Genomic Location: Scaffold_137__1_contigs__length_197557:112548...115832
NR annotation: RKU23047.1, transcription-repair coupling factor [Candidatus Poribacteria bacterium]
Species Montipora grisea · all data for this species · gene families
| CDS |
| ANN30199-RA |
| Transcript |
| ANN30199-RA |
| Protein |
| ANN30199-RA |
| UniProt accession | Description |
|---|---|
| P37474 | Transcription-repair-coupling factor OS=Bacillus subtilis (strain 168) OX=224308 GN=mfd PE=3 SV=1 |
| Q49V12 | Transcription-repair-coupling factor OS=Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229 / NCIMB 8711 / NCTC 7292 / S-41) OX=342451 GN=mfd PE=3 SV=1 |
| Q4L3G0 | Transcription-repair-coupling factor OS=Staphylococcus haemolyticus (strain JCSC1435) OX=279808 GN=mfd PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0012968 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF02559 all species → | CarD_TRCF_RID | CarD-like/TRCF RID domain | Domain | Interproscan |
| PF00270 all species → | DEAD | DEAD/DEAH box helicase | Domain | Interproscan |
| PF17757 all species → | UvrB_inter | UvrB interaction domain | Domain | Interproscan |
| PF03461 all species → | TRCF | TRCF domain | Domain | Interproscan |
| PF00271 all species → | Helicase_C | Helicase conserved C-terminal domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR003711 all species → | Domain | CarD-like/TRCF, RNAP-interacting domain | Interproscan |
| IPR014001 all species → | Domain | Helicase superfamily 1/2, ATP-binding domain | Interproscan |
| IPR011545 all species → | Domain | DEAD/DEAH box helicase domain | Interproscan |
| IPR004576 all species → | Family | Transcription-repair coupling factor | Interproscan |
| IPR027417 all species → | Homologous_superfamily | P-loop containing nucleoside triphosphate hydrolase | Interproscan |
| IPR041471 all species → | Domain | UvrB, interaction domain | Interproscan |
| IPR037235 all species → | Homologous_superfamily | TRCF-like, C-terminal D7 domain | Interproscan |
| IPR047112 all species → | Family | ATP-dependent DNA helicase RecG/Transcription-repair-coupling factor | Interproscan |
| IPR005118 all species → | Domain | Transcription-repair-coupling factor, C-terminal domain | Interproscan |
| IPR001650 all species → | Domain | Helicase, C-terminal domain-like | Interproscan |
| IPR036101 all species → | Homologous_superfamily | CarD-like/TRCF, RNAP-interacting domain superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR47964 all species → | ATP-DEPENDENT DNA HELICASE HOMOLOG RECG, CHLOROPLASTIC | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003676 all species → | Molecular Function | nucleic acid binding | Interproscan |
| GO:0005524 all species → | Molecular Function | ATP binding | Interproscan |
| GO:0003684 all species → | Molecular Function | damaged DNA binding | Interproscan |
| GO:0006281 all species → | Biological Process | DNA repair | Interproscan |
| GO:0003678 all species → | Molecular Function | DNA helicase activity | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K03723 | mfd; transcription-repair coupling factor (superfamily II helicase) | EC:5.6.2.4 | DNA repair and recombination proteins | ko03400 | deepkoala |
Genes whose expression across the transcriptome samples of Montipora grisea 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.
Whether this gene can be visualised in the single-cell atlases of Montipora grisea, 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.
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.
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 → |
