Gene detail

Detailed information of TcoG024150.mRNA1 in Tubastraea coccinea

Genomic Location: ptg001488l:404714...419549
NR annotation: no NCBI-NR hit recorded
Species Tubastraea coccinea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

TcoG024150.mRNA1

ATGGAGAGCAAAGCTTCAAAAAAGAAAGCAGATGACGGGAACACAATAAAAGGAGATTGGAGTGGCTGGGGCGAATATATGCAAGCAAAAGTGCAGAAACTAGATGCTCAGTTTAAAGAGGATGTTCCAAAAGGGCCACAGGATGTTGATGTTCCCAAAATATTTGAGAAAGTTGTTATTCACATCAATGGATACACAGTGCCGCCAGCTGATGAGTTGCGTCGCCTTGTATACTTACATGGAGGCCGTTACCAGCAGTATTACACCAAGCGTTCTGTGACGCACATTATTGCCACTAATCTACCAAACAGCAAAATTCAGGAGCTCAGGGATGAACTTGTTGTGCATCCATCATGGATTTTAGACAGCATCAAGGCTGGCAATCTGCTTCCTGTGGATCAGTATCTTCTTTACCATGGACGAAAAGCTGCGCAGAAAGTTTTAAATTTTACTTCTAAGTCAAGTTCAACCTGCACAACAACTAAACCTTTCCCTGGGGGAGTACCCCCAGTGGCAACATCACCTTCTCCAAACACAACCTTACAATCCCCTCAGGGAGGACCCTCAGTTGATATTACACCTCAATGTTCTACTGCCATACCACCCCCCACGGGAGAGCCTTTGGTGTCTTTGCTTGATGCAACAATTCATGAAGAGAGTGTAGACTTTAAAGACAGTGAAAAAGCGAGAAATATCGGTGAGGAAGATGTGTTACCAGAGTCTGAGAATTCCATAATAATTAATGAAGATGATGATTTTGGCCATAATGAAGACGATCTCGCATTTCAGATATGTAACAAGGATGAACGGCAAATTCATGATGCTAATGTCGAAAGGATGAACGATTTAGAGGGAGAAACATCAACAAATGCGTCTGACAATGCCGTATTTAAAAAGCCCGGTACGAGAAGTTTGCCACGTGCCGGCGATGCAAACTTTGTATCAGAATTCTACAACAATTCCAGATTGCATTACTTATCCACATGGGGTGCAGAATTCAAGAAGTACACAAGTGACATTATCAAGTCTTCTGCAGCCAAAGGGTGGAAGAGTAGGGGGACAGGTCGGGTGGGGCCACATGGCCGAGTTATAATGCACATAGACATGGATTCATTCTTTGTTTCTGTAACATTGCGTGACCAGCCACATCTCAGAGGAAAGCCTATTGCCGTCTGTCACGCAGGGAAAAATAGTTCAGCTACTGACCAAGCATCTGTAAACAATCTACAAACGTCACCCAATAAGCCATCATCATTCTTTAACTCCATGGCGGAGATAGCTTCCTGCAGCTATGAAGCGAGGGCCTCTGGTGTTCGCAATGGGATGTTGCTGGGCGCCGCTCGTAAGCTCTGTCCTAACATTCAGTGTGTTCCCTACCAGTTTGAGCAATATCGACAAGTATCACAGAGCCTCTATGATATTTTGGTGATGTACAGTCATGAGATCGAGGCTGTCAGCTGCGACGAGGCTTACATTGACGCGTCAGAGGCACTTGAAGAGGGTGAAACTCCAACTCAGTTCGCAGAAAAGATTCGTGCGGAGATCAAAGAAGCGACTCGATGTACCGCGTCTGTTGGTATTGGGTCTAATGTCCTGCTCGCCAGAATGTGTACCAGAGTAGCTAAACCTGATGGCTGTTATCATCTTTCACCTAATGATGATGTTAGCCAGTTTATGGGTTCCCAGAAGGTTAATGATCTCCCGGGAGTGGGTTGGAGCATGGGCCATAAACTTCAGACTCTGGGAGTAGAAACGTGTGCAGATCTACAGAAATTCAGCTCTCAAGCGCTTCAGAGAGAGTTTGGACCCAAGACAGGACTTCTGCTGTATCGGTATTGTCGGGGTATTGACGACAGAACTCTGAGAACTGAACGAGAAAGGAAGTCTGTATCAGCGGAAATCAACTATGGTATCCGTTTTACAAAGGAAAATGAAGTTATCCTATTCATCAATGAACTGGCTGAGGAGGTACAAAAGAGACTTAAGGCAGTAGATATGAAAGGAAGGTGCATTACTCTTAAGATGAAGGTACGGAAGGCAGGAGCACCAACCCCGAGAAAGTTCATGGGTCACGGAATCTGCGATAACATCGCACGCTCCTGCACCTTACCATCTGTCACGGATGAAGCACAAGTTATAGCTAAACAGTGTCACGCACTCCTGAAGCAGTTGAGTGTCACGCCAGAGGATGTTCGAGGCATGGGAATACAAGTTAGTAAGTTGATTGACAGCAATGCCTTTTCTGGTGCAAAGAATTCAAGGTCATTGTTCGATTTTATGAAACCACAAACCAACACTAATGAAGTCAACTCTGGACCAGTCGCCACGGAAAGAAAGGTTGAAATGTCTGAAGATAAACAAGCTCCGGTTGTAGAAAGAAGTCCTGAAGATCAACTAAAGAAACTTCCGCCTTTACCAAAGTTCTCTCCCCATAAAGTTCAGCAGGCTCGTGATTCCACGTCCGAAAAAAGCGTAGGTGACCTGGGTGAGAGTCTGTACTTGCCTTCTCCATCGCAGATTGATCCTGCAGTATTTGAAGCTTTACCTGAAGATATTCGAAGGAGCATCGAGAAATCGTACGCTGCAAGAAATCAAAGGATTTTACCGAATCGGTTAGGAAGACAAGAGGAAGAAGAGTTTGAGCCTCAACAGCAACCCCAGCGAAAAACTACTAAAACTAAAGTGAGCAAAACAGTGTCCAAACCTTCTCGAACACTATTTGAAACAAACACTACATCAGAAGTCGCTCAGCCTAATACGTCAGAACTCCTGCCGTCACCATCCCAAATCGACCCAGAATTCCTGGCGGCGCTTCCTGATGATGTAAGAGAGGAACTTGAGCAGGCTTACAAACGCAAGGAATCTCACGTTACACACGTTCGCATCCAGGCTCCATCGTCGGATGCCTCGGTTGTTCCACCAGAGAGAAGCATGGAAAAGAGTGCAGTGGTTGTCCAGTCGGGCGATGTCCATAAGAGAGAAGCTAAAAAGGTTAACGCCCCTCGAAAACAGGCGTGTTTAGGAGAAGCGGTTACACTTCCTGATGTGAAGCAAGTCATAAAACAGTGGACTGAAACCTATGAAGTTCCTCTGGAGGAAGATGTCGAAGTATTTAGTGATTACTTGCTCCAGCTTGTTGGAACACAAAACTTGGAGCAGCTTTGGAGAGTCTTGAAGTTCCTCGACAGGACAATTGATGGACGAGAGGATTGGCAGTGTGTCTGTTGTGCGGTTCTGGAGCAAGTTCAACAAGTACTCAGTCAGAAATACCACGCCAAACTTGCTGTGAATTCGTTAAAATTTACCAAGTAA

Transcript

TcoG024150.mRNA1

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003648 (this species only) · gene tree & orthology
Ubiquitin family	UBD\|Alpha-Helix\|UBM · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21704 all species →	POLH-Rev1_HhH	DNApol eta/Rev1, HhH motif	Motif	Interproscan
PF16727 all species →	REV1_C	DNA repair protein REV1 C-terminal domain	Domain	Interproscan
PF11799 all species →	IMS_C	impB/mucB/samB family C-terminal domain	Domain	Interproscan
PF14377 all species →	UBM	Ubiquitin binding region	Motif	Interproscan
PF00533 all species →	BRCT	BRCA1 C Terminus (BRCT) domain	Family	Interproscan
PF00817 all species →	IMS	impB/mucB/samB family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR047346 all species →	Conserved_site	DNA repair protein REV1, ubiquitin-binding motif 1/2	Interproscan
IPR012112 all species →	Family	DNA repair protein Rev1	Interproscan
IPR036420 all species →	Homologous_superfamily	BRCT domain superfamily	Interproscan
IPR043128 all species →	Homologous_superfamily	Reverse transcriptase/Diguanylate cyclase domain	Interproscan
IPR001357 all species →	Domain	BRCT domain	Interproscan
IPR031991 all species →	Domain	DNA repair protein Rev1, C-terminal	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR001126 all species →	Domain	UmuC domain	Interproscan
IPR036775 all species →	Homologous_superfamily	DNA polymerase, Y-family, little finger domain superfamily	Interproscan
IPR017961 all species →	Domain	DNA polymerase, Y-family, little finger domain	Interproscan
IPR025527 all species →	Conserved_site	HUWE1/REV1, ubiquitin-binding motif	Interproscan
IPR022880 all species →	Family	DNA polymerase IV	Interproscan
IPR038401 all species →	Homologous_superfamily	Rev1, C-terminal domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45990 all species →	DNA REPAIR PROTEIN REV1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003684 all species →	Molecular Function	damaged DNA binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0016779 all species →	Molecular Function	nucleotidyltransferase activity	Interproscan
GO:0042276 all species →	Biological Process	error-prone translesion synthesis	Interproscan
GO:0003887 all species →	Molecular Function	DNA-directed DNA polymerase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0017125 all species →	Molecular Function	deoxycytidyl transferase activity	Interproscan
GO:0070987 all species →	Biological Process	error-free translesion synthesis	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
K03515	REV1; DNA repair protein REV1	EC:2.7.7.-	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 Tubastraea coccinea 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 Tubastraea coccinea, 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 →