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mmu_circRalgapa1_934
Basic information of circular RNA
PanCircBase ID:
mmu_circRalgapa1_934
mm39_Chr. Position ID:
chr12|55720237|55724050|-
Gene name:
Ralgapa1
Transcript:
ENSMUST00000220367.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
34,33
Exon/intron offsets:
0,2951
Genomic length:
3813
Exon/intron sizes in nt:
72,862
Flanking exon/introns:
chr12:55712461-55720237|chr12:55724050-55730691
Splice length:
934
Other database IDs:
circBase: mmu_circ_0004085, CIRCpedia: MMU_CIRCpedia_23241, circAtlas: mmu-Ralgapa1_0003
circAtlas: hsa-RALGAPA1_0007, CIRCpedia: HSA_CIRCpedia_12052
Human Ortholog IDs:
Mature spliced Sequence:
TGAAAACTCAGATGCAACAAGGATTAATCTCTATAGCAGCCCGTACTGTTATTACCCATCTGGTGAATCACTTGGGCCATTATCCAATGAGTGGTGGTCCTGCTATGCTAACAAGTCAGGTGTGTGAAAATCATGACAATCATTACAGTGAAAGTACTGAACTTTCTCCTGAGCTCTTTGAAAGTCCAAACATCCAGTTCTTTGTGCTGAATAATACAACCTTAGTGTCCTGTATCCAGATAAGATCGGAAGAGAGTATGCCTGGAGGAGGTCTAGCTGCTGGCCTTGTGTCAGCCAACTCAAATGTTAGAATCATAGTACGTGATCTCTCTGGAAAGTACTCATGGGATTCTGCCATACTGTATGGACCACCCATTGTAAGTGGTTTGCCTGAACCTACATCTTTCATACTTTCAATGTCTGACCAAGAGAAACCGGAAGAGCCTCCTACATCTAACGAATGCTTAGAAGACATCGCAGTAAAAGATGGGCTTTCTCTCCAGCTTAGAAGATTTAGAGAAACTGTACCAACTTGGTCTACGATACGAGAGGAAGAAGATGTTCTTGACGAGCTCCTGCAGTATTTAGGCACTACAAGTCCTGAGTGTTTACAGAGAACGGGAATCTCCCTCAATGTTCCTGCTCCACAGCCTCTGTGCATTTCTGAAAAACAGGAGAATGATGTCATTAATGCTATCCTTAAGCAATACACGGAAGAAAAAGAGTTTGTAGAGAAGCACTTTAATGACTTAAACATGAAAGCCTCAGAACAAGATGAGCCAACACCTCAGAAACCTCAGTCAGCTTTTTATTACTGCAGATTGCTTCTTAGTATATTGGGAATGAATTCCTGGGACAAACGGAGGAGCTTTCATCTCTTGAAGAAAAATGAAAAGCTGCTCAGAGAACTTAGGAACTTGGATTCAAGGCAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGACAAACGGAGGAGCTTT
60.25
GGCCCAAGTGATTCACCAGA
59.96
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATTCCTGGGACAAACGGAGG
59.67
GGCCCAAGTGATTCACCAGA
59.96
166
PCR template sequence:
TATTGGGAATGAATTCCTGGGACAAACGGAGGAGCTTTCATCTCTTGAAGAAAAATGAAAAGCTGCTCAGAGAACTTAGGAACTTGGATTCAAGGCAATGTGAAAACTCAGATGCAACAAGGATTAATCTCTATAGCAGCCCGTACTGTTATTACCCATCTGGTGAATCACTTGGGCCATTATCCAATGAGTGGTGGTCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-30e-5p(1), mmu-miR-200c-3p(1), mmu-miR-30a-5p(1), mmu-miR-320-3p(1), mmu-miR-185-5p(1), mmu-miR-30d-5p(1), mmu-miR-362-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-335-3p(1), mmu-miR-540-3p(1), mmu-miR-544-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTCAAGGCAATGTGAAAACTCAGAT
siRNA sets
ATCTGAGTTTTCACATTGC, CTGAGTTTTCACATTGCCT, TCTGAGTTTTCACATTGCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRALGAPA1_934_ORF_1
0.7545
0.020659387
0.977641363
1050
ORF sequence:
ATGCAACAAGGATTAATCTCTATAGCAGCCCGTACTGTTATTACCCATCTGGTGAATCACTTGGGCCATTATCCAATGAGTGGTGGTCCTGCTATGCTAACAAGTCAGGTGTGTGAAAATCATGACAATCATTACAGTGAAAGTACTGAACTTTCTCCTGAGCTCTTTGAAAGTCCAAACATCCAGTTCTTTGTGCTGAATAATACAACCTTAGTGTCCTGTATCCAGATAAGATCGGAAGAGAGTATGCCTGGAGGAGGTCTAGCTGCTGGCCTTGTGTCAGCCAACTCAAATGTTAGAATCATAGTACGTGATCTCTCTGGAAAGTACTCATGGGATTCTGCCATACTGTATGGACCACCCATTGTAAGTGGTTTGCCTGAACCTACATCTTTCATACTTTCAATGTCTGACCAAGAGAAACCGGAAGAGCCTCCTACATCTAACGAATGCTTAGAAGACATCGCAGTAAAAGATGGGCTTTCTCTCCAGCTTAGAAGATTTAGAGAAACTGTACCAACTTGGTCTACGATACGAGAGGAAGAAGATGTTCTTGACGAGCTCCTGCAGTATTTAGGCACTACAAGTCCTGAGTGTTTACAGAGAACGGGAATCTCCCTCAATGTTCCTGCTCCACAGCCTCTGTGCATTTCTGAAAAACAGGAGAATGATGTCATTAATGCTATCCTTAAGCAATACACGGAAGAAAAAGAGTTTGTAGAGAAGCACTTTAATGACTTAAACATGAAAGCCTCAGAACAAGATGAGCCAACACCTCAGAAACCTCAGTCAGCTTTTTATTACTGCAGATTGCTTCTTAGTATATTGGGAATGAATTCCTGGGACAAACGGAGGAGCTTTCATCTCTTGAAGAAAAATGAAAAGCTGCTCAGAGAACTTAGGAACTTGGATTCAAGGCAATGTGAAAACTCAGATGCAACAAGGATTAATCTCTATAGCAGCCCGTACTGTTATTACCCATCTGGTGAATCACTTGGGCCATTATCCAATGAGTGGTGGTCCTGCTATGCTAACAAGTCAGGTGTGTGA
Peptide sequence:
MQQGLISIAARTVITHLVNHLGHYPMSGGPAMLTSQVCENHDNHYSESTELSPELFESPNIQFFVLNNTTLVSCIQIRSEESMPGGGLAAGLVSANSNVRIIVRDLSGKYSWDSAILYGPPIVSGLPEPTSFILSMSDQEKPEEPPTSNECLEDIAVKDGLSLQLRRFRETVPTWSTIREEEDVLDELLQYLGTTSPECLQRTGISLNVPAPQPLCISEKQENDVINAILKQYTEEKEFVEKHFNDLNMKASEQDEPTPQKPQSAFYYCRLLLSILGMNSWDKRRSFHLLKKNEKLLRELRNLDSRQCENSDATRINLYSSPYCYYPSGESLGPLSNEWWSCYANKSGV
IRESfinder result
IRESfinder score
0.675803977
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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