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mmu_circAfdn_1426

Basic information of circular RNA
PanCircBase ID:

mmu_circAfdn_1426

mm39_Chr. Position ID:

chr17|14027538|14055618|+

Gene name:

Afdn

Transcript:

ENSMUST00000137495.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

10

Exon/intron indexes:

3,4,5,6,7,8,9,10,11,12

Exon/intron offsets:

0,1655,3133,10844,14989,16014,21652,22593,25091,27961

Genomic length:

28080

Exon/intron sizes in nt:

1,16,16,41,61,15,81,12,00,00,00,00,00,000

Flanking exon/introns:

chr17:14024396-14027538|chr17:14055618-14066533

Splice length:

1426

Other database IDs:

circAtlas: hsa-MLLT4_0030, CIRCpedia: HSA_CIRCpedia_146943

Human Ortholog IDs:
Mature spliced Sequence:

AAGAAAGAAGATTGGACATTGATGAGAAACCTCTAGTTGTACAGTTGAATTGGAACAAAGATGATCGAGAGGGTCGATTCGTCCTTAAGAACGAGAATGACGCCATTCCTGCCAAGAAGGCTCAGAGTAATGGACCTGAAAAGCAGGAGAAAGAAGGTGTTATTCAGAACTTCAAAAGAACTCTCTCAAAGAAAGAAAAGAAGGAAAAAAAGAAGAAAGAGAAGGAGGCATTGAGACAAGCCTCTGATAAGGAAGAAAGGCCTTCTCAAGGGGATGACAGTGAGAACTCACGACTGGCTGCTGAAGTTTACAAAGACATGCCTGAGACCAGCTTTACTAGGACCATTTCTAACCCTGAAGTTGTCATGAAACGGCGGCGGCAGCAAAAACTGGAGAAGAGAATGCAAGAGTTTCGGAGCTCAGATGGGCGGCCTGACTCAGGTGGAACACTGAGGATATATGCAGATAGTTTAAAACCAAATATTCCATACAAGACAATCCTGCTGTCTACTACCGATACCGCAGACTTTGCTGTAGCCGAATCTTTGGAGAAGTATGGTCTGGAAAAAGAGAATCCCAAGGACTACTGTATTGCCCGGGTTATGCTTCCTCCTGGAGCCCAGCATTCTGATGAGAGAGGTGCTAAGGAAATAATTCTTGACGATGATGAATGTCCTTTACAAATCTTCAGGGAATGGCCAAGTGACAAAGGGATTTTAGTCTTTCAGTTGAAGAGGAGACCACCGGACTACATCCCAAAGAAAATGAAGAAACATGTTGAAGGGAAGTCGTTGAAGGGGAAAGACAGAGCTGACGGGTCTGGCTACGGCTCCGCTCTTCCTCCCGAGAAGCTGCCCTACTTAGTAGAGCTAAGCCCAGATGGCTCTGACTCCAGAGACAAGCCAAAGTTATACCGCCTTCAATTAAGTGTGACTGAAGTTGGGACAGAGAAATTTGATGACAATTCTATCCAGCTGTTTGGCCCCGGAATTCAGCCCCATCACTGTGATCTCACCAACATGGATGGAGTGGTCACTGTGACACCCAGAAGTATGGATGCAGAGACCTACGTGGATGGTCAGCGCATCTCAGAGACCACAATGCTGCAGAGTGGCATGAGACTGCAGTTTGGCACCTCGCATGTGTTTAAGTTTGTGGACCCCATCCAGGACCACGTTCTTTCCAAGAGATCTGTGGATGGAGGCCTGATGGTCAAGGGCCCAAGACATAAACCTGGAGCTGTTCAGGAGACAACCTTTGAATTGGGAGGAGATGTCCACAGTGGGACAGCATTGCCGGCAAGCAGGAGCACTACTAGACTGGACAGTGACAGGGTGTCCTCTGCCTCTAGCACAGCTGAGCGAGGGATGGTGAAGCCGATGATCCGACTGGACCAGGAGCAGGAATATCGACGACGAGAAAACAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AGGGTGTCCTCTGCCTCTAG

60.03

AGGACGAATCGACCCTCTCG

61.1

180

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TGAAGCCGATGATCCGACTG

59.9

AGGACGAATCGACCCTCTCG

61.1

140

PCR template sequence:

GTGACAGGGTGTCCTCTGCCTCTAGCACAGCTGAGCGAGGGATGGTGAAGCCGATGATCCGACTGGACCAGGAGCAGGAATATCGACGACGAGAAAACAGAAGAAAGAAGATTGGACATTGATGAGAAACCTCTAGTTGTACAGTTGAATTGGAACAAAGATGATCGAGAGGGTCGATTCGTCCTTAAGAACGAGAATGA

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

21

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-298-5p(1), mmu-miR-709(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

GACGAGAAAACAGAAGAAAGAAGATT

siRNA sets

TTTCTTCTGTTTTCTCGTC, TTCTTTCTTCTGTTTTCTC, TCTTTCTTCTGTTTTCTCG

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAFDN_1426_ORF_1

0.9572

0.253025472

0.996551842

1131

ORF sequence:

ATGCCTGAGACCAGCTTTACTAGGACCATTTCTAACCCTGAAGTTGTCATGAAACGGCGGCGGCAGCAAAAACTGGAGAAGAGAATGCAAGAGTTTCGGAGCTCAGATGGGCGGCCTGACTCAGGTGGAACACTGAGGATATATGCAGATAGTTTAAAACCAAATATTCCATACAAGACAATCCTGCTGTCTACTACCGATACCGCAGACTTTGCTGTAGCCGAATCTTTGGAGAAGTATGGTCTGGAAAAAGAGAATCCCAAGGACTACTGTATTGCCCGGGTTATGCTTCCTCCTGGAGCCCAGCATTCTGATGAGAGAGGTGCTAAGGAAATAATTCTTGACGATGATGAATGTCCTTTACAAATCTTCAGGGAATGGCCAAGTGACAAAGGGATTTTAGTCTTTCAGTTGAAGAGGAGACCACCGGACTACATCCCAAAGAAAATGAAGAAACATGTTGAAGGGAAGTCGTTGAAGGGGAAAGACAGAGCTGACGGGTCTGGCTACGGCTCCGCTCTTCCTCCCGAGAAGCTGCCCTACTTAGTAGAGCTAAGCCCAGATGGCTCTGACTCCAGAGACAAGCCAAAGTTATACCGCCTTCAATTAAGTGTGACTGAAGTTGGGACAGAGAAATTTGATGACAATTCTATCCAGCTGTTTGGCCCCGGAATTCAGCCCCATCACTGTGATCTCACCAACATGGATGGAGTGGTCACTGTGACACCCAGAAGTATGGATGCAGAGACCTACGTGGATGGTCAGCGCATCTCAGAGACCACAATGCTGCAGAGTGGCATGAGACTGCAGTTTGGCACCTCGCATGTGTTTAAGTTTGTGGACCCCATCCAGGACCACGTTCTTTCCAAGAGATCTGTGGATGGAGGCCTGATGGTCAAGGGCCCAAGACATAAACCTGGAGCTGTTCAGGAGACAACCTTTGAATTGGGAGGAGATGTCCACAGTGGGACAGCATTGCCGGCAAGCAGGAGCACTACTAGACTGGACAGTGACAGGGTGTCCTCTGCCTCTAGCACAGCTGAGCGAGGGATGGTGAAGCCGATGATCCGACTGGACCAGGAGCAGGAATATCGACGACGAGAAAACAGAAGAAAGAAGATTGGACATTGA

Peptide sequence:

MPETSFTRTISNPEVVMKRRRQQKLEKRMQEFRSSDGRPDSGGTLRIYADSLKPNIPYKTILLSTTDTADFAVAESLEKYGLEKENPKDYCIARVMLPPGAQHSDERGAKEIILDDDECPLQIFREWPSDKGILVFQLKRRPPDYIPKKMKKHVEGKSLKGKDRADGSGYGSALPPEKLPYLVELSPDGSDSRDKPKLYRLQLSVTEVGTEKFDDNSIQLFGPGIQPHHCDLTNMDGVVTVTPRSMDAETYVDGQRISETTMLQSGMRLQFGTSHVFKFVDPIQDHVLSKRSVDGGLMVKGPRHKPGAVQETTFELGGDVHSGTALPASRSTTRLDSDRVSSASSTAERGMVKPMIRLDQEQEYRRRENRRKKIGH

IRESfinder result

IRESfinder score

0.408492071

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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