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mmu_circRfx3_537
Basic information of circular RNA
PanCircBase ID:
mmu_circRfx3_537
mm39_Chr. Position ID:
chr19|27790977|27808192|-
Gene name:
Rfx3
Transcript:
ENSMUST00000165566.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
10,9,8,7
Exon/intron offsets:
0,1907,12455,17033
Genomic length:
17215
Exon/intron sizes in nt:
113,122,120,182
Flanking exon/introns:
chr19:27784308-27790977|chr19:27808192-27814806
Splice length:
537
Other database IDs:
CIRCpedia: MMU_CIRCpedia_215195, circAtlas: mmu-Rfx3_0005
circBase: hsa_circ_0138622, circAtlas: hsa-RFX3_0003, CIRCpedia: HSA_CIRCpedia_118178
Human Ortholog IDs:
Mature spliced Sequence:
CTGCAATGGCTGCTGGACAATTATGAGACAGCGGAGGGAGTGAGCCTGCCGAGGAGCACGCTGTACAACCACTACCTTCGACACTGCCAGGAGCACAAGCTGGACCCGGTCAATGCCGCCTCTTTCGGAAAACTAATAAGGTCCATTTTTATGGGGCTACGAACTAGGAGATTAGGCACTAGAGGAAACTCCAAATACCATTACTATGGGATTCGTGTGAAGCCAGATTCTCCTCTTAACCGTCTACAAGAAGATATGCAGTACATGGCTATGAGGCAGCAGCCCATGCAACAGAAGCAAAGGTACAAGCCTATGCAGAAAGTGGATGGGGTTGCAGATGGTTTCACAGGAAGTGGCCAACAGACAGGCACATCTGTTGAGCAAACTGTAATTGCCCAAAGTCAACATCATCAACAGTTTTTAGATGCATCTCGAGCACTTCCAGAGTTTGGAGAAGTTGAAATCTCTTCTCTGCCAGATGGTACTACCTTTGAGGATATCAAGTCACTGCAGAGTCTTTATCGAGAGCACTGTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCTTCTCTGCCAGATGGT
57.76
CCTGGCAGTGTCGAAGGTAG
60.11
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCTGCCAGATGGTACTACCT
59.75
CCTGGCAGTGTCGAAGGTAG
60.11
160
PCR template sequence:
ACTTCCAGAGTTTGGAGAAGTTGAAATCTCTTCTCTGCCAGATGGTACTACCTTTGAGGATATCAAGTCACTGCAGAGTCTTTATCGAGAGCACTGTGAGCTGCAATGGCTGCTGGACAATTATGAGACAGCGGAGGGAGTGAGCCTGCCGAGGAGCACGCTGTACAACCACTACCTTCGACACTGCCAGGAGCACAAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-let-7a-5p(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-298-5p(1), mmu-miR-196a-5p(1), mmu-let-7d-5p(1), mmu-miR-34b-5p(1), mmu-miR-98-5p(1), mmu-miR-499-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1), mmu-miR-484(1)
siRNAs for circular RNA silencing
Junction sequence
AGAGCACTGTGAGCTGCAATGGCTGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRFX3_537_ORF_1
1.0862
0.192454701
0.985320058
924
ORF sequence:
ATGGGGCTACGAACTAGGAGATTAGGCACTAGAGGAAACTCCAAATACCATTACTATGGGATTCGTGTGAAGCCAGATTCTCCTCTTAACCGTCTACAAGAAGATATGCAGTACATGGCTATGAGGCAGCAGCCCATGCAACAGAAGCAAAGGTACAAGCCTATGCAGAAAGTGGATGGGGTTGCAGATGGTTTCACAGGAAGTGGCCAACAGACAGGCACATCTGTTGAGCAAACTGTAATTGCCCAAAGTCAACATCATCAACAGTTTTTAGATGCATCTCGAGCACTTCCAGAGTTTGGAGAAGTTGAAATCTCTTCTCTGCCAGATGGTACTACCTTTGAGGATATCAAGTCACTGCAGAGTCTTTATCGAGAGCACTGTGAGCTGCAATGGCTGCTGGACAATTATGAGACAGCGGAGGGAGTGAGCCTGCCGAGGAGCACGCTGTACAACCACTACCTTCGACACTGCCAGGAGCACAAGCTGGACCCGGTCAATGCCGCCTCTTTCGGAAAACTAATAAGGTCCATTTTTATGGGGCTACGAACTAGGAGATTAGGCACTAGAGGAAACTCCAAATACCATTACTATGGGATTCGTGTGAAGCCAGATTCTCCTCTTAACCGTCTACAAGAAGATATGCAGTACATGGCTATGAGGCAGCAGCCCATGCAACAGAAGCAAAGGTACAAGCCTATGCAGAAAGTGGATGGGGTTGCAGATGGTTTCACAGGAAGTGGCCAACAGACAGGCACATCTGTTGAGCAAACTGTAATTGCCCAAAGTCAACATCATCAACAGTTTTTAGATGCATCTCGAGCACTTCCAGAGTTTGGAGAAGTTGAAATCTCTTCTCTGCCAGATGGTACTACCTTTGAGGATATCAAGTCACTGCAGAGTCTTTATCGAGAGCACTGTGAG
Peptide sequence:
MGLRTRRLGTRGNSKYHYYGIRVKPDSPLNRLQEDMQYMAMRQQPMQQKQRYKPMQKVDGVADGFTGSGQQTGTSVEQTVIAQSQHHQQFLDASRALPEFGEVEISSLPDGTTFEDIKSLQSLYREHCELQWLLDNYETAEGVSLPRSTLYNHYLRHCQEHKLDPVNAASFGKLIRSIFMGLRTRRLGTRGNSKYHYYGIRVKPDSPLNRLQEDMQYMAMRQQPMQQKQRYKPMQKVDGVADGFTGSGQQTGTSVEQTVIAQSQHHQQFLDASRALPEFGEVEISSLPDGTTFEDIKSLQSLYREHCE
IRESfinder result
IRESfinder score
0.49454244
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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