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mmu_circUbr1_964
Basic information of circular RNA
PanCircBase ID:
mmu_circUbr1_964
mm39_Chr. Position ID:
chr2|120737324|120751983|-
Gene name:
Ubr1
Transcript:
ENSMUST00000028728.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
29,28,27,26,25,24,23,22,21
Exon/intron offsets:
0,2578,4258,5154,8023,8524,9580,10977,14534
Genomic length:
14659
Exon/intron sizes in nt:
1,82,87,11,01,00,15,54,00,00,00,000
Flanking exon/introns:
chr2:120734680-120737324|chr2:120751983-120754612
Splice length:
964
Other database IDs:
circAtlas: mmu-Ubr1_0011
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_115409
Human Ortholog IDs:
Mature spliced Sequence:
GAGAACGTTATGTACCTGGAGTGGGAAATGTTACCAGAGAGGAGGTTATAATGAGAGAGATTACTCACTTACTTTGCATTGAGCCCATGCCACATAGTGCCATCGCCAGAAACCTACCTGAGAACGAAAATAATGAAACTGGCTTAGAGAATGTCATAAACAAAGTGGCCACATTTAAGAAACCAGGTGTGTCGGGCCATGGAGTTTATGAATTGAAAGATGAATCACTGAAAGACTTCAATATGTACTTTTACCATTATTCTAAAACACAGCATAGCAAGGCTGAACATATGCAGAAGAAAAGGAGAAAACAAGAAAATAAAGATGAAGCATTGCCGCCGCCACCTCCTCCGGAGTTCTGCCCTGCTTTCAGCAAAGTAGTCAACCTGCTCAGCTGTGATGTTATGATGTACATCCTCAGGACCATCTTTGAGCGGGCAGTGGACATGGAGTCTAATCTGTGGACAGAAGGGATGCTGCAGATGGCGTTCCATATATTGGCACTGGGCTTGCTGGAAGAGAAGCAGCAGCTTCAGAAAGCTCCTGAAGAGGAAGTGGCTTTTGACTTTTACCATAAGGCTTCAAGATTGGGAAGTTCAGCCATGAATGCTCAGAATATACAAATGCTCTTGGAAAAACTCAAAGGAATCCCCCAATTAGAAAGCCAGAAGGACATGATAACATGGATACTCCAGATGTTTGACACAGTGAAGCGATTAAGAGAAAAATCTTGTTTAGTTGTGGCAACCACTTCAGGACTGGAGTGCGTTAAGAGTGAGGAGATTACTCATGATAAAGAAAAGGCAGAAAGGAAGAGAAAAGCTGAGGCCGCTAGGCTTCATCGCCAGAAGATCATGGCCCAGATGTCTGCCTTACAGAAAAACTTCATTGAAACCCACAAACTCATGTATGATAATACGTCAGAAGTAACAGGGAAGGAAGACTCCATTATGGAGGAAGAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGTCAGAAGTAACAGGGAAGG
59.7
CACTATGTGGCATGGGCTCA
60.11
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGTCAGAAGTAACAGGGAAGGA
59.44
CACTATGTGGCATGGGCTCA
60.11
145
PCR template sequence:
TGTCTGCCTTACAGAAAAACTTCATTGAAACCCACAAACTCATGTATGATAATACGTCAGAAGTAACAGGGAAGGAAGACTCCATTATGGAGGAAGAGAGGAGAACGTTATGTACCTGGAGTGGGAAATGTTACCAGAGAGGAGGTTATAATGAGAGAGATTACTCACTTACTTTGCATTGAGCCCATGCCACATAGTGC
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-29b-1-5p(1), mmu-miR-676-3p(1), mmu-miR-127-5p(1), mmu-miR-183-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGGAGGAAGAGAGGAGAACGTTATGT
siRNA sets
TAACGTTCTCCTCTCTTCC, AACGTTCTCCTCTCTTCCT, CGTTCTCCTCTCTTCCTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUBR1_964_ORF_1
0.9964
0.149618392
0.987432153
996
ORF sequence:
ATGAGAGAGATTACTCACTTACTTTGCATTGAGCCCATGCCACATAGTGCCATCGCCAGAAACCTACCTGAGAACGAAAATAATGAAACTGGCTTAGAGAATGTCATAAACAAAGTGGCCACATTTAAGAAACCAGGTGTGTCGGGCCATGGAGTTTATGAATTGAAAGATGAATCACTGAAAGACTTCAATATGTACTTTTACCATTATTCTAAAACACAGCATAGCAAGGCTGAACATATGCAGAAGAAAAGGAGAAAACAAGAAAATAAAGATGAAGCATTGCCGCCGCCACCTCCTCCGGAGTTCTGCCCTGCTTTCAGCAAAGTAGTCAACCTGCTCAGCTGTGATGTTATGATGTACATCCTCAGGACCATCTTTGAGCGGGCAGTGGACATGGAGTCTAATCTGTGGACAGAAGGGATGCTGCAGATGGCGTTCCATATATTGGCACTGGGCTTGCTGGAAGAGAAGCAGCAGCTTCAGAAAGCTCCTGAAGAGGAAGTGGCTTTTGACTTTTACCATAAGGCTTCAAGATTGGGAAGTTCAGCCATGAATGCTCAGAATATACAAATGCTCTTGGAAAAACTCAAAGGAATCCCCCAATTAGAAAGCCAGAAGGACATGATAACATGGATACTCCAGATGTTTGACACAGTGAAGCGATTAAGAGAAAAATCTTGTTTAGTTGTGGCAACCACTTCAGGACTGGAGTGCGTTAAGAGTGAGGAGATTACTCATGATAAAGAAAAGGCAGAAAGGAAGAGAAAAGCTGAGGCCGCTAGGCTTCATCGCCAGAAGATCATGGCCCAGATGTCTGCCTTACAGAAAAACTTCATTGAAACCCACAAACTCATGTATGATAATACGTCAGAAGTAACAGGGAAGGAAGACTCCATTATGGAGGAAGAGAGGAGAACGTTATGTACCTGGAGTGGGAAATGTTACCAGAGAGGAGGTTATAATGAGAGAGATTACTCACTTACTTTGCATTGA
Peptide sequence:
MREITHLLCIEPMPHSAIARNLPENENNETGLENVINKVATFKKPGVSGHGVYELKDESLKDFNMYFYHYSKTQHSKAEHMQKKRRKQENKDEALPPPPPPEFCPAFSKVVNLLSCDVMMYILRTIFERAVDMESNLWTEGMLQMAFHILALGLLEEKQQLQKAPEEEVAFDFYHKASRLGSSAMNAQNIQMLLEKLKGIPQLESQKDMITWILQMFDTVKRLREKSCLVVATTSGLECVKSEEITHDKEKAERKRKAEAARLHRQKIMAQMSALQKNFIETHKLMYDNTSEVTGKEDSIMEEERRTLCTWSGKCYQRGGYNERDYSLTLH
IRESfinder result
IRESfinder score
0.510130457
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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