top of page
mmu_circRufy1_621
Basic information of circular RNA
PanCircBase ID:
mmu_circRufy1_621
mm39_Chr. Position ID:
chr11|50292264|50305409|-
Gene name:
Rufy1
Transcript:
ENSMUST00000020643.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
12,11,10,9,8,7
Exon/intron offsets:
0,3016,4929,6385,9128,13079
Genomic length:
13145
Exon/intron sizes in nt:
98,168,117,102,70,66
Flanking exon/introns:
chr11:50289317-50292264|chr11:50305409-50307066
Splice length:
621
Other database IDs:
circAtlas: mmu-Rufy1_0004
circBase: hsa_circ_0075272, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_102441
Human Ortholog IDs:
Mature spliced Sequence:
GCATGAAAGAATTACCGATGTCCTTGATCAGAAAAATTACGTGGAGGAACTTAACCGGCACCTAAGCTGCACAGTTGGGGATCTTCAGACGAAGATAGATGGCTTGGAAAAGACGAACTCAAAGCTTCAAGAAGAGCTTTCAGCTGCAACAGACCGAATTTGTTCCCTACAAAAAGAACAACAGCAGCTGAGAGAACAGAACGAAGTAATTCGAGAAAGAAGCGAGAAGAGCGTGGAGATAACAAAACAGGACACCAAGGTTGAACTGGAGACTTATAAGCAGACCCGGCAGGGCCTGGATGAAATGTACAGCGATGTGTGGAAACAGCTGAAGGAGGAGAAGAAAGTCCGACTGGAACTGGAAAAGGAGCTGGAGTTGCAGATTGGAATGAAGACGGAGATGGAGATCGCCATGAAGTTGCTGGAGAAGGACACCCATGAGAAGCAAGACACGCTCGTTGCCCTCCGCCAGCAGCTGGAGGAAGTCAAAGCTATTAACTTACAGATGTTTCACAAAGTTCAGAGTGCAGAGAGCAGTTTACAGCAGAAGAATGAAGCCATCGCATCTTTTGAAGGAAAAACCACTCAGGTGATGTCCAGCATGAAGCAAATGGAGGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGAAGAATGAAGCCATCGC
60.27
TCCCCAACTGTGCAGCTTAG
59.96
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGAAGAATGAAGCCATCGC
60.27
CCCAACTGTGCAGCTTAGGT
60.25
157
PCR template sequence:
AGAGTGCAGAGAGCAGTTTACAGCAGAAGAATGAAGCCATCGCATCTTTTGAAGGAAAAACCACTCAGGTGATGTCCAGCATGAAGCAAATGGAGGAAAGGCATGAAAGAATTACCGATGTCCTTGATCAGAAAAATTACGTGGAGGAACTTAACCGGCACCTAAGCTGCACAGTTGGGGATCTTCAGACGAAGATAGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-135a-5p(1), mmu-miR-136-5p(1), mmu-miR-127-5p(1), mmu-miR-207(1), mmu-miR-3105-3p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAATGGAGGAAAGGCATGAAAGAATT
siRNA sets
AATTCTTTCATGCCTTTCC, TCTTTCATGCCTTTCCTCC, ATTCTTTCATGCCTTTCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRUFY1_621_ORF_1
1.2457
0.487825483
0.996961684
936
ORF sequence:
ATGTACAGCGATGTGTGGAAACAGCTGAAGGAGGAGAAGAAAGTCCGACTGGAACTGGAAAAGGAGCTGGAGTTGCAGATTGGAATGAAGACGGAGATGGAGATCGCCATGAAGTTGCTGGAGAAGGACACCCATGAGAAGCAAGACACGCTCGTTGCCCTCCGCCAGCAGCTGGAGGAAGTCAAAGCTATTAACTTACAGATGTTTCACAAAGTTCAGAGTGCAGAGAGCAGTTTACAGCAGAAGAATGAAGCCATCGCATCTTTTGAAGGAAAAACCACTCAGGTGATGTCCAGCATGAAGCAAATGGAGGAAAGGCATGAAAGAATTACCGATGTCCTTGATCAGAAAAATTACGTGGAGGAACTTAACCGGCACCTAAGCTGCACAGTTGGGGATCTTCAGACGAAGATAGATGGCTTGGAAAAGACGAACTCAAAGCTTCAAGAAGAGCTTTCAGCTGCAACAGACCGAATTTGTTCCCTACAAAAAGAACAACAGCAGCTGAGAGAACAGAACGAAGTAATTCGAGAAAGAAGCGAGAAGAGCGTGGAGATAACAAAACAGGACACCAAGGTTGAACTGGAGACTTATAAGCAGACCCGGCAGGGCCTGGATGAAATGTACAGCGATGTGTGGAAACAGCTGAAGGAGGAGAAGAAAGTCCGACTGGAACTGGAAAAGGAGCTGGAGTTGCAGATTGGAATGAAGACGGAGATGGAGATCGCCATGAAGTTGCTGGAGAAGGACACCCATGAGAAGCAAGACACGCTCGTTGCCCTCCGCCAGCAGCTGGAGGAAGTCAAAGCTATTAACTTACAGATGTTTCACAAAGTTCAGAGTGCAGAGAGCAGTTTACAGCAGAAGAATGAAGCCATCGCATCTTTTGAAGGAAAAACCACTCAGGTGATGTCCAGCATGAAGCAAATGGAGGAA
Peptide sequence:
MYSDVWKQLKEEKKVRLELEKELELQIGMKTEMEIAMKLLEKDTHEKQDTLVALRQQLEEVKAINLQMFHKVQSAESSLQQKNEAIASFEGKTTQVMSSMKQMEERHERITDVLDQKNYVEELNRHLSCTVGDLQTKIDGLEKTNSKLQEELSAATDRICSLQKEQQQLREQNEVIRERSEKSVEITKQDTKVELETYKQTRQGLDEMYSDVWKQLKEEKKVRLELEKELELQIGMKTEMEIAMKLLEKDTHEKQDTLVALRQQLEEVKAINLQMFHKVQSAESSLQQKNEAIASFEGKTTQVMSSMKQMEE
IRESfinder result
IRESfinder score
0.305833262
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page