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mmu_circAmph_812

Basic information of circular RNA
PanCircBase ID:

mmu_circAmph_812

mm39_Chr. Position ID:

chr13|19268374|19288529|+

Gene name:

Amph

Transcript:

ENSMUST00000239207.2

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

8

Exon/intron indexes:

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

Exon/intron offsets:

0,2318,10548,11802,15688,16367,18667,20026

Genomic length:

20155

Exon/intron sizes in nt:

95,96,10,88,67,68,31,30,000

Flanking exon/introns:

chr13:19261555-19268374|chr13:19288529-19297272

Splice length:

812

Other database IDs:

CIRCpedia: MMU_CIRCpedia_225705, circAtlas: mmu-Amph_0006

circAtlas: hsa-AMPH_0005

Human Ortholog IDs:
Mature spliced Sequence:

GTATGCAGGAGGCCTCAATGAAGCTCACTGAATCTCTACATGAAGTCTACGAGCCAGACTGGTATGGACGGGAAGATGTAAAGATGGTTGGTGAGAAGTGTGATGTGCTGTGGGAAGACTTCCATCAAAAGCTAGTGGATGGCTCCTTGCTGACACTGGACACCTACCTGGGCCAGTTTCCTGACATAAAGAATCGCATCGCTAAGCGCAGCAGGAAGCTTGTGGATTATGATAGTGCTCGCCATCACCTGGAGGCTCTGCAGAGTTCCAAACGGAAAGATGAGAGTCGGATCTCTAAGGCAGAAGAGGAGTTTCAGAAAGCACAGAAAGTGTTTGAAGAGTTCAATGTTGACTTACAAGAAGAGTTGCCGTCATTGTGGTCAAGTCGAGTTGGCTTTTACGTCAATACTTTCAAAAATGTCTCCAGCCTTGAGGCCAAGTTTCATAAGGAAATCGCAGTGCTTTGCCACAAGCTCTATGAAGTGATGACGAAACTCGGTGATCAGCATGCTGACAAGGCCTTCAGCATTCAAGGAGCTCCCAGTGACTCGGGTCCTCTTCGCATTGCAAAGACACCATCACCTCCAGAGGAGCCTTCTCCCCTGCCCAGCCCCACGGCTAGTCCCAACCACACATTAGCACCTGCATCTCCTGCCCCAGTGCGACCCAGATCACCTTCACAGACAAGGAAAGGGCCTCCTGTCCCACCTCTGCCTAAAGTCACCCCAACAAAGGAACTGAAACAGGAGAACATCATCAATTTCTTTGAGGACAACTTTGTACCAGAAATCAATGTGACAACACCTTCCCAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TCACCCCAACAAAGGAACTGA

59.43

GTCCATACCAGTCTGGCTCG

59.9

161

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TCACCCCAACAAAGGAACTGA

59.43

CGTCCATACCAGTCTGGCTC

59.9

162

PCR template sequence:

GCCTAAAGTCACCCCAACAAAGGAACTGAAACAGGAGAACATCATCAATTTCTTTGAGGACAACTTTGTACCAGAAATCAATGTGACAACACCTTCCCAGGTATGCAGGAGGCCTCAATGAAGCTCACTGAATCTCTACATGAAGTCTACGAGCCAGACTGGTATGGACGGGAAGATGTAAAGATGGTTGGTGAGAAGTG

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-298-5p(1), mmu-miR-149-5p(1), mmu-miR-382-5p(1), mmu-miR-193b-3p(1)

siRNAs for circular RNA silencing
Junction sequence

AACACCTTCCCAGGTATGCAGGAGGC

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAMPH_812_ORF_1

1.0307

0.290497366

0.978545824

831

ORF sequence:

ATGCAGGAGGCCTCAATGAAGCTCACTGAATCTCTACATGAAGTCTACGAGCCAGACTGGTATGGACGGGAAGATGTAAAGATGGTTGGTGAGAAGTGTGATGTGCTGTGGGAAGACTTCCATCAAAAGCTAGTGGATGGCTCCTTGCTGACACTGGACACCTACCTGGGCCAGTTTCCTGACATAAAGAATCGCATCGCTAAGCGCAGCAGGAAGCTTGTGGATTATGATAGTGCTCGCCATCACCTGGAGGCTCTGCAGAGTTCCAAACGGAAAGATGAGAGTCGGATCTCTAAGGCAGAAGAGGAGTTTCAGAAAGCACAGAAAGTGTTTGAAGAGTTCAATGTTGACTTACAAGAAGAGTTGCCGTCATTGTGGTCAAGTCGAGTTGGCTTTTACGTCAATACTTTCAAAAATGTCTCCAGCCTTGAGGCCAAGTTTCATAAGGAAATCGCAGTGCTTTGCCACAAGCTCTATGAAGTGATGACGAAACTCGGTGATCAGCATGCTGACAAGGCCTTCAGCATTCAAGGAGCTCCCAGTGACTCGGGTCCTCTTCGCATTGCAAAGACACCATCACCTCCAGAGGAGCCTTCTCCCCTGCCCAGCCCCACGGCTAGTCCCAACCACACATTAGCACCTGCATCTCCTGCCCCAGTGCGACCCAGATCACCTTCACAGACAAGGAAAGGGCCTCCTGTCCCACCTCTGCCTAAAGTCACCCCAACAAAGGAACTGAAACAGGAGAACATCATCAATTTCTTTGAGGACAACTTTGTACCAGAAATCAATGTGACAACACCTTCCCAGGTATGCAGGAGGCCTCAATGA

Peptide sequence:

MQEASMKLTESLHEVYEPDWYGREDVKMVGEKCDVLWEDFHQKLVDGSLLTLDTYLGQFPDIKNRIAKRSRKLVDYDSARHHLEALQSSKRKDESRISKAEEEFQKAQKVFEEFNVDLQEELPSLWSSRVGFYVNTFKNVSSLEAKFHKEIAVLCHKLYEVMTKLGDQHADKAFSIQGAPSDSGPLRIAKTPSPPEEPSPLPSPTASPNHTLAPASPAPVRPRSPSQTRKGPPVPPLPKVTPTKELKQENIINFFEDNFVPEINVTTPSQVCRRPQ

IRESfinder result

IRESfinder score

0.527195871

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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