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mmu_circPrex1_417
Basic information of circular RNA
PanCircBase ID:
mmu_circPrex1_417
mm39_Chr. Position ID:
chr2|166451657|166455180|-
Gene name:
Prex1
Transcript:
ENSMUST00000036719.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
10,9,8
Exon/intron offsets:
0,1890,3404
Genomic length:
3523
Exon/intron sizes in nt:
14,81,50,119
Flanking exon/introns:
chr2:166444836-166451657|chr2:166455180-166459752
Splice length:
417
Other database IDs:
circBase: mmu_circ_0009580, CIRCpedia: MMU_CIRCpedia_11602, circAtlas: mmu-Prex1_0002
circBase: hsa_circ_0003539, circAtlas: hsa-PREX1_0002, CIRCpedia: HSA_CIRCpedia_68050
Human Ortholog IDs:
Mature spliced Sequence:
GGTCACTGGGAGCAAGAAATCTACCAAAAGGACCAAGTCCATCAACGGCTCCCTGTACATCTTTAGGGGTCGGATCAACACTGAGGTCATGGAAGTGGAGAATGTGGAGGATGGGACAGCCGATTACCACAGCAATGGCTACACTGTCACCAATGGCTGGAAGATCCACAACACCGCCAAAAACAAGTGGTTCGTGTGTATGGCCAAGACGGCGGAGGAGAAACAGAAGTGGCTGGATGCCCTGATCCGAGAGCGGGAGCAGCGAGAGAGCCTGAAGCTGGGCATGGAGCGTGACGCGTACGTCATGATTGCGGAGAAGGGGGAGAAGCTGTATCACATGATGATGAGCAAGAAGGTGAACTTGATCAAGGACCGCCGGCGGAAGCTGAGCACCGTCCCCAAGTGCTTCCTTGGCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACTTGATCAAGGACCGCCG
60.67
CTCAGTGTTGATCCGACCCC
60.11
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACTTGATCAAGGACCGCCG
60.67
CCTCAGTGTTGATCCGACCC
60.11
145
PCR template sequence:
AGGGGGAGAAGCTGTATCACATGATGATGAGCAAGAAGGTGAACTTGATCAAGGACCGCCGGCGGAAGCTGAGCACCGTCCCCAAGTGCTTCCTTGGCAAGGTCACTGGGAGCAAGAAATCTACCAAAAGGACCAAGTCCATCAACGGCTCCCTGTACATCTTTAGGGGTCGGATCAACACTGAGGTCATGGAAGTGGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-34c-5p(1), mmu-miR-207(1), mmu-miR-484(1)
siRNAs for circular RNA silencing
Junction sequence
GCTTCCTTGGCAAGGTCACTGGGAGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPREX1_417_ORF_1
1.231
0.649993575
0.993651033
744
ORF sequence:
ATGGAAGTGGAGAATGTGGAGGATGGGACAGCCGATTACCACAGCAATGGCTACACTGTCACCAATGGCTGGAAGATCCACAACACCGCCAAAAACAAGTGGTTCGTGTGTATGGCCAAGACGGCGGAGGAGAAACAGAAGTGGCTGGATGCCCTGATCCGAGAGCGGGAGCAGCGAGAGAGCCTGAAGCTGGGCATGGAGCGTGACGCGTACGTCATGATTGCGGAGAAGGGGGAGAAGCTGTATCACATGATGATGAGCAAGAAGGTGAACTTGATCAAGGACCGCCGGCGGAAGCTGAGCACCGTCCCCAAGTGCTTCCTTGGCAAGGTCACTGGGAGCAAGAAATCTACCAAAAGGACCAAGTCCATCAACGGCTCCCTGTACATCTTTAGGGGTCGGATCAACACTGAGGTCATGGAAGTGGAGAATGTGGAGGATGGGACAGCCGATTACCACAGCAATGGCTACACTGTCACCAATGGCTGGAAGATCCACAACACCGCCAAAAACAAGTGGTTCGTGTGTATGGCCAAGACGGCGGAGGAGAAACAGAAGTGGCTGGATGCCCTGATCCGAGAGCGGGAGCAGCGAGAGAGCCTGAAGCTGGGCATGGAGCGTGACGCGTACGTCATGATTGCGGAGAAGGGGGAGAAGCTGTATCACATGATGATGAGCAAGAAGGTGAACTTGATCAAGGACCGCCGGCGGAAGCTGAGCACCGTCCCCAAGTGCTTCCTTGGC
Peptide sequence:
MEVENVEDGTADYHSNGYTVTNGWKIHNTAKNKWFVCMAKTAEEKQKWLDALIREREQRESLKLGMERDAYVMIAEKGEKLYHMMMSKKVNLIKDRRRKLSTVPKCFLGKVTGSKKSTKRTKSINGSLYIFRGRINTEVMEVENVEDGTADYHSNGYTVTNGWKIHNTAKNKWFVCMAKTAEEKQKWLDALIREREQRESLKLGMERDAYVMIAEKGEKLYHMMMSKKVNLIKDRRRKLSTVPKCFLG
IRESfinder result
IRESfinder score
0.13730405
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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