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mmu_circNek4_1489
Basic information of circular RNA
PanCircBase ID:
mmu_circNek4_1489
mm39_Chr. Position ID:
chr14|30675759|30697784|+
Gene name:
Nek4
Transcript:
ENSMUST00000226551.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
2,3,4,5,6,7,8,9
Exon/intron offsets:
0,3078,3459,5338,10130,16360,21420,21958
Genomic length:
22025
Exon/intron sizes in nt:
267,198,108,155,142,402,150,67
Flanking exon/introns:
chr14:30673675-30675759|chr14:30697784-30699402
Splice length:
1489
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TATGTCATCAAAAAGCTGAACCTCCGAAATGCCTCCAGCCGAGAGCGTCGAGCTGCTGAGCAGGAAGCTCAGCTCCTATCTCAGTTGAAGCACCCCAACATTGTCACCTACAAAGAATCATGGGAGGGAGGAGACGGTCTGCTCTACATTGTCATGGGCTTCTGCGAAGGAGGTGATCTGTACCGGAAGCTCAAGGAGCAGAAAGGGCAGCTTCTGCCTGAGAGTCAGGTGGTGGAGTGGTTTGTCCAGATCGCCATGGCCTTGCAGTATTTACATGAGAAACACATCCTTCATCGAGATCTGAAAACTCAGAATGTCTTCTTAACAAGAACAAACATCATCAAAGTGGGGGACCTAGGAATTGCCCGCGTCTTAGAGAATCACGGTGACATGGCGAGCACCCTCATTGGCACACCCTATTACATGAGCCCTGAGCTGTTCTCCAACAAACCCTACAACTATAAGTCGGATGTTTGGGCTTTGGGATGCTGTGTATATGAAATGGCCACCCTGAAGCACGCTTTTAATGCAAAAGACATGAATTCTTTAGTTTATCGGATTATTGAAGGAAAGTTGCCGCCAATGCCAAAAGTTTACAGCACAGAGCTGGCTGAGCTGATAAGAACAATGCTGAGCAGAAGGCCTGAGGAGAGGCCCTCTGTGCGGAGCATCCTGAGGCAGCCCTACATAAAACACCACATCTCCTTGTTCTTGGAGGCCACCAAGGCAAAAACTTCCAAAAATAATGTTAAAAACTGTGACTCCAGAGCCAAGCCTGTTGCTGCTGTAGTTTCCAGAAAGGAAGAATCAAATACTGACGTGATACACTACCAGCCACGCTCTTCTGAGGGCTCTGCTTTGCATGTCATGGGTGAAGATAAATGTTTGTCCCAAGAGAAACCAGTGGACATTGGTCCCTTGAGATCACCGGCTAGTCTTGAAGGCCACACTGGCAAACAAGACATGAACAATACTGGGGAGTCATGTGCCACAATCAGTAGGATAAATATCGATATCTTACCTGCAGAAAGGAGGGACTCAGCGAACGCTGGTGTAGTTCAGGAGAGCCAACCACAACACGTGGATGCCGCTGATGAAGTAGACAGTCAGTGCAGTATTTCTCAAGAGAAGGAGAGGCTACAGGGCAATACCAAGTCCAGTGATCAGCCTGGAAATCTCCTTCCCAGACGGTCCTCTGATGGTGGTGATGGGGAAGGGAGTGAACTGGTGAAGCCATTGTATCCCTCAAATAAAGACCAAAAGCCAGACCAGTTCCAAGAATTACCCCCTCGGCTTTTGCCTTCTTATCCTGGTATTGGGAAAGTGGATATCATAGCAACACAGCAAAATGATGGAAACCAAGGTGGACCTGTGGCTGGGTGTGTAAACAGTTCAAGGACCAGCTCAACAGCATCAGCAAAGGATCGACCATTATCAGCCAGAGAGAGGAGACGGCTAAAGCAGTCACAGGAGGAGATGCTGCCCTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGAGAGAGGAGACGGCTA
59.82
TGTTGGGGTGCTTCAACTGA
59.74
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGCCAGAGAGAGGAGACG
60.39
TGTTGGGGTGCTTCAACTGA
59.74
155
PCR template sequence:
AGTTCAAGGACCAGCTCAACAGCATCAGCAAAGGATCGACCATTATCAGCCAGAGAGAGGAGACGGCTAAAGCAGTCACAGGAGGAGATGCTGCCCTCAGTATGTCATCAAAAAGCTGAACCTCCGAAATGCCTCCAGCCGAGAGCGTCGAGCTGCTGAGCAGGAAGCTCAGCTCCTATCTCAGTTGAAGCACCCCAACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-200b-3p(2), mmu-miR-134-5p(1), mmu-miR-15a-5p(1), mmu-miR-27b-3p(1), mmu-miR-199a-5p(1), mmu-miR-429-3p(1), mmu-miR-200c-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-342-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-1198-5p(1), mmu-miR-129-5p(1), mmu-miR-300-3p(1), mmu-miR-539-5p(1), mmu-miR-1199-5p(1), mmu-miR-1904(1), mmu-miR-544-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGCTGCCCTCAGTATGTCATCAAAA
siRNA sets
TTGATGACATACTGAGGGC, TTTTGATGACATACTGAGG, TGATGACATACTGAGGGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNEK4_1489_ORF_1
0.7423
0.168145059
0.998911578
1395
ORF sequence:
ATGGGCTTCTGCGAAGGAGGTGATCTGTACCGGAAGCTCAAGGAGCAGAAAGGGCAGCTTCTGCCTGAGAGTCAGGTGGTGGAGTGGTTTGTCCAGATCGCCATGGCCTTGCAGTATTTACATGAGAAACACATCCTTCATCGAGATCTGAAAACTCAGAATGTCTTCTTAACAAGAACAAACATCATCAAAGTGGGGGACCTAGGAATTGCCCGCGTCTTAGAGAATCACGGTGACATGGCGAGCACCCTCATTGGCACACCCTATTACATGAGCCCTGAGCTGTTCTCCAACAAACCCTACAACTATAAGTCGGATGTTTGGGCTTTGGGATGCTGTGTATATGAAATGGCCACCCTGAAGCACGCTTTTAATGCAAAAGACATGAATTCTTTAGTTTATCGGATTATTGAAGGAAAGTTGCCGCCAATGCCAAAAGTTTACAGCACAGAGCTGGCTGAGCTGATAAGAACAATGCTGAGCAGAAGGCCTGAGGAGAGGCCCTCTGTGCGGAGCATCCTGAGGCAGCCCTACATAAAACACCACATCTCCTTGTTCTTGGAGGCCACCAAGGCAAAAACTTCCAAAAATAATGTTAAAAACTGTGACTCCAGAGCCAAGCCTGTTGCTGCTGTAGTTTCCAGAAAGGAAGAATCAAATACTGACGTGATACACTACCAGCCACGCTCTTCTGAGGGCTCTGCTTTGCATGTCATGGGTGAAGATAAATGTTTGTCCCAAGAGAAACCAGTGGACATTGGTCCCTTGAGATCACCGGCTAGTCTTGAAGGCCACACTGGCAAACAAGACATGAACAATACTGGGGAGTCATGTGCCACAATCAGTAGGATAAATATCGATATCTTACCTGCAGAAAGGAGGGACTCAGCGAACGCTGGTGTAGTTCAGGAGAGCCAACCACAACACGTGGATGCCGCTGATGAAGTAGACAGTCAGTGCAGTATTTCTCAAGAGAAGGAGAGGCTACAGGGCAATACCAAGTCCAGTGATCAGCCTGGAAATCTCCTTCCCAGACGGTCCTCTGATGGTGGTGATGGGGAAGGGAGTGAACTGGTGAAGCCATTGTATCCCTCAAATAAAGACCAAAAGCCAGACCAGTTCCAAGAATTACCCCCTCGGCTTTTGCCTTCTTATCCTGGTATTGGGAAAGTGGATATCATAGCAACACAGCAAAATGATGGAAACCAAGGTGGACCTGTGGCTGGGTGTGTAAACAGTTCAAGGACCAGCTCAACAGCATCAGCAAAGGATCGACCATTATCAGCCAGAGAGAGGAGACGGCTAAAGCAGTCACAGGAGGAGATGCTGCCCTCAGTATGTCATCAAAAAGCTGAACCTCCGAAATGCCTCCAGCCGAGAGCGTCGAGCTGCTGA
Peptide sequence:
MGFCEGGDLYRKLKEQKGQLLPESQVVEWFVQIAMALQYLHEKHILHRDLKTQNVFLTRTNIIKVGDLGIARVLENHGDMASTLIGTPYYMSPELFSNKPYNYKSDVWALGCCVYEMATLKHAFNAKDMNSLVYRIIEGKLPPMPKVYSTELAELIRTMLSRRPEERPSVRSILRQPYIKHHISLFLEATKAKTSKNNVKNCDSRAKPVAAVVSRKEESNTDVIHYQPRSSEGSALHVMGEDKCLSQEKPVDIGPLRSPASLEGHTGKQDMNNTGESCATISRINIDILPAERRDSANAGVVQESQPQHVDAADEVDSQCSISQEKERLQGNTKSSDQPGNLLPRRSSDGGDGEGSELVKPLYPSNKDQKPDQFQELPPRLLPSYPGIGKVDIIATQQNDGNQGGPVAGCVNSSRTSSTASAKDRPLSARERRRLKQSQEEMLPSVCHQKAEPPKCLQPRASSC
IRESfinder result
IRESfinder score
0.402466753
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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