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mmu_circAbce1_640

Basic information of circular RNA
PanCircBase ID:

mmu_circAbce1_640

mm39_Chr. Position ID:

chr8|80427541|80435181|-

Gene name:

Abce1

Transcript:

ENSMUST00000080536.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

6

Exon/intron indexes:

7,6,5,4,3,2

Exon/intron offsets:

0,202,861,2091,6321,7510

Genomic length:

7640

Exon/intron sizes in nt:

70,13,81,18,98,86,130

Flanking exon/introns:

chr8:80427311-80427541|chr8:80435181-80438171

Splice length:

640

Other database IDs:

circAtlas: mmu-Abce1_0011

Human Ortholog IDs:
Mature spliced Sequence:

AAGAACTGGATATTCTTTGTTACAATTATGGCAGACAAATTAACAAGAATTGCTATTGTCAACCACGACAAATGCAAACCTAAGAAATGTCGACAGGAGTGCAAAAAGAGTTGCCCTGTGGTTCGGATGGGAAAATTGTGCATAGAAGTTACACCCCAGAGCAAAATAGCATGGATTTCTGAAACTCTCTGTATTGGTTGTGGTATTTGTATTAAGAAATGTCCCTTTGGCGCCTTATCAATTGTCAATTTGCCAAGCAACTTGGAAAAAGAAACAACACATCGCTACTGTGCCAATGCCTTCAAGCTTCACAGGTTGCCTATCCCTCGTCCAGGTGAAGTTTTGGGATTAGTTGGAACTAATGGTATTGGAAAGTCAACTGCACTAAAAATTTTAGCAGGAAAACAAAAGCCAAACCTTGGAAAGTATGATGATCCACCTGATTGGCAAGAGATTTTGACTTATTTCCGTGGATCTGAATTACAAAATTACTTTACCAAGATTCTCGAAGATGACCTAAAAGCCATTATCAAACCTCAATATGTAGACCAAATTCCCAAGGCTGCAAAGGGGACAGTGGGCTCTATTCTGGACCGAAAAGATGAAACAAAGACACAGGCAATTGTATGTCAGCAGCTTG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AGGGGACAGTGGGCTCTATT

59.96

TGCATTTGTCGTGGTTGACA

58.62

148

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

AAGGGGACAGTGGGCTCTAT

59.96

TGCATTTGTCGTGGTTGACA

58.62

149

PCR template sequence:

TATGTAGACCAAATTCCCAAGGCTGCAAAGGGGACAGTGGGCTCTATTCTGGACCGAAAAGATGAAACAAAGACACAGGCAATTGTATGTCAGCAGCTTGAAGAACTGGATATTCTTTGTTACAATTATGGCAGACAAATTAACAAGAATTGCTATTGTCAACCACGACAAATGCAAACCTAAGAAATGTCGACAGGAGT

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

4

Interacting miRNAs (#binding sites)

mmu-miR-135a-5p(1), mmu-miR-127-5p(1), mmu-miR-96-5p(1), mmu-miR-129-5p(1)

siRNAs for circular RNA silencing
Junction sequence

TGTCAGCAGCTTGAAGAACTGGATAT

siRNA sets

ATATCCAGTTCTTCAAGCT, GTTCTTCAAGCTGCTGACA, AGTTCTTCAAGCTGCTGAC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCABCE1_640_ORF_1

0.722

0.0000462

0.748827586

696

ORF sequence:

ATGGCAGACAAATTAACAAGAATTGCTATTGTCAACCACGACAAATGCAAACCTAAGAAATGTCGACAGGAGTGCAAAAAGAGTTGCCCTGTGGTTCGGATGGGAAAATTGTGCATAGAAGTTACACCCCAGAGCAAAATAGCATGGATTTCTGAAACTCTCTGTATTGGTTGTGGTATTTGTATTAAGAAATGTCCCTTTGGCGCCTTATCAATTGTCAATTTGCCAAGCAACTTGGAAAAAGAAACAACACATCGCTACTGTGCCAATGCCTTCAAGCTTCACAGGTTGCCTATCCCTCGTCCAGGTGAAGTTTTGGGATTAGTTGGAACTAATGGTATTGGAAAGTCAACTGCACTAAAAATTTTAGCAGGAAAACAAAAGCCAAACCTTGGAAAGTATGATGATCCACCTGATTGGCAAGAGATTTTGACTTATTTCCGTGGATCTGAATTACAAAATTACTTTACCAAGATTCTCGAAGATGACCTAAAAGCCATTATCAAACCTCAATATGTAGACCAAATTCCCAAGGCTGCAAAGGGGACAGTGGGCTCTATTCTGGACCGAAAAGATGAAACAAAGACACAGGCAATTGTATGTCAGCAGCTTGAAGAACTGGATATTCTTTGTTACAATTATGGCAGACAAATTAACAAGAATTGCTATTGTCAACCACGACAAATGCAAACCTAA

Peptide sequence:

MADKLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTPQSKIAWISETLCIGCGICIKKCPFGALSIVNLPSNLEKETTHRYCANAFKLHRLPIPRPGEVLGLVGTNGIGKSTALKILAGKQKPNLGKYDDPPDWQEILTYFRGSELQNYFTKILEDDLKAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAIVCQQLEELDILCYNYGRQINKNCYCQPRQMQT

IRESfinder result

IRESfinder score

0.519232168

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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