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mmu_circNfxl1_838
Basic information of circular RNA
PanCircBase ID:
mmu_circNfxl1_838
mm39_Chr. Position ID:
chr5|72686726|72697996|-
Gene name:
Nfxl1
Transcript:
ENSMUST00000087216.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
13,12,11,10,9,8,7
Exon/intron offsets:
0,3661,7982,8766,10222,10910,11108
Genomic length:
11270
Exon/intron sizes in nt:
1,21,91,12,31,25,11,51,00,000
Flanking exon/introns:
chr5:72686514-72686726|chr5:72697996-72698196
Splice length:
838
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTCCCTGCCCTCCTTGTCCAAAGATGGTCACAACCACTTGTTACTGTAAGAAAGCCAAGCCTATCCCTCGCAGGTGCAGTGCCAAGCAGTGGTCCTGTCAGCTGCCATGTGGGCGAAAGCTGCTTTGTGGACATCATAAGTGTGAAAATCCTTGCCATGCAGGAAACTGTCAGCCTTGTCCAAGAGTTAGTAGACAAAAATGTGTATGTGGCAAAAAAGTAGCAGAAAGAAGTTGTGCAAGCCCAGTGTGGCATTGTGATCAAGTATGTGGAAAGACACTGCCATGTGGTAATCATACATGTGAGCAAGTTTGTCATGTTGGTGCTTGTGGAGAGTGTCCTCGATCTGGGAAGAGGTCCTGTCCATGTCAGAAATCAAAGTTTTCTTTGCCTTGTACAGAAGATGTACCAACTTGTGGAGACAGCTGTGACAAAATACTTGAATGTGGAATCCATAGGTGTTCACAGCGTTGCCACCGAGGTCCTTGTGAAACATGCAGACAAGAAGTGGAAAAACAGTGTCGTTGTGGAAAGCACACAAAGCGAATGCCTTGTCACAAGCCTTACCTTTGTGAAACAAAGTGTGTTAAAATGCGGGACTGTCAAAAGCATCAGTGTAGGAGAAAGTGTTGCCCTGGAAACTGTCCACCTTGTGATCAAAATTGTGGACGGACTTTAGGATGTAGAAACCATAAGTGTCCGTCTGTCTGCCATAGAGGCAGTTGCTATCCATGTCCAGAAACGGTAGATGTGAAGTGCAATTGTGGTAATGCAAAGGTGACAGTACCCTGTGGCCGAGAGCGGACCACAAGGCCACCTAAGTGCAAAGAGCTGTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCAAAGGTGACAGTACCCT
59.29
CGAGGGATAGGCTTGGCTTT
59.82
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAAAGGTGACAGTACCCT
58.86
CTGCACCTGCGAGGGATAG
59.93
148
PCR template sequence:
AAACGGTAGATGTGAAGTGCAATTGTGGTAATGCAAAGGTGACAGTACCCTGTGGCCGAGAGCGGACCACAAGGCCACCTAAGTGCAAAGAGCTGTGCAGGTCCCTGCCCTCCTTGTCCAAAGATGGTCACAACCACTTGTTACTGTAAGAAAGCCAAGCCTATCCCTCGCAGGTGCAGTGCCAAGCAGTGGTCCTGTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-96-5p(2), mmu-miR-140-5p(1), mmu-miR-32-5p(1), mmu-miR-34a-5p(1), mmu-miR-92a-3p(1), mmu-miR-29a-3p(1), mmu-miR-25-3p(1), mmu-miR-363-3p(1), mmu-miR-26b-5p(1), mmu-miR-218-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-802-5p(1), mmu-miR-673-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGAGCTGTGCAGGTCCCTGCCCTCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNFXL1_838_ORF_1
1.0346
-0.140054409
0.90920861
864
ORF sequence:
ATGGTCACAACCACTTGTTACTGTAAGAAAGCCAAGCCTATCCCTCGCAGGTGCAGTGCCAAGCAGTGGTCCTGTCAGCTGCCATGTGGGCGAAAGCTGCTTTGTGGACATCATAAGTGTGAAAATCCTTGCCATGCAGGAAACTGTCAGCCTTGTCCAAGAGTTAGTAGACAAAAATGTGTATGTGGCAAAAAAGTAGCAGAAAGAAGTTGTGCAAGCCCAGTGTGGCATTGTGATCAAGTATGTGGAAAGACACTGCCATGTGGTAATCATACATGTGAGCAAGTTTGTCATGTTGGTGCTTGTGGAGAGTGTCCTCGATCTGGGAAGAGGTCCTGTCCATGTCAGAAATCAAAGTTTTCTTTGCCTTGTACAGAAGATGTACCAACTTGTGGAGACAGCTGTGACAAAATACTTGAATGTGGAATCCATAGGTGTTCACAGCGTTGCCACCGAGGTCCTTGTGAAACATGCAGACAAGAAGTGGAAAAACAGTGTCGTTGTGGAAAGCACACAAAGCGAATGCCTTGTCACAAGCCTTACCTTTGTGAAACAAAGTGTGTTAAAATGCGGGACTGTCAAAAGCATCAGTGTAGGAGAAAGTGTTGCCCTGGAAACTGTCCACCTTGTGATCAAAATTGTGGACGGACTTTAGGATGTAGAAACCATAAGTGTCCGTCTGTCTGCCATAGAGGCAGTTGCTATCCATGTCCAGAAACGGTAGATGTGAAGTGCAATTGTGGTAATGCAAAGGTGACAGTACCCTGTGGCCGAGAGCGGACCACAAGGCCACCTAAGTGCAAAGAGCTGTGCAGGTCCCTGCCCTCCTTGTCCAAAGATGGTCACAACCACTTGTTACTGTAA
Peptide sequence:
MVTTTCYCKKAKPIPRRCSAKQWSCQLPCGRKLLCGHHKCENPCHAGNCQPCPRVSRQKCVCGKKVAERSCASPVWHCDQVCGKTLPCGNHTCEQVCHVGACGECPRSGKRSCPCQKSKFSLPCTEDVPTCGDSCDKILECGIHRCSQRCHRGPCETCRQEVEKQCRCGKHTKRMPCHKPYLCETKCVKMRDCQKHQCRRKCCPGNCPPCDQNCGRTLGCRNHKCPSVCHRGSCYPCPETVDVKCNCGNAKVTVPCGRERTTRPPKCKELCRSLPSLSKDGHNHLLL
IRESfinder result
IRESfinder score
0.499026147
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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