top of page
mmu_circRabep1_462
Basic information of circular RNA
PanCircBase ID:
mmu_circRabep1_462
mm39_Chr. Position ID:
chr11|70810002|70816738|+
Gene name:
Rabep1
Transcript:
ENSMUST00000076270.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
10,11,12,13
Exon/intron offsets:
0,1675,3966,6595
Genomic length:
6736
Exon/intron sizes in nt:
105,117,99,141
Flanking exon/introns:
chr11:70808608-70810002|chr11:70816738-70825230
Splice length:
462
Other database IDs:
CIRCpedia: MMU_CIRCpedia_27656, circAtlas: mmu-Rabep1_0041
circBase: hsa_circ_0041685, circAtlas: hsa-RABEP1_0124, CIRCpedia: HSA_CIRCpedia_167368
Human Ortholog IDs:
Mature spliced Sequence:
GTACATAATGCTGGAAATAAGCTTGGTAGACGTTGTGATATGTGTTCCAATTATGAAAAACAGTTACAAGGAATTCAGATTCAGGAAGCTGAAACAAGAGACCAGGTGAAAAAACTGCAGTTAATGCTCAGGCAAGCTAATGACCAGCTTGAGAAGACGATGAAAGAGAAGCAGGAGCTGGAGGACTTCCTCAAGCAGAGTGCGGAGGACTCAAGCCACCAGATATCTGCACTTGTTTTAAGAGCCCAAGCCTCTGAGGTCTTACTTGAAGAGTTACAACAGAGCTTTTCCCAAGCAAAGAGGGACGTTCAGGAGCAGATGGCGGTGCTGATGCAGTCACGTGAACAGGTTTCAGAAGAGTTGGTGAGGTTACAGAAAGACAACGACAGCCTCCAGGGGAAGCACAGCTTGCATGTGTCATTACAGCTAGCAGAAGACTTCATTCTTCCAGACACTGTGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGACAACGACAGCCTCCAG
59.97
TCAGCTTCCTGAATCTGAATTCCT
59.77
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGACAACGACAGCCTCCAG
59.97
TCAGCTTCCTGAATCTGAATTCC
58.48
178
PCR template sequence:
GGTGAGGTTACAGAAAGACAACGACAGCCTCCAGGGGAAGCACAGCTTGCATGTGTCATTACAGCTAGCAGAAGACTTCATTCTTCCAGACACTGTGGAGGTACATAATGCTGGAAATAAGCTTGGTAGACGTTGTGATATGTGTTCCAATTATGAAAAACAGTTACAAGGAATTCAGATTCAGGAAGCTGAAACAAGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-26a-5p(1), mmu-miR-217-5p(1), mmu-miR-26b-5p(1), mmu-miR-335-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AGACACTGTGGAGGTACATAATGCTG
siRNA sets
CAGCATTATGTACCTCCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRABEP1_462_ORF_1
1.2012
0.239022548
0.98703964
885
ORF sequence:
ATGTGTTCCAATTATGAAAAACAGTTACAAGGAATTCAGATTCAGGAAGCTGAAACAAGAGACCAGGTGAAAAAACTGCAGTTAATGCTCAGGCAAGCTAATGACCAGCTTGAGAAGACGATGAAAGAGAAGCAGGAGCTGGAGGACTTCCTCAAGCAGAGTGCGGAGGACTCAAGCCACCAGATATCTGCACTTGTTTTAAGAGCCCAAGCCTCTGAGGTCTTACTTGAAGAGTTACAACAGAGCTTTTCCCAAGCAAAGAGGGACGTTCAGGAGCAGATGGCGGTGCTGATGCAGTCACGTGAACAGGTTTCAGAAGAGTTGGTGAGGTTACAGAAAGACAACGACAGCCTCCAGGGGAAGCACAGCTTGCATGTGTCATTACAGCTAGCAGAAGACTTCATTCTTCCAGACACTGTGGAGGTACATAATGCTGGAAATAAGCTTGGTAGACGTTGTGATATGTGTTCCAATTATGAAAAACAGTTACAAGGAATTCAGATTCAGGAAGCTGAAACAAGAGACCAGGTGAAAAAACTGCAGTTAATGCTCAGGCAAGCTAATGACCAGCTTGAGAAGACGATGAAAGAGAAGCAGGAGCTGGAGGACTTCCTCAAGCAGAGTGCGGAGGACTCAAGCCACCAGATATCTGCACTTGTTTTAAGAGCCCAAGCCTCTGAGGTCTTACTTGAAGAGTTACAACAGAGCTTTTCCCAAGCAAAGAGGGACGTTCAGGAGCAGATGGCGGTGCTGATGCAGTCACGTGAACAGGTTTCAGAAGAGTTGGTGAGGTTACAGAAAGACAACGACAGCCTCCAGGGGAAGCACAGCTTGCATGTGTCATTACAGCTAGCAGAAGACTTCATTCTTCCAGACACTGTGGAG
Peptide sequence:
MCSNYEKQLQGIQIQEAETRDQVKKLQLMLRQANDQLEKTMKEKQELEDFLKQSAEDSSHQISALVLRAQASEVLLEELQQSFSQAKRDVQEQMAVLMQSREQVSEELVRLQKDNDSLQGKHSLHVSLQLAEDFILPDTVEVHNAGNKLGRRCDMCSNYEKQLQGIQIQEAETRDQVKKLQLMLRQANDQLEKTMKEKQELEDFLKQSAEDSSHQISALVLRAQASEVLLEELQQSFSQAKRDVQEQMAVLMQSREQVSEELVRLQKDNDSLQGKHSLHVSLQLAEDFILPDTVE
IRESfinder result
IRESfinder score
0.456809962
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page