RECENT UPDATES:
- Jul 2017 - Maass et al. H.sapiens circRNAs
- Dec 2015 - Ashwal-Fluss et al. D.melanogaster circRNAs
- Jun 2015 - Ivanov et al. C.elegans circRNAs
- May 2015 - Rybak-Wolf et al. human and mouse CNS samples
Welcome to circBase
Thousands of circular RNAs (circRNAs) have recently been shown to be expressed in eukaryotic cells [Salzman et al. 2012, Jeck et al. 2013, Memczak et al. 2013, Salzman et al. 2013]. Here you can explore public circRNA datasets and download the custom python scripts needed to discover circRNAs in your own (ribominus) RNA-seq data.
New:
- Sequence-based search
- Search the database by identifier, gene description, genomic position, or their lists.
- Retrieve dataset slices by defining a set of conditions (table browser).
- Export tables in a variety of formats.
- Export FASTA files containing genomic sequence. Please refer to documentation for further info.
- HTML tables from circBase 0.1 are available here.
- Custom python scripts used to report circRNAs can be downloaded here.
-
Glažar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA. 2014 Sep 18.
Stats:
| circRNA study | organism | sample | # circRNAs |
|---|---|---|---|
| Maass 2017 | H.sapiens (hg19) | cortex | 339 |
| plasma | 57 | ||
| serum | 39 | ||
| neutrophils | 274 | ||
| platelets | 3324 | ||
| right atrium | 340 | ||
| vena cava | 702 | ||
| umbilical cord | 85 | ||
| HUVEC | 22 | ||
| HUAEC | 211 | ||
| EPC | 159 | ||
| fat | 507 | ||
| MSC | 55 | ||
| chondrocytes | 148 | ||
| osteocytes | 104 | ||
| VSMC | 137 | ||
| placenta | 63 | ||
| decidua | 173 | ||
| fibroblasts | 99 | ||
| muscle | 184 | ||
| ADA-SCID | 257 | ||
| LCL | 295 | ||
| MSC_047 | 112 | ||
| WAS2 | 1071 | ||
| Ivanov 2015 | C.elegans (ce6) | pooled | 757 |
| Ashwal-Fluss 2014 | D.melanogaster (dm3) | S2 | 1280 |
| head | 4515 | ||
| Rybak-Wolf 2015 | H.sapiens (hg19) | cerebellum[0] | 21071 |
| diencephalon[1] | 24632 | ||
| frontal cortex[2] | 38983 | ||
| occipital lobe[3] | 31085 | ||
| parietal lobe[4] | 23303 | ||
| temporal lobe[5] | 21835 | ||
| SH-SY5Y | 4264 | ||
| M.musculus (mm9) | forebrain[6] | 6614 | |
| midbrain[7] | 3758 | ||
| hindbrain[8] | 3382 | ||
| cerebellum | 2407 | ||
| prefrontal cortex | 1677 | ||
| hippocampus | 1212 | ||
| olfactory bulb | 1771 | ||
| P19 | 2735 | ||
| primary cortical neurons | 5267 | ||
| synaptoneurosomes | 1773 | ||
| Nitsche 2013 | L.chalumnae (latCha1)[9] | muscle | 767 |
| L.menadoensis (latCha1)[10] | liver | 581 | |
| testis | 806 | ||
| Zhang 2013 | H.sapiens[11] (hg19) | H9 | 103 |
| Jeck 2013 | H.sapiens (hg19) | Hs68 | 7771 |
| Salzman 2013 | H.sapiens (hg19)[12] | A549 | 14970 |
| AG04450 | 16808 | ||
| BJ | 12705 | ||
| GM12878 | 18274 | ||
| H1-hESC | 16017 | ||
| HeLa S3 | 15195 | ||
| HepG2 | 14024 | ||
| HMEC | 1107 | ||
| HSMM | 2940 | ||
| HUVEC | 8143 | ||
| K562 | 27307 | ||
| MCF-7 | 5331 | ||
| NHEK | 13760 | ||
| NHLF | 2209 | ||
| SK-N-SH RA | 12745 | ||
| Memczak 2013 | H.sapiens (hg19) | CD19+[13] | 1303 |
| CD34+[14] | 528 | ||
| HEK293 | 239 | ||
| Neutrophil[13] | 417 | ||
| M.musculus (mm9)[14][6] | brain1 | 970 | |
| brain2 | 537 | ||
| ES | 761 | ||
| head | 1184 | ||
| C.elegans (ce6) | 1cell | 217 | |
| 2cell | 178 | ||
| fem1 (oocytes) | 316 | ||
| spe9 (oocytes) | 364 | ||
| sperm | 270 | ||
| sperm_act | 297 |
HTML5/CSS3 compatible web browser is required for optimal performance. Please report misbehaviour and suggest further modifications/upgrades to petar.glazar@mdc-berlin.de. When reporting a bug, please include all the information necessary to reproduce it (operating system, browser type/version, input data).