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mmu_circAfdn_1191
Basic information of circular RNA
PanCircBase ID:
mmu_circAfdn_1191
mm39_Chr. Position ID:
chr17|14029193|14052699|+
Gene name:
Afdn
Transcript:
ENSMUST00000170827.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
4,5,6,7,8,9,10,11
Exon/intron offsets:
0,1478,9189,13334,14359,19997,20938,23436
Genomic length:
23506
Exon/intron sizes in nt:
164,161,158,112,168,95,263,70
Flanking exon/introns:
chr17:14027654-14029193|chr17:14052699-14055499
Splice length:
1191
Other database IDs:
CIRCpedia: MMU_CIRCpedia_8604, circAtlas: mmu-Mllt4_0080
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
AAGGCTCAGAGTAATGGACCTGAAAAGCAGGAGAAAGAAGGTGTTATTCAGAACTTCAAAAGAACTCTCTCAAAGAAAGAAAAGAAGGAAAAAAAGAAGAAAGAGAAGGAGGCATTGAGACAAGCCTCTGATAAGGAAGAAAGGCCTTCTCAAGGGGATGACAGTGAGAACTCACGACTGGCTGCTGAAGTTTACAAAGACATGCCTGAGACCAGCTTTACTAGGACCATTTCTAACCCTGAAGTTGTCATGAAACGGCGGCGGCAGCAAAAACTGGAGAAGAGAATGCAAGAGTTTCGGAGCTCAGATGGGCGGCCTGACTCAGGTGGAACACTGAGGATATATGCAGATAGTTTAAAACCAAATATTCCATACAAGACAATCCTGCTGTCTACTACCGATACCGCAGACTTTGCTGTAGCCGAATCTTTGGAGAAGTATGGTCTGGAAAAAGAGAATCCCAAGGACTACTGTATTGCCCGGGTTATGCTTCCTCCTGGAGCCCAGCATTCTGATGAGAGAGGTGCTAAGGAAATAATTCTTGACGATGATGAATGTCCTTTACAAATCTTCAGGGAATGGCCAAGTGACAAAGGGATTTTAGTCTTTCAGTTGAAGAGGAGACCACCGGACTACATCCCAAAGAAAATGAAGAAACATGTTGAAGGGAAGTCGTTGAAGGGGAAAGACAGAGCTGACGGGTCTGGCTACGGCTCCGCTCTTCCTCCCGAGAAGCTGCCCTACTTAGTAGAGCTAAGCCCAGATGGCTCTGACTCCAGAGACAAGCCAAAGTTATACCGCCTTCAATTAAGTGTGACTGAAGTTGGGACAGAGAAATTTGATGACAATTCTATCCAGCTGTTTGGCCCCGGAATTCAGCCCCATCACTGTGATCTCACCAACATGGATGGAGTGGTCACTGTGACACCCAGAAGTATGGATGCAGAGACCTACGTGGATGGTCAGCGCATCTCAGAGACCACAATGCTGCAGAGTGGCATGAGACTGCAGTTTGGCACCTCGCATGTGTTTAAGTTTGTGGACCCCATCCAGGACCACGTTCTTTCCAAGAGATCTGTGGATGGAGGCCTGATGGTCAAGGGCCCAAGACATAAACCTGGAGCTGTTCAGGAGACAACCTTTGAATTGGGAGGAGATGTCCACAGTGGGACAGCATTGCCGGCAAGCAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTCAAGGGCCCAAGACATA
59.38
ACACCTTCTTTCTCCTGCTT
56.67
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTCAAGGGCCCAAGACATA
59.38
AACACCTTCTTTCTCCTGCT
56.67
142
PCR template sequence:
GATGGTCAAGGGCCCAAGACATAAACCTGGAGCTGTTCAGGAGACAACCTTTGAATTGGGAGGAGATGTCCACAGTGGGACAGCATTGCCGGCAAGCAGGAAGGCTCAGAGTAATGGACCTGAAAAGCAGGAGAAAGAAGGTGTTATTCAGAACTTCAAAAGAACTCTCTCAAAGAAAGAAAAGAAGGAAAAAAAGAAGA
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-27b-3p(2), mmu-miR-27a-3p(2), mmu-miR-181a-5p(1), mmu-miR-103-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-320-3p(1), mmu-miR-181b-5p(1), mmu-miR-128-3p(1), mmu-miR-136-5p(1), mmu-miR-107-3p(1), mmu-miR-27a-5p(1), mmu-miR-129-5p(1), mmu-miR-207(1), mmu-miR-452-3p(1), mmu-miR-3470b(1), mmu-miR-1199-5p(1), mmu-miR-670-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCGGCAAGCAGGAAGGCTCAGAGTA
siRNA sets
TACTCTGAGCCTTCCTGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFDN_1191_ORF_1
0.9963
0.248725607
0.999998342
2181
ORF sequence:
ATGCCTGAGACCAGCTTTACTAGGACCATTTCTAACCCTGAAGTTGTCATGAAACGGCGGCGGCAGCAAAAACTGGAGAAGAGAATGCAAGAGTTTCGGAGCTCAGATGGGCGGCCTGACTCAGGTGGAACACTGAGGATATATGCAGATAGTTTAAAACCAAATATTCCATACAAGACAATCCTGCTGTCTACTACCGATACCGCAGACTTTGCTGTAGCCGAATCTTTGGAGAAGTATGGTCTGGAAAAAGAGAATCCCAAGGACTACTGTATTGCCCGGGTTATGCTTCCTCCTGGAGCCCAGCATTCTGATGAGAGAGGTGCTAAGGAAATAATTCTTGACGATGATGAATGTCCTTTACAAATCTTCAGGGAATGGCCAAGTGACAAAGGGATTTTAGTCTTTCAGTTGAAGAGGAGACCACCGGACTACATCCCAAAGAAAATGAAGAAACATGTTGAAGGGAAGTCGTTGAAGGGGAAAGACAGAGCTGACGGGTCTGGCTACGGCTCCGCTCTTCCTCCCGAGAAGCTGCCCTACTTAGTAGAGCTAAGCCCAGATGGCTCTGACTCCAGAGACAAGCCAAAGTTATACCGCCTTCAATTAAGTGTGACTGAAGTTGGGACAGAGAAATTTGATGACAATTCTATCCAGCTGTTTGGCCCCGGAATTCAGCCCCATCACTGTGATCTCACCAACATGGATGGAGTGGTCACTGTGACACCCAGAAGTATGGATGCAGAGACCTACGTGGATGGTCAGCGCATCTCAGAGACCACAATGCTGCAGAGTGGCATGAGACTGCAGTTTGGCACCTCGCATGTGTTTAAGTTTGTGGACCCCATCCAGGACCACGTTCTTTCCAAGAGATCTGTGGATGGAGGCCTGATGGTCAAGGGCCCAAGACATAAACCTGGAGCTGTTCAGGAGACAACCTTTGAATTGGGAGGAGATGTCCACAGTGGGACAGCATTGCCGGCAAGCAGGAAGGCTCAGAGTAATGGACCTGAAAAGCAGGAGAAAGAAGGTGTTATTCAGAACTTCAAAAGAACTCTCTCAAAGAAAGAAAAGAAGGAAAAAAAGAAGAAAGAGAAGGAGGCATTGAGACAAGCCTCTGATAAGGAAGAAAGGCCTTCTCAAGGGGATGACAGTGAGAACTCACGACTGGCTGCTGAAGTTTACAAAGACATGCCTGAGACCAGCTTTACTAGGACCATTTCTAACCCTGAAGTTGTCATGAAACGGCGGCGGCAGCAAAAACTGGAGAAGAGAATGCAAGAGTTTCGGAGCTCAGATGGGCGGCCTGACTCAGGTGGAACACTGAGGATATATGCAGATAGTTTAAAACCAAATATTCCATACAAGACAATCCTGCTGTCTACTACCGATACCGCAGACTTTGCTGTAGCCGAATCTTTGGAGAAGTATGGTCTGGAAAAAGAGAATCCCAAGGACTACTGTATTGCCCGGGTTATGCTTCCTCCTGGAGCCCAGCATTCTGATGAGAGAGGTGCTAAGGAAATAATTCTTGACGATGATGAATGTCCTTTACAAATCTTCAGGGAATGGCCAAGTGACAAAGGGATTTTAGTCTTTCAGTTGAAGAGGAGACCACCGGACTACATCCCAAAGAAAATGAAGAAACATGTTGAAGGGAAGTCGTTGAAGGGGAAAGACAGAGCTGACGGGTCTGGCTACGGCTCCGCTCTTCCTCCCGAGAAGCTGCCCTACTTAGTAGAGCTAAGCCCAGATGGCTCTGACTCCAGAGACAAGCCAAAGTTATACCGCCTTCAATTAAGTGTGACTGAAGTTGGGACAGAGAAATTTGATGACAATTCTATCCAGCTGTTTGGCCCCGGAATTCAGCCCCATCACTGTGATCTCACCAACATGGATGGAGTGGTCACTGTGACACCCAGAAGTATGGATGCAGAGACCTACGTGGATGGTCAGCGCATCTCAGAGACCACAATGCTGCAGAGTGGCATGAGACTGCAGTTTGGCACCTCGCATGTGTTTAAGTTTGTGGACCCCATCCAGGACCACGTTCTTTCCAAGAGATCTGTGGATGGAGGCCTGATGGTCAAGGGCCCAAGACATAAACCTGGAGCTGTTCAGGAGACAACCTTTGAATTGGGAGGAGATGTCCACAGTGGGACAGCATTGCCGGCAAGCAGG
Peptide sequence:
MPETSFTRTISNPEVVMKRRRQQKLEKRMQEFRSSDGRPDSGGTLRIYADSLKPNIPYKTILLSTTDTADFAVAESLEKYGLEKENPKDYCIARVMLPPGAQHSDERGAKEIILDDDECPLQIFREWPSDKGILVFQLKRRPPDYIPKKMKKHVEGKSLKGKDRADGSGYGSALPPEKLPYLVELSPDGSDSRDKPKLYRLQLSVTEVGTEKFDDNSIQLFGPGIQPHHCDLTNMDGVVTVTPRSMDAETYVDGQRISETTMLQSGMRLQFGTSHVFKFVDPIQDHVLSKRSVDGGLMVKGPRHKPGAVQETTFELGGDVHSGTALPASRKAQSNGPEKQEKEGVIQNFKRTLSKKEKKEKKKKEKEALRQASDKEERPSQGDDSENSRLAAEVYKDMPETSFTRTISNPEVVMKRRRQQKLEKRMQEFRSSDGRPDSGGTLRIYADSLKPNIPYKTILLSTTDTADFAVAESLEKYGLEKENPKDYCIARVMLPPGAQHSDERGAKEIILDDDECPLQIFREWPSDKGILVFQLKRRPPDYIPKKMKKHVEGKSLKGKDRADGSGYGSALPPEKLPYLVELSPDGSDSRDKPKLYRLQLSVTEVGTEKFDDNSIQLFGPGIQPHHCDLTNMDGVVTVTPRSMDAETYVDGQRISETTMLQSGMRLQFGTSHVFKFVDPIQDHVLSKRSVDGGLMVKGPRHKPGAVQETTFELGGDVHSGTALPASR
IRESfinder result
IRESfinder score
0.434376172
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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