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mmu_circAfdn_2294
Basic information of circular RNA
PanCircBase ID:
mmu_circAfdn_2294
mm39_Chr. Position ID:
chr17|14038382|14082117|+
Gene name:
Afdn
Transcript:
ENSMUST00000170827.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
17
Exon/intron indexes:
6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
Exon/intron offsets:
0,4145,5170,10808,11749,14247,17117,28151,28313,30987,31447,32659,34195,37093,41752,43605,43654
Genomic length:
43735
Exon/intron sizes in nt:
158,112,168,95,263,70,119,62,206,146,95,266,144,199,108,2,81
Flanking exon/introns:
chr17:14030832-14038382|chr17:14082117-14101546
Splice length:
2294
Other database IDs:
CIRCpedia: MMU_CIRCpedia_8645, circAtlas: mmu-Mllt4_0044
Human Ortholog IDs:
Mature spliced Sequence:
GTGGAACACTGAGGATATATGCAGATAGTTTAAAACCAAATATTCCATACAAGACAATCCTGCTGTCTACTACCGATACCGCAGACTTTGCTGTAGCCGAATCTTTGGAGAAGTATGGTCTGGAAAAAGAGAATCCCAAGGACTACTGTATTGCCCGGGTTATGCTTCCTCCTGGAGCCCAGCATTCTGATGAGAGAGGTGCTAAGGAAATAATTCTTGACGATGATGAATGTCCTTTACAAATCTTCAGGGAATGGCCAAGTGACAAAGGGATTTTAGTCTTTCAGTTGAAGAGGAGACCACCGGACTACATCCCAAAGAAAATGAAGAAACATGTTGAAGGGAAGTCGTTGAAGGGGAAAGACAGAGCTGACGGGTCTGGCTACGGCTCCGCTCTTCCTCCCGAGAAGCTGCCCTACTTAGTAGAGCTAAGCCCAGATGGCTCTGACTCCAGAGACAAGCCAAAGTTATACCGCCTTCAATTAAGTGTGACTGAAGTTGGGACAGAGAAATTTGATGACAATTCTATCCAGCTGTTTGGCCCCGGAATTCAGCCCCATCACTGTGATCTCACCAACATGGATGGAGTGGTCACTGTGACACCCAGAAGTATGGATGCAGAGACCTACGTGGATGGTCAGCGCATCTCAGAGACCACAATGCTGCAGAGTGGCATGAGACTGCAGTTTGGCACCTCGCATGTGTTTAAGTTTGTGGACCCCATCCAGGACCACGTTCTTTCCAAGAGATCTGTGGATGGAGGCCTGATGGTCAAGGGCCCAAGACATAAACCTGGAGCTGTTCAGGAGACAACCTTTGAATTGGGAGGAGATGTCCACAGTGGGACAGCATTGCCGGCAAGCAGGAGCACTACTAGACTGGACAGTGACAGGGTGTCCTCTGCCTCTAGCACAGCTGAGCGAGGGATGGTGAAGCCGATGATCCGACTGGACCAGGAGCAGGAATATCGACGACGAGAAAACAGGACTCAGGATGCTACTGGGCCTGAACTGATACTGCCTGCCAGCATTGAATTCAGGGAAAGCTCTGAAGACTCTTTTTTATCTGCCATTATAAACTATACCAATAGTTCTACAGTTCATTTTAAGTTGTCACCTACATATGTGTTATACATGGCATGCCGGTATGTATTGTCCAGCCAGCACAGGCCCGACATCAGTCCTACAGAGCGTACACATAAGGCCATTGCTGTTGTCAACAAGATGGTGAGCATGATGGAAGGGGTCATCCAGAAACAGAAGAACATTGCAGGAGCACTTGCTTTTTGGATGGCAAATGCATCTGAGCTTCTCAACTTCATCAAGCAGGACCGAGACCTTAGTCGGATCACGCTGGATGCCCAGGATGTCCTAGCACACTTGGTTCAGATGGCATTTAAGTACTTGGTTCATTGCCTTCAGTCAGAACTTAATAACTACATGCCAGCCTTTCTGGATGATCCTGAGGAGAACAGTCTGCAAAGACCAAAAATAGATGATGTGCTGCACACACTCACAGGAGCCATGTCCTTGCTGCGGCGCTGCAGAGTCAATGCTGCCTTGACCATCCAGCTCTTCTCTCAGCTTTTCCACTTCATCAATATGTGGCTGTTCAACAGACTGGTGACTGACCCAGATTCAGGCCTGTGCTCCCACTACTGGGGTGCCATTATCCGCCAGCAGCTGGGGCATATTGAAGCGTGGGCAGAGAAGCAGGGGCTAGAGCTGGCAGCTGACTGTCACTTGAGCAGAATTGTACAGGCTACAACATTGCTTACGATGGATAAGTATGTACCTGATGACATTCCAAATATAAACAGCACATGCTTTAAGTTAAATTCTCTGCAGCTTCAAGCCTTGTTACAAAATTACCACTGTGCACCCGATGAGCCTTTTATTCCTACGGATCTCATAGAAAATGTTGTGGCTGTTGCTGAGAACACAGCTGATGAGCTCGCCCGCAGTGATGGCAGAGACGTGCAGCTGGAGGAAGACCCAGACCTACAGCTGCCTTTTCTTCTGCCAGAAGATGGCTATTCCTGTGATGTTGTCAGAAACATTCCAAATGGTTTACAAGAATTTTTAGACCCTCTGTGCCAGAGAGGATTTTGTAGATTGGTTCCTCACACACGTTCACCAGGTACCTGGACAATATATTTTGAAGGAGCAGATTATGAAAGTCACCTTATGCGTGAGAACGCAGAACTGGCAACACCTCTGAGGAAGGAGCCTGAGATAATCACTGTGACTCTGAAGAAGCAGAATGGAATGGGCCTCAGCATCGTTGCAGCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCAACACCTCTGAGGAAGG
60.32
GCAAAGTCTGCGGTATCGGT
60.74
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCTGAGGAAGGAGCCTGA
60.33
GCAAAGTCTGCGGTATCGGT
60.74
172
PCR template sequence:
GAACGCAGAACTGGCAACACCTCTGAGGAAGGAGCCTGAGATAATCACTGTGACTCTGAAGAAGCAGAATGGAATGGGCCTCAGCATCGTTGCAGCCAAGGTGGAACACTGAGGATATATGCAGATAGTTTAAAACCAAATATTCCATACAAGACAATCCTGCTGTCTACTACCGATACCGCAGACTTTGCTGTAGCCGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
33
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(3), mmu-miR-27a-3p(3), mmu-miR-103-3p(2), mmu-miR-107-3p(2), mmu-miR-484(2), mmu-miR-670-5p(2), mmu-miR-697(2), mmu-miR-1904(2), mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-miR-181a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-15b-5p(1), mmu-miR-298-5p(1), mmu-miR-709(1), mmu-miR-320-3p(1), mmu-miR-326-3p(1), mmu-miR-181b-5p(1), mmu-miR-128-3p(1), mmu-miR-136-5p(1), mmu-miR-22-3p(1), mmu-miR-127-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-466d-3p(1), mmu-miR-27a-5p(1), mmu-miR-335-3p(1), mmu-miR-452-3p(1), mmu-miR-3470b(1), mmu-miR-1199-5p(1), mmu-miR-574-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGTTGCAGCCAAGGTGGAACACTGAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFDN_2294_ORF_1
1.1236
0.218819058
0.999997981
2145
ORF sequence:
ATGCTTCCTCCTGGAGCCCAGCATTCTGATGAGAGAGGTGCTAAGGAAATAATTCTTGACGATGATGAATGTCCTTTACAAATCTTCAGGGAATGGCCAAGTGACAAAGGGATTTTAGTCTTTCAGTTGAAGAGGAGACCACCGGACTACATCCCAAAGAAAATGAAGAAACATGTTGAAGGGAAGTCGTTGAAGGGGAAAGACAGAGCTGACGGGTCTGGCTACGGCTCCGCTCTTCCTCCCGAGAAGCTGCCCTACTTAGTAGAGCTAAGCCCAGATGGCTCTGACTCCAGAGACAAGCCAAAGTTATACCGCCTTCAATTAAGTGTGACTGAAGTTGGGACAGAGAAATTTGATGACAATTCTATCCAGCTGTTTGGCCCCGGAATTCAGCCCCATCACTGTGATCTCACCAACATGGATGGAGTGGTCACTGTGACACCCAGAAGTATGGATGCAGAGACCTACGTGGATGGTCAGCGCATCTCAGAGACCACAATGCTGCAGAGTGGCATGAGACTGCAGTTTGGCACCTCGCATGTGTTTAAGTTTGTGGACCCCATCCAGGACCACGTTCTTTCCAAGAGATCTGTGGATGGAGGCCTGATGGTCAAGGGCCCAAGACATAAACCTGGAGCTGTTCAGGAGACAACCTTTGAATTGGGAGGAGATGTCCACAGTGGGACAGCATTGCCGGCAAGCAGGAGCACTACTAGACTGGACAGTGACAGGGTGTCCTCTGCCTCTAGCACAGCTGAGCGAGGGATGGTGAAGCCGATGATCCGACTGGACCAGGAGCAGGAATATCGACGACGAGAAAACAGGACTCAGGATGCTACTGGGCCTGAACTGATACTGCCTGCCAGCATTGAATTCAGGGAAAGCTCTGAAGACTCTTTTTTATCTGCCATTATAAACTATACCAATAGTTCTACAGTTCATTTTAAGTTGTCACCTACATATGTGTTATACATGGCATGCCGGTATGTATTGTCCAGCCAGCACAGGCCCGACATCAGTCCTACAGAGCGTACACATAAGGCCATTGCTGTTGTCAACAAGATGGTGAGCATGATGGAAGGGGTCATCCAGAAACAGAAGAACATTGCAGGAGCACTTGCTTTTTGGATGGCAAATGCATCTGAGCTTCTCAACTTCATCAAGCAGGACCGAGACCTTAGTCGGATCACGCTGGATGCCCAGGATGTCCTAGCACACTTGGTTCAGATGGCATTTAAGTACTTGGTTCATTGCCTTCAGTCAGAACTTAATAACTACATGCCAGCCTTTCTGGATGATCCTGAGGAGAACAGTCTGCAAAGACCAAAAATAGATGATGTGCTGCACACACTCACAGGAGCCATGTCCTTGCTGCGGCGCTGCAGAGTCAATGCTGCCTTGACCATCCAGCTCTTCTCTCAGCTTTTCCACTTCATCAATATGTGGCTGTTCAACAGACTGGTGACTGACCCAGATTCAGGCCTGTGCTCCCACTACTGGGGTGCCATTATCCGCCAGCAGCTGGGGCATATTGAAGCGTGGGCAGAGAAGCAGGGGCTAGAGCTGGCAGCTGACTGTCACTTGAGCAGAATTGTACAGGCTACAACATTGCTTACGATGGATAAGTATGTACCTGATGACATTCCAAATATAAACAGCACATGCTTTAAGTTAAATTCTCTGCAGCTTCAAGCCTTGTTACAAAATTACCACTGTGCACCCGATGAGCCTTTTATTCCTACGGATCTCATAGAAAATGTTGTGGCTGTTGCTGAGAACACAGCTGATGAGCTCGCCCGCAGTGATGGCAGAGACGTGCAGCTGGAGGAAGACCCAGACCTACAGCTGCCTTTTCTTCTGCCAGAAGATGGCTATTCCTGTGATGTTGTCAGAAACATTCCAAATGGTTTACAAGAATTTTTAGACCCTCTGTGCCAGAGAGGATTTTGTAGATTGGTTCCTCACACACGTTCACCAGGTACCTGGACAATATATTTTGAAGGAGCAGATTATGAAAGTCACCTTATGCGTGAGAACGCAGAACTGGCAACACCTCTGAGGAAGGAGCCTGAGATAATCACTGTGACTCTGAAGAAGCAGAATGGAATGGGCCTCAGCATCGTTGCAGCCAAGGTGGAACACTGA
Peptide sequence:
MLPPGAQHSDERGAKEIILDDDECPLQIFREWPSDKGILVFQLKRRPPDYIPKKMKKHVEGKSLKGKDRADGSGYGSALPPEKLPYLVELSPDGSDSRDKPKLYRLQLSVTEVGTEKFDDNSIQLFGPGIQPHHCDLTNMDGVVTVTPRSMDAETYVDGQRISETTMLQSGMRLQFGTSHVFKFVDPIQDHVLSKRSVDGGLMVKGPRHKPGAVQETTFELGGDVHSGTALPASRSTTRLDSDRVSSASSTAERGMVKPMIRLDQEQEYRRRENRTQDATGPELILPASIEFRESSEDSFLSAIINYTNSSTVHFKLSPTYVLYMACRYVLSSQHRPDISPTERTHKAIAVVNKMVSMMEGVIQKQKNIAGALAFWMANASELLNFIKQDRDLSRITLDAQDVLAHLVQMAFKYLVHCLQSELNNYMPAFLDDPEENSLQRPKIDDVLHTLTGAMSLLRRCRVNAALTIQLFSQLFHFINMWLFNRLVTDPDSGLCSHYWGAIIRQQLGHIEAWAEKQGLELAADCHLSRIVQATTLLTMDKYVPDDIPNINSTCFKLNSLQLQALLQNYHCAPDEPFIPTDLIENVVAVAENTADELARSDGRDVQLEEDPDLQLPFLLPEDGYSCDVVRNIPNGLQEFLDPLCQRGFCRLVPHTRSPGTWTIYFEGADYESHLMRENAELATPLRKEPEIITVTLKKQNGMGLSIVAAKVEH
IRESfinder result
IRESfinder score
0.500765472
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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