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mmu_circN4bp2_3017
Basic information of circular RNA
PanCircBase ID:
mmu_circN4bp2_3017
mm39_Chr. Position ID:
chr5|65955433|65972213|+
Gene name:
N4bp2
Transcript:
ENSMUST00000201489.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
9,10,11,12,13,14,15
Exon/intron offsets:
0,5330,8099,11064,11673,13872,16661
Genomic length:
16780
Exon/intron sizes in nt:
77,14,72,35,48,64,61,80,000
Flanking exon/introns:
chr5:65951952-65955433|chr5:65972213-65974504
Splice length:
3017
Other database IDs:
circAtlas: mmu-N4bp2_0016
Human Ortholog IDs:
Mature spliced Sequence:
TCTCAAAAGCATAAATATAAGGTCCTTTTCCGGGAGCCAGACACGTGGTGGAAGTTCAAGCCGAAGGAGCTTGCGAGACGTAATATTCATGGAGTAAGCAAAGAGAAAATATCAAGAATGCTGGAGCACTATCAGCGCTTTGTCTCCGTGCCGATAATCATGAGCTCTTCCGATCCAGAGAAAACCGAGCGCATTGAGTTGTGTGCATACGCTTCTGACGACAGCCCAAGAGACAGTGAAGCTATTAGCTCTGCAAAAGAAGACAGTGTCTCATCTGCGTCTCCGAAGCACTCAGAGCTAACGGAAGAGAAGACCCTTGAGGTGGCCACACAAGCAGTGTTATCTGTGCGTGATCCCCAGCTCCCTTGTCCTGGTTTAAACAGAGGAAGAAAGGAGTTGGGTGACGTGAGTCACGGTGGTCATAACCCCTTCTTTCAGGAAGCCCCGAGCACCTATTTTCCTAACCCTGAAAGCAAAGGTCAAGCCACAGATAGAAGTGAGGAAGAACAAGAGATGGTGTCTGAAAAAGAACATTGTGAAGCAGATGCGTGGAGGCCTGCGGGGGGAGCGTCATCAGATGGGCGCTGTGCTGATGATAATCAAGAAGCCTGTGGGTCTGCAGGTGCAGCCGCGCTTCCAGGTGAGACCCCCTCGCCTCCTGAAATGCTGGAAGAAAGAACGGCAGGAAAGAAAAAGACCATTGGAAAACAAAAAGGCAAATCATCTTTGGAAAAAATCCCCAAACAAGAGCTATCAAATTTTGTTGGTGACTGGCCAGTTGATAAGACAATTAGCCAGAGAACCAAAAGGAACCGGAAAACTGAAAAAGGCTTATCTGTACAAAGTGACAAAAAAGGTAACCTCCCGCAGTCCCACAAAGTATTAGATGCTAGGGTCTCTGTGAATACAGATCCTGTCCAGCCCCAAGGATCTTCACATGGGAACGACGATCTTTCAGAAGTGCCCAGTAGCTATCACTATGATCCTTACAGAAGTACCGAGCAAAGCTCACTTAGTGCTGTGAGCGACTGGCCTTCCTCTGCTTCCTTAGCTCCGAGAGAGCACAGACCGAGAATGCCAAAAGCTGACTTAAGTGAACCCAGCGTGGAATTTGGAACTAATGACAACCTGGGTGAAATACCCTTATATCCAGCACACGAGGCCTACTGGGGGACAAGCCCTGAGGAGCTGAAGACGTTGAGTTCCAGCCTTCGAAGTTCTGAGATGCTGCCCAGTCAAACAGCTCCTGAGCATCATCCGACCTCCCTGAATCCACTGGCTCACAGCCAGCACGCGCTGCCCCTGACCTTCCCCAGTAGTGCAGCAGCTCTTCCTGGAGTAGTGGGTCCCCGGTCTCTAACAGAATTTCCAGTGGGGGTGTCTGGAATTGTCTCTGGAGTAGATACAGGCACTTGTACCCAGACTGAACCCCAAGATTTTGCTCTCTTGTGGAAAATAGAAAAGAATAAAATCAATGTTTCAGATTCTGTCAGAGTGTTGACAGGAAGATTGGATGGGTTTAAGCCCAAAGATTTCACTCTTAATAGAAAAGTAAATGTCCAAGAAACAATTCCCTACAGAGTAATGCATGATAAAAGTACATTCGTTGAAGAAAGTGAGCTTACCAGTGCTGATGAGTCTGAAAATCTTAACATCCTTTGCAAACTATTCGGATCCTTTTCCTTAGAAGCCTTGAAGGATTTATATGAGCGATGTAATAAAGACATTATTTGGGCCACAAGTCTCTTGTTGGATTCTGAGACTAAACTGTGCGAGGACACTGCGGTTGAGAGCTCCCCCAAGTCGTACAGCGAGTCACAGGTTGGGCCGTTTTCTATGGGCTTGGACCTGAAGGAAATTATTAGCCACAGAGGAACCTCAGAAGGTTCTAATTCTTCTGTATCAGAATTTAGTCCTGGAATTGGTATCCGGAACACCAGTGCACGGTCTGCTGGTAACCCAGGAAAGGGGACCTCAGAGCAGGAAGGGAGAAGAGCTATGAATCCTGAAAACCCTGAATTAATAACTAGAGTATTCCCCAATGCTGCTGTAAAGGTCAAGAGTAATAATGAGACACTGCCTGACCGTCAGGCTGAACTGCCAGGCGCGTACACCTTTAAGCAGCCTCTTTCACTTACTCCACGATCTTATATCCCTAAAGATGTTAGTGAGATAGAAAAAAATCTAGTAATGACAGAGACTAGAGACAATATGCATTCATTTCTAAATTTATCTGATATTATAAACTCTGCAACAAGCACTTCAAATCCTGAATTAAATGAAGATGTTTATCTTACTGGCTCTTTGGAAGTAAAGAAAAATGAAAATCTTCCTAAGGATTATGTGAAATTTGCAAACATGGAAGAATTTATCAATGAAGATAAACAGGAAATGGAGAAAAATCTAATGCCAGGAAGTGGTTGGTCAGCAGGAGTTAGTGAAGAGGGTAAAGCTGAGGTATTGACTCCCACGCCAGTGACAGCCACATCTCTGACCATAGACTGTCTGGAGCTGGCGTTACCCCCTGAGCTGGCTTTCCAACTTAATGAGCTGTTTGGCCCAGTTGGTATTGATTCAGGGTCTCTAACAGTCGAGGACTGTGTGGTTCATATAGATCTGAATCTGGCTAAAGTGATTCATGAGAAATGGAGAGAATCTGTAATGGAGCGACAGAGACAGGAGGAGGTTTCTCGAGGCAAGCGCACACAAGATCCTTTGCTGGCTGGACATACTGGTCTTGATAATTTTGAACAAAAATCATCTCAGAAAACAGGCAAAAGGTTATTGAAGACTTTAGCAGCACCTGAGACCCTGGATCACTGGAACACTCAAACAAAAAAAGTTTCACTTCGAGAAATAATGTCAGAAGAAATTGCCTTACAGGAGAAACATGACTTGAAAAGGGAGACACTTATGTTTGAAAAAGACTGTGCCACAAAACTAAAGGAAAAGCAGCTCTTTAAAATATTTCCAGCCATTAATCAAAATTTCCTGGTGGACATTTTCAAAGATCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGTGCCACAAAACTAAAGGA
58.37
TACGTCTCGCAAGCTCCTTC
59.83
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACTGTGCCACAAAACTAAAGGA
59.37
TACGTCTCGCAAGCTCCTTC
59.83
174
PCR template sequence:
TTGAAAAAGACTGTGCCACAAAACTAAAGGAAAAGCAGCTCTTTAAAATATTTCCAGCCATTAATCAAAATTTCCTGGTGGACATTTTCAAAGATCACAGTCTCAAAAGCATAAATATAAGGTCCTTTTCCGGGAGCCAGACACGTGGTGGAAGTTCAAGCCGAAGGAGCTTGCGAGACGTAATATTCATGGAGTAAGCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
29
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(2), mmu-miR-34a-5p(2), mmu-miR-136-5p(2), mmu-miR-107-3p(2), mmu-miR-207(2), mmu-miR-335-3p(2), mmu-miR-669d-5p(2), mmu-miR-9-5p(1), mmu-miR-20b-5p(1), mmu-miR-200a-3p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-106b-5p(1), mmu-miR-298-5p(1), mmu-miR-196a-5p(1), mmu-miR-709(1), mmu-miR-433-3p(1), mmu-miR-467b-5p(1), mmu-miR-362-5p(1), mmu-miR-690(1), mmu-miR-673-5p(1), mmu-miR-5101(1), mmu-miR-3065-5p(1), mmu-miR-540-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAAAGATCACAGTCTCAAAAGCATA
siRNA sets
TATGCTTTTGAGACTGTGA, TTGAGACTGTGATCTTTGA, ATGCTTTTGAGACTGTGAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCN4BP2_3017_ORF_1
1.0315
0.096263144
0.999999991
2997
ORF sequence:
ATGCTGGAGCACTATCAGCGCTTTGTCTCCGTGCCGATAATCATGAGCTCTTCCGATCCAGAGAAAACCGAGCGCATTGAGTTGTGTGCATACGCTTCTGACGACAGCCCAAGAGACAGTGAAGCTATTAGCTCTGCAAAAGAAGACAGTGTCTCATCTGCGTCTCCGAAGCACTCAGAGCTAACGGAAGAGAAGACCCTTGAGGTGGCCACACAAGCAGTGTTATCTGTGCGTGATCCCCAGCTCCCTTGTCCTGGTTTAAACAGAGGAAGAAAGGAGTTGGGTGACGTGAGTCACGGTGGTCATAACCCCTTCTTTCAGGAAGCCCCGAGCACCTATTTTCCTAACCCTGAAAGCAAAGGTCAAGCCACAGATAGAAGTGAGGAAGAACAAGAGATGGTGTCTGAAAAAGAACATTGTGAAGCAGATGCGTGGAGGCCTGCGGGGGGAGCGTCATCAGATGGGCGCTGTGCTGATGATAATCAAGAAGCCTGTGGGTCTGCAGGTGCAGCCGCGCTTCCAGGTGAGACCCCCTCGCCTCCTGAAATGCTGGAAGAAAGAACGGCAGGAAAGAAAAAGACCATTGGAAAACAAAAAGGCAAATCATCTTTGGAAAAAATCCCCAAACAAGAGCTATCAAATTTTGTTGGTGACTGGCCAGTTGATAAGACAATTAGCCAGAGAACCAAAAGGAACCGGAAAACTGAAAAAGGCTTATCTGTACAAAGTGACAAAAAAGGTAACCTCCCGCAGTCCCACAAAGTATTAGATGCTAGGGTCTCTGTGAATACAGATCCTGTCCAGCCCCAAGGATCTTCACATGGGAACGACGATCTTTCAGAAGTGCCCAGTAGCTATCACTATGATCCTTACAGAAGTACCGAGCAAAGCTCACTTAGTGCTGTGAGCGACTGGCCTTCCTCTGCTTCCTTAGCTCCGAGAGAGCACAGACCGAGAATGCCAAAAGCTGACTTAAGTGAACCCAGCGTGGAATTTGGAACTAATGACAACCTGGGTGAAATACCCTTATATCCAGCACACGAGGCCTACTGGGGGACAAGCCCTGAGGAGCTGAAGACGTTGAGTTCCAGCCTTCGAAGTTCTGAGATGCTGCCCAGTCAAACAGCTCCTGAGCATCATCCGACCTCCCTGAATCCACTGGCTCACAGCCAGCACGCGCTGCCCCTGACCTTCCCCAGTAGTGCAGCAGCTCTTCCTGGAGTAGTGGGTCCCCGGTCTCTAACAGAATTTCCAGTGGGGGTGTCTGGAATTGTCTCTGGAGTAGATACAGGCACTTGTACCCAGACTGAACCCCAAGATTTTGCTCTCTTGTGGAAAATAGAAAAGAATAAAATCAATGTTTCAGATTCTGTCAGAGTGTTGACAGGAAGATTGGATGGGTTTAAGCCCAAAGATTTCACTCTTAATAGAAAAGTAAATGTCCAAGAAACAATTCCCTACAGAGTAATGCATGATAAAAGTACATTCGTTGAAGAAAGTGAGCTTACCAGTGCTGATGAGTCTGAAAATCTTAACATCCTTTGCAAACTATTCGGATCCTTTTCCTTAGAAGCCTTGAAGGATTTATATGAGCGATGTAATAAAGACATTATTTGGGCCACAAGTCTCTTGTTGGATTCTGAGACTAAACTGTGCGAGGACACTGCGGTTGAGAGCTCCCCCAAGTCGTACAGCGAGTCACAGGTTGGGCCGTTTTCTATGGGCTTGGACCTGAAGGAAATTATTAGCCACAGAGGAACCTCAGAAGGTTCTAATTCTTCTGTATCAGAATTTAGTCCTGGAATTGGTATCCGGAACACCAGTGCACGGTCTGCTGGTAACCCAGGAAAGGGGACCTCAGAGCAGGAAGGGAGAAGAGCTATGAATCCTGAAAACCCTGAATTAATAACTAGAGTATTCCCCAATGCTGCTGTAAAGGTCAAGAGTAATAATGAGACACTGCCTGACCGTCAGGCTGAACTGCCAGGCGCGTACACCTTTAAGCAGCCTCTTTCACTTACTCCACGATCTTATATCCCTAAAGATGTTAGTGAGATAGAAAAAAATCTAGTAATGACAGAGACTAGAGACAATATGCATTCATTTCTAAATTTATCTGATATTATAAACTCTGCAACAAGCACTTCAAATCCTGAATTAAATGAAGATGTTTATCTTACTGGCTCTTTGGAAGTAAAGAAAAATGAAAATCTTCCTAAGGATTATGTGAAATTTGCAAACATGGAAGAATTTATCAATGAAGATAAACAGGAAATGGAGAAAAATCTAATGCCAGGAAGTGGTTGGTCAGCAGGAGTTAGTGAAGAGGGTAAAGCTGAGGTATTGACTCCCACGCCAGTGACAGCCACATCTCTGACCATAGACTGTCTGGAGCTGGCGTTACCCCCTGAGCTGGCTTTCCAACTTAATGAGCTGTTTGGCCCAGTTGGTATTGATTCAGGGTCTCTAACAGTCGAGGACTGTGTGGTTCATATAGATCTGAATCTGGCTAAAGTGATTCATGAGAAATGGAGAGAATCTGTAATGGAGCGACAGAGACAGGAGGAGGTTTCTCGAGGCAAGCGCACACAAGATCCTTTGCTGGCTGGACATACTGGTCTTGATAATTTTGAACAAAAATCATCTCAGAAAACAGGCAAAAGGTTATTGAAGACTTTAGCAGCACCTGAGACCCTGGATCACTGGAACACTCAAACAAAAAAAGTTTCACTTCGAGAAATAATGTCAGAAGAAATTGCCTTACAGGAGAAACATGACTTGAAAAGGGAGACACTTATGTTTGAAAAAGACTGTGCCACAAAACTAAAGGAAAAGCAGCTCTTTAAAATATTTCCAGCCATTAATCAAAATTTCCTGGTGGACATTTTCAAAGATCACAGTCTCAAAAGCATAAATATAAGGTCCTTTTCCGGGAGCCAGACACGTGGTGGAAGTTCAAGCCGAAGGAGCTTGCGAGACGTAATATTCATGGAGTAA
Peptide sequence:
MLEHYQRFVSVPIIMSSSDPEKTERIELCAYASDDSPRDSEAISSAKEDSVSSASPKHSELTEEKTLEVATQAVLSVRDPQLPCPGLNRGRKELGDVSHGGHNPFFQEAPSTYFPNPESKGQATDRSEEEQEMVSEKEHCEADAWRPAGGASSDGRCADDNQEACGSAGAAALPGETPSPPEMLEERTAGKKKTIGKQKGKSSLEKIPKQELSNFVGDWPVDKTISQRTKRNRKTEKGLSVQSDKKGNLPQSHKVLDARVSVNTDPVQPQGSSHGNDDLSEVPSSYHYDPYRSTEQSSLSAVSDWPSSASLAPREHRPRMPKADLSEPSVEFGTNDNLGEIPLYPAHEAYWGTSPEELKTLSSSLRSSEMLPSQTAPEHHPTSLNPLAHSQHALPLTFPSSAAALPGVVGPRSLTEFPVGVSGIVSGVDTGTCTQTEPQDFALLWKIEKNKINVSDSVRVLTGRLDGFKPKDFTLNRKVNVQETIPYRVMHDKSTFVEESELTSADESENLNILCKLFGSFSLEALKDLYERCNKDIIWATSLLLDSETKLCEDTAVESSPKSYSESQVGPFSMGLDLKEIISHRGTSEGSNSSVSEFSPGIGIRNTSARSAGNPGKGTSEQEGRRAMNPENPELITRVFPNAAVKVKSNNETLPDRQAELPGAYTFKQPLSLTPRSYIPKDVSEIEKNLVMTETRDNMHSFLNLSDIINSATSTSNPELNEDVYLTGSLEVKKNENLPKDYVKFANMEEFINEDKQEMEKNLMPGSGWSAGVSEEGKAEVLTPTPVTATSLTIDCLELALPPELAFQLNELFGPVGIDSGSLTVEDCVVHIDLNLAKVIHEKWRESVMERQRQEEVSRGKRTQDPLLAGHTGLDNFEQKSSQKTGKRLLKTLAAPETLDHWNTQTKKVSLREIMSEEIALQEKHDLKRETLMFEKDCATKLKEKQLFKIFPAINQNFLVDIFKDHSLKSINIRSFSGSQTRGGSSSRRSLRDVIFME
IRESfinder result
IRESfinder score
0.620202091
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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