Gene detail

Detailed information of ANN00334-RA in Leptoseris scabra

Genomic Location: Scaffold_3__1_contigs__length_63507380:5692477...5710938
NR annotation: XP_020603181.1, DNA polymerase subunit gamma-1-like [Orbicella faveolata]
Species Leptoseris scabra · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ANN00334-RA

ATGTATCGCTCACTTGCAGCGATTTTACGTAAAACTGGAAGGCTATATCCAGCTCAGCTACGCATGCCTAGTCTCTCAAGACGCAAGTGTTCATCAACTTCATCAACATCGCTTACCGAAGATGTCACCCCGCCAAATGAAGAACTCAAAGAAAAGAGGTTCAATCCCCTCGAAATACAGATGCTTTCTAGTTCATTACACGATCAAGTTTTCCACGGAAAAACCGAAACCTACGATCCCGCAGTTGTCGACAAATGCCAAGAACATTTGAAGGTCCATAACTTGTGGAACAAAAGTGGGACTGTCCTTCCTGAAGTCGATTTTGAACTCCCGCCTTTACTGGGATCAAACGTCGATGAGCATTTTAGAAAGATCGCAGAGCAACAAAGCAAACCTTACTTTGAAAAGGCTCAAATGTTGGCGAATCTCACATTGTCTGCTATGCCAGATGAGTGGAGTTTCTCTCCAGGGTGGACTAAGTATGTTTACAGTGACGAGGGGCTAATGACATCACCAGTGGATTTCCCTCAGGAAGATGCCCTGATCTTTGATGTTGAGGTCTGCGTCAATGAAGGCCCCTTCCCTGTGATTGCTGTAGCGGCTTCTCCTACTGCATGGTACTGTTGGGTGAGTCCCAGACTTGTGGAAGACAAGAGTTACCAGTGGTTGGTCCGCTCAGCCCCTAAGCTGTATATTCCATTGGAAATTCCTGATAGTCAGGATTGGGGCAAGGCAGAGTGGCGAGAGAGGCTCATAGTCGGTCATTCTGTAGGATATGATAGATCATTTATAAAAGAGCAATATTATATCAAGGGACCAAAAACTTATTTCCTGGACACTCTGAGTCTGCACATGTGCATCTCTGGTTTAACAAGTCTCCAACGAGGCCTGTGGGAATCAGCAAATGCGGGACGCATTGGGAAGGTGCCATGGATGCTTGTTGGCTCAGGGAACAAACTGGCGAACCTTCACCAGTTATACTGTGGTGGTGACGAGATGGACAAATCCATGGTGAAGATTTTCATTGAAGGAACGCTTGATGATGTGAAGGAAAATTTCCAGGATTTAGTAACATACTGTGCAAAAGACACTGTTGCAACTCAGGAGGTATTCGCTGCCCTTTGGCCCAAATTCCTGGATAGGTTTCCACACCCAGTGTCTTTTGCCGGGATGCTAGAGATGGGATCAGCATACCTCCCTGTTGATCGTTCCTGGGAAAACTACATCAGAGATGCGGATGACACTTATGAAGACTTGGAGAAGGAGATGAAGTGCTCATTAATGAAACTAGCAGATGACTCGTGCAACTACCTTCATGGCAAAAGCTCAGATTCTCCAGAGGTTTTGCATGTGGCCTTCAGTTTCTTCAGAAAACATTGTCCCAATCCAAGGTATGCAGAGGACCCCTGGCTTTGGGAGTTGGATTGGGCAGTCCAGGATATACGAACAAAAAAACTCAAACCTCCAAAAAAGAAAAGGAAAACCAAAGCGAAAGAAGACGCGGTTGTTTCAGGTGAAGATTCTGCGACTGATGCAAGCACACCTGGAGAGACCATTTCTGACATTTTAAGTGAAGATGAAATGCTTGATGATAACAACATTGAAGTAGTGGAGGGGTTGAAAAACTCTTCAGACATCTTGGCAACCATTCCTTCAGCTGTTGATGTGATGTACAAGAGACGACAGAACATGCCGGGGTACCCTAATTGGTACAGATCTCTCTGCATTGGACCATCAGACAAGGAGGAGTGGAGGGAAGGGCCTGTACACATCAGCCCACAGTGTCAAGTGGCGCCCATGCTATTGCGCATGACATGGGATGGCTTTCCACTGCACCACAGCCGTAAACATGGATGGGGATATTTGGTGCCTGGTAGGACAGATAATCTGAGAACCAATCACATCACGTTACAAGACAACGAGGAAGAGCAAGTGGAAACAAAAAAGGCAGAAGCACCTTTTCCAACGAGAGCATTTGAAAATCTTTGGAAAAGCCACCGTATGAACAAAGCTCAACAGCGTCTCAACACGGACGCGAAGTTTGACAACGGCGAGATGGACGTGTACAATCTTAGCGAAGATCAGCTGTGGGCGTCGTCAGAGCTTGAAGAAATGAGGAAACCGAAAAGCTCTAAAGCCAAGAAATCTCCAGCTGTGTCGATCGAAACTGAGGATGTAGAAGAAGAGAAGAAGGCAGCCGCGAAGAAGAAGACATCTCGAGCGCAAACTCAAGGAACAAACTCGGCCACAGAGAGCAGTCCTGATTTTTATCATGGCGTCGGGCCTTTTAATGATATCAACTTTCCTGGAGTATGGTTCTTCCGGATACCACATAAGGCCGGGGTCAAAATTCGTGGTTTGGTACCCCTTAGGAAGCTAGAATCTAAAATGGCTTCCGTCAAAAGTATGGTGAATGGTGAAAACTACCGTTGTGGAAACCCTCTAGCCAAGGACTATATCAGCAAGATTGAGGATGGAACATTGGTGGCGTCTGGTGATAATAGTGCTCACAAAACGCTGATTGTCAACAAGATGATTTCTTCCTGGAGAAACGCTCAGAAAAGAGTCAGATCTCAGTTAGCTGTTTGGTTCGACAAAGACGACTTGCCGACAGAAATATCTGGTTCCGACAAGTACAGCGCTGATAATATGCTTGGCGCCATCTTGCCGCGGGTCATTACAGCTGGGACGGTGACAAGGCGAGCAGTAGAACCTACTTGGTTGACGGCTAGCAACCCAAGAGAGGACCGTGTCGGCTCTGAGCTGAAGGCCATGGTCCGGGCTCCTCCAGGGTACTGTTTAGTAGGGGCTGATGTAGACAGCCAAGAGCTCTGGATTGCGGCCATCTTGGGGGATGCTCACTTTGCTGGGATACATGGCAGTACTGCATTTGGCTGGATGACTCTACAGGGTAAAAAATCAGAGGGTACAGACCTGCACAGTAAAACGGCAGAGACCATTGGCATAAGCCGTGACCATGCCAAGATTTTCAACTATGGCCGTATTTATGGAGCAGGACAGAAGTACGCGGAGAAGTTGCTTTTGCAGTTCAACCATCGCCTGACGGAGAGCGAAGCGAAACAGAAAGCAGAGACACTGTACGCAAACACCAAGGGTGTGGCCAAGTTTCTTCTCACTGATTACGGAAAAGCAATGGCAGAAAAATTTGGCTTCGCTGAAGACGTGGATGAAAACGGTTGCGTTGTCACCAAAGTTTACTACCAGTTACTGCGGAAAACGTCTCGAAAAGGACGTTCTTCTGCAAACAGCATTGACAGTGGACGAAGATGGTGCGGAGGAAGTGAGTCTCAGATGTTTAACAAATTGGAAAGCATCGCACAGTCAGACGAGCCGAGAACACCTGTGTTGGGCTGCAGAATCAGCAGATCACTGGAGCCATCAGCTGTGGGCACTGAGTTCATGACCAGTCGAGTCAACTGGGTTGTCCAAAGCTCTGCCGTGGACTATCTGCATCTCATGTTAGTCAGCATGAAATGGCTCTTCACCAAGTATAACATCGACGGACGTTTCTGTATCAGCATCCACGACGAGGTTCGTTATCTGGTAGCAAGCAAGGACAAGTATCGCGCTGCCCTGGCACTACAAATAACCAATCTTCTCACAAGGGCAATGTTCGCGCACAAACTGGGAATGAGCGACCTCCCTCAGTCAGTGGCATTCTTCAGTGCAGTTGATATAGATACCGTGTTACGGAAAGAAGTGTCCTTGGATTGTAAAACTCCTTCAAATCCGTTAGGCCTCCACAAGGGTCAAGGCATACCACCAGGTTTGACGCTTATTATTTTCAATTTTTCTTGCATTAATACCCTCTTCTTGCCATGCATATTTACTATTATTTGTCATGTTTATTCGCGTTTAGTCACTTTCTCAGATCACTCGGAGCCTTTCTTTACTAAAATTTGA

Transcript

ANN00334-RA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9QYV8	DNA polymerase subunit gamma-1 OS=Rattus norvegicus OX=10116 GN=Polg PE=2 SV=1
P54098	DNA polymerase subunit gamma-1 OS=Homo sapiens OX=9606 GN=POLG PE=1 SV=1
P54099	DNA polymerase subunit gamma-1 OS=Mus musculus OX=10090 GN=Polg PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002983 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00476 all species →	DNA_pol_A	DNA polymerase family A	Family	Interproscan
PF18136 all species →	DNApol_Exo	DNA mitochondrial polymerase exonuclease domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001098 all species →	Domain	DNA-directed DNA polymerase, family A, palm domain	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR002297 all species →	Family	DNA-directed DNA-polymerase, family A, mitochondria	Interproscan
IPR019760 all species →	Conserved_site	DNA-directed DNA polymerase, family A, conserved site	Interproscan
IPR047580 all species →	Domain	DNA polymerase gamma, palm domain	Interproscan
IPR041336 all species →	Domain	DNA mitochondrial polymerase, exonuclease domain	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10267 all species →	DNA POLYMERASE SUBUNIT GAMMA-1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003887 all species →	Molecular Function	DNA-directed DNA polymerase activity	Interproscan
GO:0006260 all species →	Biological Process	DNA replication	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0005760 all species →	Cellular Component	gamma DNA polymerase complex	Interproscan
GO:0006264 all species →	Biological Process	mitochondrial DNA replication	Interproscan
GO:0008408 all species →	Molecular Function	3'-5' exonuclease 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
K02332	POLG; DNA polymerase gamma 1	EC:2.7.7.7	Mitochondrial biogenesis	ko03029	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 Leptoseris scabra 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 Leptoseris scabra, 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 →