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mmu_circRere_434
Basic information of circular RNA
PanCircBase ID:
mmu_circRere_434
mm39_Chr. Position ID:
chr4|150523799|150561925|+
Gene name:
Rere
Transcript:
ENSMUST00000105682.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
4,5,6,7
Exon/intron offsets:
0,29352,30952,38021
Genomic length:
38126
Exon/intron sizes in nt:
126,106,97,105
Flanking exon/introns:
chr4:150516050-150523799|chr4:150561925-150584459
Splice length:
434
Other database IDs:
circBase: mmu_circ_0001298, CIRCpedia: MMU_CIRCpedia_10079, circAtlas: mmu-Rere_0007
circBase: hsa_circ_0008501, circAtlas: hsa-RERE_0006, CIRCpedia: HSA_CIRCpedia_33040
Human Ortholog IDs:
Mature spliced Sequence:
GTCCACAGCTCCCAGGCCTGTTGCAGATCTCCAGCTCCTGCTTTCTGTGACCCCCCAGCATGCTCTCTGCCGGTGGCACCACAGCCACCACAGCACCTCTCTGAAGCCGGGAGAGGGCCTGGAGGGAGTAAGAGGGACCATCTACTCATGAACGTCAAATGGTACTACCGTCAGTCTGAAGTCCCAGATTCTGTCTATCAGCATTTGGTTCAGGATCGGCATAATGAAAACGACTCTGGAAGAGAGCTTGTCATCACAGATCCAGTCATCAAGAATCGGGAACTCTTCATTTCTGATTATGTTGACACCTACCATGCTGCTGCCCTAAGAGGGAAGTGTAACATCTCCCATTTTTCTGACATATTTGCTGCTCGAGAGTTTAAAGCCCGAGTGGACTCATTTTTCTACATATTAGGATACAACCCTGAGACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCCGAGTGGACTCATTTT
59.31
GAGGTGCTGTGGTGGCTG
60.67
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCCCGAGTGGACTCATTT
59.31
GAGGTGCTGTGGTGGCTG
60.67
151
PCR template sequence:
AGTGTAACATCTCCCATTTTTCTGACATATTTGCTGCTCGAGAGTTTAAAGCCCGAGTGGACTCATTTTTCTACATATTAGGATACAACCCTGAGACAAGGTCCACAGCTCCCAGGCCTGTTGCAGATCTCCAGCTCCTGCTTTCTGTGACCCCCCAGCATGCTCTCTGCCGGTGGCACCACAGCCACCACAGCACCTCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-103-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-107-3p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCCTGAGACAAGGTCCACAGCTCCC
siRNA sets
GAGCTGTGGACCTTGTCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRERE_434_ORF_1
0.8521
0.181899966
0.556172898
438
ORF sequence:
ATGAACGTCAAATGGTACTACCGTCAGTCTGAAGTCCCAGATTCTGTCTATCAGCATTTGGTTCAGGATCGGCATAATGAAAACGACTCTGGAAGAGAGCTTGTCATCACAGATCCAGTCATCAAGAATCGGGAACTCTTCATTTCTGATTATGTTGACACCTACCATGCTGCTGCCCTAAGAGGGAAGTGTAACATCTCCCATTTTTCTGACATATTTGCTGCTCGAGAGTTTAAAGCCCGAGTGGACTCATTTTTCTACATATTAGGATACAACCCTGAGACAAGGTCCACAGCTCCCAGGCCTGTTGCAGATCTCCAGCTCCTGCTTTCTGTGACCCCCCAGCATGCTCTCTGCCGGTGGCACCACAGCCACCACAGCACCTCTCTGAAGCCGGGAGAGGGCCTGGAGGGAGTAAGAGGGACCATCTACTCATGA
Peptide sequence:
MNVKWYYRQSEVPDSVYQHLVQDRHNENDSGRELVITDPVIKNRELFISDYVDTYHAAALRGKCNISHFSDIFAAREFKARVDSFFYILGYNPETRSTAPRPVADLQLLLSVTPQHALCRWHHSHHSTSLKPGEGLEGVRGTIYS
IRESfinder result
IRESfinder score
0.792237892
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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