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mmu_circNrxn1_2199
Basic information of circular RNA
PanCircBase ID:
mmu_circNrxn1_2199
mm39_Chr. Position ID:
chr17|91008171|91397033|-
Gene name:
Nrxn1
Transcript:
ENSMUST00000160844.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
8,7,6,5,4,3,2
Exon/intron offsets:
0,1244,3322,290623,291371,294717,387211
Genomic length:
388862
Exon/intron sizes in nt:
1,62,24,30,21,23,01,81,000
Flanking exon/introns:
chr17:90950857-91008171|chr17:91397033-91400026
Splice length:
2199
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATTTCTGAGTTCTTATAAACGTCAAAATAAAATCAAAATGCATCACCAACATACAACCAACTGACATGCTGGAGTCTTAGGGTGGCCTTGCAGAGACAGAAAAAAGAAGAGTTTGAGGGATTGATTTCACCATCTAACAGCTTCTGGCTACTTCACAGCAGGGTTTGAGACCTACCTACAGGGCTCCTAAACATAAAGCGAATCAGCCTGGGAGGGCATGCACAGGAAATTTGGCCTTGGCTTTAGTGGTGCTGGAAGCCCATGATATGACAGAAGTAGGCCTCTGAAGCTATTCTGGTGTCTCACTCTGTCCTTTCTCCTTCTGTGCTTGGAGCCAACATCTGGAGGGGCCTCGAGGCCTGCCAAGCAGCCAAAGATCCTGGCTCAGTGTTGACTTCGTGTTCCTCTCCGAGAAAAGTGTGTTTCTTCCGATTCTGCTCTCCTACTGCTGGCACCGCGCCGGTGGTACTTTGAAGGTTTTGGTCCTGGGATAGTTGAAGTACCTGTTGGTGCCACAGATGCCCTCACTTAAACATCATCGGATGCAAATGGATCAGTGATCGCTCTTGAGCCTCGGTGGCCCTCTTTTTCAGAACGTTGCCTCCAAAGTGTATCCCCCCTTTGGCCTGGAAGTTCTGCAGCTATCCCATAGGACTGGGGTCTCCGCTTTCCAGTTGGAAGGAGACTACTGGGAGAGAGGAAGGGGCTGCTGGAAGAGAAGAAGAAGGAAAAAAGAGCTGAAGGAGGGTGCGCCCCTCCCACTGCCGCCTCCCCCCTCCCTCCCACTCCTCTGCGGACCCCCATTTCTCTGTGAAGGTGTCCAGGACCGCTTCGACCCTGTCGCCCCCGGCTCCCCCCCGCCGCACCCCAGCCCCGAGCATGGGGACGGCGCTGGTCCAGCGCGGGGGCTGCTGTCTCCTCTGCCTGTCGCTGCTGCTGCTGGGCTGCTGGGCAGAGCTGGGCAGCGGGCTGGAGTTCCCGGGCGCCGAGGGCCAGTGGACGCGCTTCCCCAAGTGGAACGCGTGCTGCGAGAGCGAGATGAGCTTCCAGCTGAAGACGCGCAGTGCCCGCGGCCTCGTGCTCTACTTCGACGACGAGGGCTTCTGCGACTTCCTCGAGCTCATCCTGACGCGCGGCGGCCGCCTGCAGCTCAGCTTCTCCATCTTCTGCGCCGAGCCCGCCACGCTGTTGGCCGACACGCCGGTCAACGACGGCGCCTGGCACAGCGTGCGCATCCGCCGCCAGTTCCGCAACACCACGCTCTACATCGACCGCGCCGAGGCCAAGTGGGTGGAGGTCAAGTCCAAGCGCAGGGACATGACGGTGTTCAGCGGGCTCTTCGTGGGCGGCCTGCCACCCGAACTGCGCGCCGCGGCCCTCAAGCTCACGCTGGCCTCGGTGCGCGAGCGCGAGCCCTTCAAGGGCTGGATCCGTGACGTCCGGGTCAACTCGTCACAGGCCCTGCCGGTGGACGGCGGCGAGGTCAAGCTGGACGACGAGCCTCCCAACAGCGGTGGCGGGAGCCCATGCGAGGCGGGCGAAGAAGGCGAGGGCGGCGTGTGCCTCAACGGGGGCGTGTGCTCCGTGGTCGACGACCAGGCCGTATGCGACTGCTCGAGGACCGGCTTCCGTGGCAAGGACTGCAGCCAAGAAGACAACAATGTGGAAGGTCTGGCACACCTGATGATGGGCGACCAAGGTAAAAGTAAAGGAAAAGAAGAGTATATTGCCACGTTCAAGGGATCTGAATACTTCTGCTACGACTTATCTCAAAACCCCATTCAAAGCAGCAGTGATGAAATAACTCTGTCCTTTAAAACTCTTCAAAGGAACGGACTGATGCTTCACACAGGGAAATCAGCTGATTATGTCAATCTTGCATTGAAAAATGGAGCTGTCTCTCTGGTCATTAATTTGGGATCAGGGGCCTTTGAAGCACTAGTGGAGCCTGTGAATGGAAAGTTTAATGATAATGCCTGGCATGATGTGAAAGTCACCAGGAATCTGCGTCAGCACTCAGGCATTGGACACGCTATGGTGACAATATCAGTGGATGGAATTCTTACCACAACGGGCTACACGCAAGAAGATTACACCATGCTGGGGTCTGATGACTTTTTCTATGTTGGAGGCAGCCCCAGCACAGCCGACCTTCCAGGGTCACCAGTCAGTAACAACTTTATGGGCTGTCTCAAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTATGTTGGAGGCAGCCC
59.74
AAGGCCACCCTAAGACTCCA
60.18
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTATGTTGGAGGCAGCCC
59.74
CAAGGCCACCCTAAGACTCC
59.75
171
PCR template sequence:
GCTGGGGTCTGATGACTTTTTCTATGTTGGAGGCAGCCCCAGCACAGCCGACCTTCCAGGGTCACCAGTCAGTAACAACTTTATGGGCTGTCTCAAAGAGATTTCTGAGTTCTTATAAACGTCAAAATAAAATCAAAATGCATCACCAACATACAACCAACTGACATGCTGGAGTCTTAGGGTGGCCTTGCAGAGACAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
25
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(2), mmu-miR-136-5p(2), mmu-miR-382-5p(2), mmu-miR-705(2), mmu-miR-338-3p(2), mmu-miR-23b-3p(1), mmu-miR-106a-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-335-5p(1), mmu-miR-29c-3p(1), mmu-miR-328-3p(1), mmu-miR-125b-5p(1), mmu-miR-23a-3p(1), mmu-miR-127-3p(1), mmu-miR-382-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-370-3p(1), mmu-miR-297a-5p(1), mmu-miR-666-5p(1), mmu-miR-499-5p(1), mmu-miR-680(1), mmu-miR-335-3p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGTCTCAAAGAGATTTCTGAGTTCT
siRNA sets
GAACTCAGAAATCTCTTTG, AGAAATCTCTTTGAGACAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNRXN1_2199_ORF_1
1.1749
0.446154906
0.999756121
1338
ORF sequence:
ATGGGGACGGCGCTGGTCCAGCGCGGGGGCTGCTGTCTCCTCTGCCTGTCGCTGCTGCTGCTGGGCTGCTGGGCAGAGCTGGGCAGCGGGCTGGAGTTCCCGGGCGCCGAGGGCCAGTGGACGCGCTTCCCCAAGTGGAACGCGTGCTGCGAGAGCGAGATGAGCTTCCAGCTGAAGACGCGCAGTGCCCGCGGCCTCGTGCTCTACTTCGACGACGAGGGCTTCTGCGACTTCCTCGAGCTCATCCTGACGCGCGGCGGCCGCCTGCAGCTCAGCTTCTCCATCTTCTGCGCCGAGCCCGCCACGCTGTTGGCCGACACGCCGGTCAACGACGGCGCCTGGCACAGCGTGCGCATCCGCCGCCAGTTCCGCAACACCACGCTCTACATCGACCGCGCCGAGGCCAAGTGGGTGGAGGTCAAGTCCAAGCGCAGGGACATGACGGTGTTCAGCGGGCTCTTCGTGGGCGGCCTGCCACCCGAACTGCGCGCCGCGGCCCTCAAGCTCACGCTGGCCTCGGTGCGCGAGCGCGAGCCCTTCAAGGGCTGGATCCGTGACGTCCGGGTCAACTCGTCACAGGCCCTGCCGGTGGACGGCGGCGAGGTCAAGCTGGACGACGAGCCTCCCAACAGCGGTGGCGGGAGCCCATGCGAGGCGGGCGAAGAAGGCGAGGGCGGCGTGTGCCTCAACGGGGGCGTGTGCTCCGTGGTCGACGACCAGGCCGTATGCGACTGCTCGAGGACCGGCTTCCGTGGCAAGGACTGCAGCCAAGAAGACAACAATGTGGAAGGTCTGGCACACCTGATGATGGGCGACCAAGGTAAAAGTAAAGGAAAAGAAGAGTATATTGCCACGTTCAAGGGATCTGAATACTTCTGCTACGACTTATCTCAAAACCCCATTCAAAGCAGCAGTGATGAAATAACTCTGTCCTTTAAAACTCTTCAAAGGAACGGACTGATGCTTCACACAGGGAAATCAGCTGATTATGTCAATCTTGCATTGAAAAATGGAGCTGTCTCTCTGGTCATTAATTTGGGATCAGGGGCCTTTGAAGCACTAGTGGAGCCTGTGAATGGAAAGTTTAATGATAATGCCTGGCATGATGTGAAAGTCACCAGGAATCTGCGTCAGCACTCAGGCATTGGACACGCTATGGTGACAATATCAGTGGATGGAATTCTTACCACAACGGGCTACACGCAAGAAGATTACACCATGCTGGGGTCTGATGACTTTTTCTATGTTGGAGGCAGCCCCAGCACAGCCGACCTTCCAGGGTCACCAGTCAGTAACAACTTTATGGGCTGTCTCAAAGAGATTTCTGAGTTCTTATAA
Peptide sequence:
MGTALVQRGGCCLLCLSLLLLGCWAELGSGLEFPGAEGQWTRFPKWNACCESEMSFQLKTRSARGLVLYFDDEGFCDFLELILTRGGRLQLSFSIFCAEPATLLADTPVNDGAWHSVRIRRQFRNTTLYIDRAEAKWVEVKSKRRDMTVFSGLFVGGLPPELRAAALKLTLASVREREPFKGWIRDVRVNSSQALPVDGGEVKLDDEPPNSGGGSPCEAGEEGEGGVCLNGGVCSVVDDQAVCDCSRTGFRGKDCSQEDNNVEGLAHLMMGDQGKSKGKEEYIATFKGSEYFCYDLSQNPIQSSSDEITLSFKTLQRNGLMLHTGKSADYVNLALKNGAVSLVINLGSGAFEALVEPVNGKFNDNAWHDVKVTRNLRQHSGIGHAMVTISVDGILTTTGYTQEDYTMLGSDDFFYVGGSPSTADLPGSPVSNNFMGCLKEISEFL
IRESfinder result
IRESfinder score
0.323303936
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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