top of page
mmu_circRfx3_2035
Basic information of circular RNA
PanCircBase ID:
mmu_circRfx3_2035
mm39_Chr. Position ID:
chr19|27764013|27900666|-
Gene name:
Rfx3
Transcript:
ENSMUST00000165566.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
15
Exon/intron indexes:
16,15,14,13,12,11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,6997,13503,15768,19574,20179,26964,28871,39419,43997,50793,63097,80899,114165,136594
Genomic length:
136653
Exon/intron sizes in nt:
154,209,150,98,155,116,113,122,120,182,75,259,98,125,59
Flanking exon/introns:
chr19:27748071-27764013|chr19:27900666-27960253
Splice length:
2035
Other database IDs:
circAtlas: mmu-Rfx3_0061
Human Ortholog IDs:
Mature spliced Sequence:
AGATTTTTATCAGAGGAATGTAGACTGGAATCTGCAATGGTTCTCAAAATCCCAAAGTGAGACCATCATGCAGACTTCAGAGACGGGTTCAGACACAGGTTCGACAGTGACTCTGCAGACGTCTGTGGCTAGCCAAGCAGCAGTGCCTACACAGGTGGTACAGCAAGTGCCAGTGCAGCAGCAGGTGCAGCAGGTACAGACAGTTCAGCAGGTCCAACATGTCTACCCAGCTCAGGTGCAGTATGTGGAAGGAAGTGATACTGTCTATACCAATGGAGCAATCCGAACAACAACTTATCCCTACACAGAAACACAGATGTACAGCCAAAACACTGGAGGAAATTACTTTGATACTCAAGGAAGTTCTGCCCAGGTGACAACTGTGGTGTCCTCCCACAGTATGGTGGGTACTGGTGGGATTCAGATGGGCGTCACAGGAGGACAACTCATCAGCAGCTCGGGAGGAACCTATTTGATCGGCAATTCAATGGAGAACTCTGGTCACTCAGTGACACACACAACTCGGGCCTCCCCAGCAACAATTGAAATGGCGATTGAGACGCTGCAAAAGTCTGACGGTCTGTCCACTCACAGAAGCTCTCTTCTCAACAGCCATCTGCAATGGCTGCTGGACAATTATGAGACAGCGGAGGGAGTGAGCCTGCCGAGGAGCACGCTGTACAACCACTACCTTCGACACTGCCAGGAGCACAAGCTGGACCCGGTCAATGCCGCCTCTTTCGGAAAACTAATAAGGTCCATTTTTATGGGGCTACGAACTAGGAGATTAGGCACTAGAGGAAACTCCAAATACCATTACTATGGGATTCGTGTGAAGCCAGATTCTCCTCTTAACCGTCTACAAGAAGATATGCAGTACATGGCTATGAGGCAGCAGCCCATGCAACAGAAGCAAAGGTACAAGCCTATGCAGAAAGTGGATGGGGTTGCAGATGGTTTCACAGGAAGTGGCCAACAGACAGGCACATCTGTTGAGCAAACTGTAATTGCCCAAAGTCAACATCATCAACAGTTTTTAGATGCATCTCGAGCACTTCCAGAGTTTGGAGAAGTTGAAATCTCTTCTCTGCCAGATGGTACTACCTTTGAGGATATCAAGTCACTGCAGAGTCTTTATCGAGAGCACTGTGAGGCAATACTGGACGTTGTTGTGAATCTTCAGTTTAGCCTGATAGAAAAACTGTGGCAAACATTCTGGCGCTATTCCCCATCTACTCCAGCCGACGGCACTACCATCACGGAATCAAGCAATCTGAGTGAAATAGAAAGTCGACTTCCGAAAGCAAAGCTGATAACTCTGTGCAAACATGAGTCTATCCTGAAATGGATGTGTAACTGTGACCATGGGATGTACCAGGCTTTGGTGGAGATTCTCATCCCCGACGTCCTTAGACCCATTCCTAGTGCCTTGACCCAAGCCATTCGAAATTTCGCAAAAAGCCTAGAAGGTTGGCTTTCAAATGCCATGAACAATATTCCACAGAGAATGATTCAAACCAAGGTTGCCGCTGTAAGTGCCTTTGCTCAGACTCTGCGAAGATACACATCGCTCAATCACCTGGCCCAGGCAGCCCGCGCAGTGCTTCAGAACACTTCCCAGATCAACCAGATGCTCAGTGACCTCAACCGCGTTGACTTTGCCAATGTCCAGGAGCAGGCTTCCTGGGTGTGCCAGTGTGATGACAACATGGTTCAGAGACTAGAAACAGACTTCAAGATGACCCTGCAGCAGCAGAGCACTCTGGAGCAGTGGGCTGCTTGGCTGGACAATGTGATGATGCAAGCGCTGAAGCCCTATGAAGGAAGGCCCAGCTTCCCGAAGGCTGCTCGGCAGTTTCTGCTCAAGTGGTCTTTCTACAGCTCCATGGTTATCCGGGACTTAACCTTGCGCAGTGCTGCTAGCTTTGGCTCCTTTCACCTGATCCGGCTGCTCTATGATGAGTACATGTTCTACTTAGTAGAGCATCGTGTTGCTCAAGTGACAGGAGAGACACCGATAGCAGTGATGGGTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGTGTTGCTCAAGTGACAGG
59.42
CCTGTGTCTGAACCCGTCTC
60.04
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCATCGTGTTGCTCAAGTGA
59.13
CCTGTGTCTGAACCCGTCTC
60.04
151
PCR template sequence:
TCACCTGATCCGGCTGCTCTATGATGAGTACATGTTCTACTTAGTAGAGCATCGTGTTGCTCAAGTGACAGGAGAGACACCGATAGCAGTGATGGGTGAGAGATTTTTATCAGAGGAATGTAGACTGGAATCTGCAATGGTTCTCAAAATCCCAAAGTGAGACCATCATGCAGACTTCAGAGACGGGTTCAGACACAGGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
30
Interacting miRNAs (#binding sites)
mmu-miR-136-5p(2), mmu-miR-370-3p(2), mmu-miR-29b-2-5p(2), mmu-miR-124-3p(1), mmu-miR-23b-3p(1), mmu-miR-140-5p(1), mmu-miR-134-5p(1), mmu-let-7a-5p(1), mmu-miR-199a-5p(1), mmu-miR-375-3p(1), mmu-miR-103-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-let-7c-5p(1), mmu-miR-15b-5p(1), mmu-miR-298-5p(1), mmu-miR-196a-5p(1), mmu-miR-23a-3p(1), mmu-let-7d-5p(1), mmu-miR-382-5p(1), mmu-miR-34b-5p(1), mmu-miR-107-3p(1), mmu-miR-98-5p(1), mmu-miR-499-5p(1), mmu-miR-207(1), mmu-miR-5101(1), mmu-miR-484(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGTGATGGGTGAGAGATTTTTATCAG
siRNA sets
AAATCTCTCACCCATCACT, AAAATCTCTCACCCATCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRFX3_2035_ORF_1
0.913
0.233940119
0.999993546
2028
ORF sequence:
ATGCAGACTTCAGAGACGGGTTCAGACACAGGTTCGACAGTGACTCTGCAGACGTCTGTGGCTAGCCAAGCAGCAGTGCCTACACAGGTGGTACAGCAAGTGCCAGTGCAGCAGCAGGTGCAGCAGGTACAGACAGTTCAGCAGGTCCAACATGTCTACCCAGCTCAGGTGCAGTATGTGGAAGGAAGTGATACTGTCTATACCAATGGAGCAATCCGAACAACAACTTATCCCTACACAGAAACACAGATGTACAGCCAAAACACTGGAGGAAATTACTTTGATACTCAAGGAAGTTCTGCCCAGGTGACAACTGTGGTGTCCTCCCACAGTATGGTGGGTACTGGTGGGATTCAGATGGGCGTCACAGGAGGACAACTCATCAGCAGCTCGGGAGGAACCTATTTGATCGGCAATTCAATGGAGAACTCTGGTCACTCAGTGACACACACAACTCGGGCCTCCCCAGCAACAATTGAAATGGCGATTGAGACGCTGCAAAAGTCTGACGGTCTGTCCACTCACAGAAGCTCTCTTCTCAACAGCCATCTGCAATGGCTGCTGGACAATTATGAGACAGCGGAGGGAGTGAGCCTGCCGAGGAGCACGCTGTACAACCACTACCTTCGACACTGCCAGGAGCACAAGCTGGACCCGGTCAATGCCGCCTCTTTCGGAAAACTAATAAGGTCCATTTTTATGGGGCTACGAACTAGGAGATTAGGCACTAGAGGAAACTCCAAATACCATTACTATGGGATTCGTGTGAAGCCAGATTCTCCTCTTAACCGTCTACAAGAAGATATGCAGTACATGGCTATGAGGCAGCAGCCCATGCAACAGAAGCAAAGGTACAAGCCTATGCAGAAAGTGGATGGGGTTGCAGATGGTTTCACAGGAAGTGGCCAACAGACAGGCACATCTGTTGAGCAAACTGTAATTGCCCAAAGTCAACATCATCAACAGTTTTTAGATGCATCTCGAGCACTTCCAGAGTTTGGAGAAGTTGAAATCTCTTCTCTGCCAGATGGTACTACCTTTGAGGATATCAAGTCACTGCAGAGTCTTTATCGAGAGCACTGTGAGGCAATACTGGACGTTGTTGTGAATCTTCAGTTTAGCCTGATAGAAAAACTGTGGCAAACATTCTGGCGCTATTCCCCATCTACTCCAGCCGACGGCACTACCATCACGGAATCAAGCAATCTGAGTGAAATAGAAAGTCGACTTCCGAAAGCAAAGCTGATAACTCTGTGCAAACATGAGTCTATCCTGAAATGGATGTGTAACTGTGACCATGGGATGTACCAGGCTTTGGTGGAGATTCTCATCCCCGACGTCCTTAGACCCATTCCTAGTGCCTTGACCCAAGCCATTCGAAATTTCGCAAAAAGCCTAGAAGGTTGGCTTTCAAATGCCATGAACAATATTCCACAGAGAATGATTCAAACCAAGGTTGCCGCTGTAAGTGCCTTTGCTCAGACTCTGCGAAGATACACATCGCTCAATCACCTGGCCCAGGCAGCCCGCGCAGTGCTTCAGAACACTTCCCAGATCAACCAGATGCTCAGTGACCTCAACCGCGTTGACTTTGCCAATGTCCAGGAGCAGGCTTCCTGGGTGTGCCAGTGTGATGACAACATGGTTCAGAGACTAGAAACAGACTTCAAGATGACCCTGCAGCAGCAGAGCACTCTGGAGCAGTGGGCTGCTTGGCTGGACAATGTGATGATGCAAGCGCTGAAGCCCTATGAAGGAAGGCCCAGCTTCCCGAAGGCTGCTCGGCAGTTTCTGCTCAAGTGGTCTTTCTACAGCTCCATGGTTATCCGGGACTTAACCTTGCGCAGTGCTGCTAGCTTTGGCTCCTTTCACCTGATCCGGCTGCTCTATGATGAGTACATGTTCTACTTAGTAGAGCATCGTGTTGCTCAAGTGACAGGAGAGACACCGATAGCAGTGATGGGTGAGAGATTTTTATCAGAGGAATGTAGACTGGAATCTGCAATGGTTCTCAAAATCCCAAAGTGA
Peptide sequence:
MQTSETGSDTGSTVTLQTSVASQAAVPTQVVQQVPVQQQVQQVQTVQQVQHVYPAQVQYVEGSDTVYTNGAIRTTTYPYTETQMYSQNTGGNYFDTQGSSAQVTTVVSSHSMVGTGGIQMGVTGGQLISSSGGTYLIGNSMENSGHSVTHTTRASPATIEMAIETLQKSDGLSTHRSSLLNSHLQWLLDNYETAEGVSLPRSTLYNHYLRHCQEHKLDPVNAASFGKLIRSIFMGLRTRRLGTRGNSKYHYYGIRVKPDSPLNRLQEDMQYMAMRQQPMQQKQRYKPMQKVDGVADGFTGSGQQTGTSVEQTVIAQSQHHQQFLDASRALPEFGEVEISSLPDGTTFEDIKSLQSLYREHCEAILDVVVNLQFSLIEKLWQTFWRYSPSTPADGTTITESSNLSEIESRLPKAKLITLCKHESILKWMCNCDHGMYQALVEILIPDVLRPIPSALTQAIRNFAKSLEGWLSNAMNNIPQRMIQTKVAAVSAFAQTLRRYTSLNHLAQAARAVLQNTSQINQMLSDLNRVDFANVQEQASWVCQCDDNMVQRLETDFKMTLQQQSTLEQWAAWLDNVMMQALKPYEGRPSFPKAARQFLLKWSFYSSMVIRDLTLRSAASFGSFHLIRLLYDEYMFYLVEHRVAQVTGETPIAVMGERFLSEECRLESAMVLKIPK
IRESfinder result
IRESfinder score
0.506411806
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page