAGCTGACTGTTGCCATGCGCAAACACATTAAGGAATATTACATGGGATGGCAGAAATGTGATGACCCGTCCTGTGGTTACATTAGTCGACAGGTGTCTCTGACACATCAGCGGGGTGCCCCATGTGTACCTCGTGCTTCAAGGCTCACTTGCACCCTGTGTACTCGGACACGGCGCTCTATACTCAACTCTTGTACTACTCACGTCTGTTTGACTATGATTACGCTCTCAAGAACTCTAAAGAAGACGCCAAGAAAGTTCCATACGACTTGCGCCAGGCTCCGCCATTCTACACCGCCGTTCACTCCACAGTCTCCAAAGTTCTGA

Transcript

PcrG019185.mRNA1

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001753 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08996 all species →	zf-DNA_Pol	DNA Polymerase alpha zinc finger	Domain	Interproscan
PF03104 all species →	DNA_pol_B_exo1	DNA polymerase family B, exonuclease domain	Family	Interproscan
PF00136 all species →	DNA_pol_B	DNA polymerase family B	Family	Interproscan
PF12254 all species →	DNA_pol_alpha_N	DNA polymerase alpha subunit p180 N terminal	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017964 all species →	Conserved_site	DNA-directed DNA polymerase, family B, conserved site	Interproscan
IPR038256 all species →	Homologous_superfamily	DNA polymerase alpha, zinc finger domain superfamily	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR042087 all species →	Homologous_superfamily	DNA polymerase family B, thumb domain	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR015088 all species →	Domain	Zinc finger, DNA-directed DNA polymerase, family B, alpha	Interproscan
IPR006133 all species →	Domain	DNA-directed DNA polymerase, family B, exonuclease domain	Interproscan
IPR006172 all species →	Family	DNA-directed DNA polymerase, family B	Interproscan
IPR045846 all species →	Domain	DNA polymerase alpha catalytic subunit, catalytic domain	Interproscan
IPR006134 all species →	Domain	DNA-directed DNA polymerase, family B, multifunctional domain	Interproscan
IPR023211 all species →	Homologous_superfamily	DNA polymerase, palm domain superfamily	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR024647 all species →	Domain	DNA polymerase alpha catalytic subunit, N-terminal domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45861 all species →	DNA POLYMERASE ALPHA 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:0006260 all species →	Biological Process	DNA replication	Interproscan
GO:1902975 all species →	Biological Process	mitotic DNA replication initiation	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003682 all species →	Molecular Function	chromatin binding	Interproscan
GO:0003688 all species →	Molecular Function	DNA replication origin binding	Interproscan
GO:0003697 all species →	Molecular Function	single-stranded DNA binding	Interproscan
GO:0005658 all species →	Cellular Component	alpha DNA polymerase:primase complex	Interproscan
GO:0006272 all species →	Biological Process	leading strand elongation	Interproscan
GO:0006273 all species →	Biological Process	lagging strand elongation	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
K02320	POLA1; DNA polymerase alpha subunit A	EC:2.7.7.7	DNA replication proteins	ko03032	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 Podabacia crustacea 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 Podabacia crustacea, 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 →