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mmu_circAfdn_1627
Basic information of circular RNA
PanCircBase ID:
mmu_circAfdn_1627
mm39_Chr. Position ID:
chr17|14069829|14105769|+
Gene name:
Afdn
Transcript:
ENSMUST00000170827.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
13
Exon/intron indexes:
16,17,18,19,20,21,22,23,24,25,26,27,28
Exon/intron offsets:
0,1212,2748,5646,10305,12158,12207,31717,32283,32815,34173,35001,35754
Genomic length:
35940
Exon/intron sizes in nt:
95,266,144,199,108,2,81,66,74,119,195,92,186
Flanking exon/introns:
chr17:14069515-14069829|chr17:14105769-14108243
Splice length:
1627
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTACTTGGTTCATTGCCTTCAGTCAGAACTTAATAACTACATGCCAGCCTTTCTGGATGATCCTGAGGAGAACAGTCTGCAAAGACCAAAAATAGATGATGTGCTGCACACACTCACAGGAGCCATGTCCTTGCTGCGGCGCTGCAGAGTCAATGCTGCCTTGACCATCCAGCTCTTCTCTCAGCTTTTCCACTTCATCAATATGTGGCTGTTCAACAGACTGGTGACTGACCCAGATTCAGGCCTGTGCTCCCACTACTGGGGTGCCATTATCCGCCAGCAGCTGGGGCATATTGAAGCGTGGGCAGAGAAGCAGGGGCTAGAGCTGGCAGCTGACTGTCACTTGAGCAGAATTGTACAGGCTACAACATTGCTTACGATGGATAAGTATGTACCTGATGACATTCCAAATATAAACAGCACATGCTTTAAGTTAAATTCTCTGCAGCTTCAAGCCTTGTTACAAAATTACCACTGTGCACCCGATGAGCCTTTTATTCCTACGGATCTCATAGAAAATGTTGTGGCTGTTGCTGAGAACACAGCTGATGAGCTCGCCCGCAGTGATGGCAGAGACGTGCAGCTGGAGGAAGACCCAGACCTACAGCTGCCTTTTCTTCTGCCAGAAGATGGCTATTCCTGTGATGTTGTCAGAAACATTCCAAATGGTTTACAAGAATTTTTAGACCCTCTGTGCCAGAGAGGATTTTGTAGATTGGTTCCTCACACACGTTCACCAGGTACCTGGACAATATATTTTGAAGGAGCAGATTATGAAAGTCACCTTATGCGTGAGAACGCAGAACTGGCAACACCTCTGAGGAAGGAGCCTGAGATAATCACTGTGACTCTGAAGAAGCAGAATGGAATGGGCCTCAGCATCGTTGCAGCCAAGGGTGCTGGCCAGGATAAACTGGGAATCTACGTTAAGTCGGTTGTCAAAGGAGGTGCTGCAGATGTGGATGGACGATTAGCTGCTGGTGACCAACTCCTCAGTGTGGATGGACGAAGTCTGGTTGGACTTTCTCAGGAAAGGGCAGCAGAACTCATGACAAGAACCAGTTCCGTGGTTACACTGGAAGTTGCAAAGCAAGGTGCCATCTATCACGGCCTGGCCACCCTCCTTAACCAGCCGTCCCCCATGATGCAAAGAATTTCAGATCGTCGTGGCTCAGGTAAACCCAGACCAAAGAGTGAAGGTTTTGAGCTCTATAATAATTCAGCTCAAAATGGCTCCCCAGAGAGTCCTCAGATGCCTTGGACAGAGTACAGTGAGCCAAAGAAACTGCCTGGGGATGACAGGCTGATGAAAAACAGAGCGGACCACCGTTCCAGCCCCAATGTGGCAAATCAGCCTCCTAGCCCTGGAGGGAAGGGTCCATATACATCTGGAACAGCAGCTAAGATAACATCTGTCTCCACTGGAAACCTCTGCACTGAGGAGCAGTCCCCTCCACCCAGACCTGAAGCCTATCCTATCCCTACTCAGACATACACCAGAGAGTATTTTACCTTTCCAGCTTCAAAGTCGCAGGATCGGATGGCTCCTCCTCAGAGCCAGTGGCCAAATTATGAGGAAAAACCACATGTGCACACAGAAAGTAATCATTCCAGTATTGCAATCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GATCGGATGGCTCCTCCTCA
60.83
TGCAGACTGTTCTCCTCAGG
59.03
174
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCGGATGGCTCCTCCTCAG
60.83
TGCAGACTGTTCTCCTCAGG
59.03
173
PCR template sequence:
GTCGCAGGATCGGATGGCTCCTCCTCAGAGCCAGTGGCCAAATTATGAGGAAAAACCACATGTGCACACAGAAAGTAATCATTCCAGTATTGCAATCCAGGTACTTGGTTCATTGCCTTCAGTCAGAACTTAATAACTACATGCCAGCCTTTCTGGATGATCCTGAGGAGAACAGTCTGCAAAGACCAAAAATAGATGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
20
Interacting miRNAs (#binding sites)
mmu-miR-1904(3), mmu-miR-127-5p(2), mmu-miR-140-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-miR-103-3p(1), mmu-miR-15b-5p(1), mmu-miR-320-3p(1), mmu-miR-326-3p(1), mmu-miR-22-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-297a-5p(1), mmu-miR-107-3p(1), mmu-miR-680(1), mmu-miR-335-3p(1), mmu-miR-484(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TATTGCAATCCAGGTACTTGGTTCAT
siRNA sets
ATGAACCAAGTACCTGGAT, ACCAAGTACCTGGATTGCA, GAACCAAGTACCTGGATTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFDN_1627_ORF_1
1.0353
0.165650931
0.999919606
1683
ORF sequence:
ATGAGGAAAAACCACATGTGCACACAGAAAGTAATCATTCCAGTATTGCAATCCAGGTACTTGGTTCATTGCCTTCAGTCAGAACTTAATAACTACATGCCAGCCTTTCTGGATGATCCTGAGGAGAACAGTCTGCAAAGACCAAAAATAGATGATGTGCTGCACACACTCACAGGAGCCATGTCCTTGCTGCGGCGCTGCAGAGTCAATGCTGCCTTGACCATCCAGCTCTTCTCTCAGCTTTTCCACTTCATCAATATGTGGCTGTTCAACAGACTGGTGACTGACCCAGATTCAGGCCTGTGCTCCCACTACTGGGGTGCCATTATCCGCCAGCAGCTGGGGCATATTGAAGCGTGGGCAGAGAAGCAGGGGCTAGAGCTGGCAGCTGACTGTCACTTGAGCAGAATTGTACAGGCTACAACATTGCTTACGATGGATAAGTATGTACCTGATGACATTCCAAATATAAACAGCACATGCTTTAAGTTAAATTCTCTGCAGCTTCAAGCCTTGTTACAAAATTACCACTGTGCACCCGATGAGCCTTTTATTCCTACGGATCTCATAGAAAATGTTGTGGCTGTTGCTGAGAACACAGCTGATGAGCTCGCCCGCAGTGATGGCAGAGACGTGCAGCTGGAGGAAGACCCAGACCTACAGCTGCCTTTTCTTCTGCCAGAAGATGGCTATTCCTGTGATGTTGTCAGAAACATTCCAAATGGTTTACAAGAATTTTTAGACCCTCTGTGCCAGAGAGGATTTTGTAGATTGGTTCCTCACACACGTTCACCAGGTACCTGGACAATATATTTTGAAGGAGCAGATTATGAAAGTCACCTTATGCGTGAGAACGCAGAACTGGCAACACCTCTGAGGAAGGAGCCTGAGATAATCACTGTGACTCTGAAGAAGCAGAATGGAATGGGCCTCAGCATCGTTGCAGCCAAGGGTGCTGGCCAGGATAAACTGGGAATCTACGTTAAGTCGGTTGTCAAAGGAGGTGCTGCAGATGTGGATGGACGATTAGCTGCTGGTGACCAACTCCTCAGTGTGGATGGACGAAGTCTGGTTGGACTTTCTCAGGAAAGGGCAGCAGAACTCATGACAAGAACCAGTTCCGTGGTTACACTGGAAGTTGCAAAGCAAGGTGCCATCTATCACGGCCTGGCCACCCTCCTTAACCAGCCGTCCCCCATGATGCAAAGAATTTCAGATCGTCGTGGCTCAGGTAAACCCAGACCAAAGAGTGAAGGTTTTGAGCTCTATAATAATTCAGCTCAAAATGGCTCCCCAGAGAGTCCTCAGATGCCTTGGACAGAGTACAGTGAGCCAAAGAAACTGCCTGGGGATGACAGGCTGATGAAAAACAGAGCGGACCACCGTTCCAGCCCCAATGTGGCAAATCAGCCTCCTAGCCCTGGAGGGAAGGGTCCATATACATCTGGAACAGCAGCTAAGATAACATCTGTCTCCACTGGAAACCTCTGCACTGAGGAGCAGTCCCCTCCACCCAGACCTGAAGCCTATCCTATCCCTACTCAGACATACACCAGAGAGTATTTTACCTTTCCAGCTTCAAAGTCGCAGGATCGGATGGCTCCTCCTCAGAGCCAGTGGCCAAATTATGAGGAAAAACCACATGTGCACACAGAAAGTAATCATTCCAGTATTGCAATCCAG
Peptide sequence:
MRKNHMCTQKVIIPVLQSRYLVHCLQSELNNYMPAFLDDPEENSLQRPKIDDVLHTLTGAMSLLRRCRVNAALTIQLFSQLFHFINMWLFNRLVTDPDSGLCSHYWGAIIRQQLGHIEAWAEKQGLELAADCHLSRIVQATTLLTMDKYVPDDIPNINSTCFKLNSLQLQALLQNYHCAPDEPFIPTDLIENVVAVAENTADELARSDGRDVQLEEDPDLQLPFLLPEDGYSCDVVRNIPNGLQEFLDPLCQRGFCRLVPHTRSPGTWTIYFEGADYESHLMRENAELATPLRKEPEIITVTLKKQNGMGLSIVAAKGAGQDKLGIYVKSVVKGGAADVDGRLAAGDQLLSVDGRSLVGLSQERAAELMTRTSSVVTLEVAKQGAIYHGLATLLNQPSPMMQRISDRRGSGKPRPKSEGFELYNNSAQNGSPESPQMPWTEYSEPKKLPGDDRLMKNRADHRSSPNVANQPPSPGGKGPYTSGTAAKITSVSTGNLCTEEQSPPPRPEAYPIPTQTYTREYFTFPASKSQDRMAPPQSQWPNYEEKPHVHTESNHSSIAIQ
IRESfinder result
IRESfinder score
0.505377631
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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