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mmu_circRabep1_256
Basic information of circular RNA
PanCircBase ID:
mmu_circRabep1_256
mm39_Chr. Position ID:
chr11|70784394|70791433|+
Gene name:
Rabep1
Transcript:
ENSMUST00000076270.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
5,6
Exon/intron offsets:
0,6903
Genomic length:
7039
Exon/intron sizes in nt:
1,20,136
Flanking exon/introns:
chr11:70777997-70784394|chr11:70791433-70795430
Splice length:
256
Other database IDs:
CIRCpedia: MMU_CIRCpedia_27639, circAtlas: mmu-Rabep1_0023
circBase: hsa_circ_0141357, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_21430
Human Ortholog IDs:
Mature spliced Sequence:
GCCCAAGAGGATGCTGAAAAGCTTCGTTCTGTCGTGATGCCCATGGAGAAGGAAATTGCAGCTCTGAAAGATAAACTGACAGAAGCTGAAGACAAGATTAAAGAGCTGGAGGCCTCAAAGGTTAAGGAGCTGAATCATTATCTGGAGGCCGAGAAGTCTTGCAGGACTGACCTGGAGATGTACGTAGCTGTTTTGAACACTCAGAAATCTGTGCTACAGGAAGATGCTGAGAAATTGAGGAAAGAACTGCATGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGACTGACCTGGAGATGTACG
59.59
TTCTCCATGGGCATCACGAC
60.11
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGACTGACCTGGAGATGTACG
59.59
CTTCTCCATGGGCATCACGA
59.82
144
PCR template sequence:
TCTTGCAGGACTGACCTGGAGATGTACGTAGCTGTTTTGAACACTCAGAAATCTGTGCTACAGGAAGATGCTGAGAAATTGAGGAAAGAACTGCATGAAGGCCCAAGAGGATGCTGAAAAGCTTCGTTCTGTCGTGATGCCCATGGAGAAGGAAATTGCAGCTCTGAAAGATAAACTGACAGAAGCTGAAGACAAGATTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-223-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
GAACTGCATGAAGGCCCAAGAGGATG
siRNA sets
TCCTCTTGGGCCTTCATGC, TCTTGGGCCTTCATGCAGT, ATCCTCTTGGGCCTTCATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRABEP1_256_ORF_1
1.2143
0.415351368
0.64215624
261
ORF sequence:
ATGAAGGCCCAAGAGGATGCTGAAAAGCTTCGTTCTGTCGTGATGCCCATGGAGAAGGAAATTGCAGCTCTGAAAGATAAACTGACAGAAGCTGAAGACAAGATTAAAGAGCTGGAGGCCTCAAAGGTTAAGGAGCTGAATCATTATCTGGAGGCCGAGAAGTCTTGCAGGACTGACCTGGAGATGTACGTAGCTGTTTTGAACACTCAGAAATCTGTGCTACAGGAAGATGCTGAGAAATTGAGGAAAGAACTGCATGAA
Peptide sequence:
MKAQEDAEKLRSVVMPMEKEIAALKDKLTEAEDKIKELEASKVKELNHYLEAEKSCRTDLEMYVAVLNTQKSVLQEDAEKLRKELHE
IRESfinder result
IRESfinder score
0.409830805
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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