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mmu_circUsh2a_772_1

Basic information of circular RNA
PanCircBase ID:

mmu_circUsh2a_772_1

mm39_Chr. Position ID:

chr1|188447237|188460936|+

Gene name:

Ush2a

Transcript:

ENSMUST00000060479.14

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

2

Exon/intron indexes:

39,40

Exon/intron offsets:

0,13070

Genomic length:

13699

Exon/intron sizes in nt:

1,43,629

Flanking exon/introns:

chr1:188446651-188447237|chr1:188460936-188465629

Splice length:

772

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

ATTATTCCCCATTCCTTCTGCATCGTTAAGCTACGAAGTGACTGGTCTCCAGCCGTTCACAGTGTATGAGTTTCGGTTGGTTGCCACCAATGGCTTTGGCACTGCATACAGTGCTTGGACTCCGCTCATGACTACAGAGGACAAGCCTGGACCTATAGATGCTCCAATTCTTATCAATGTGAAAGCTAGGATGTTGTCGGTCATCTGGAGGCAGCCTGCAAAGTGCAATGGGGCCATTACCCATTATAACATCTACCTGCATGGCCGTCTCTACTTAACAGTCTCTGGACGAGTCACTAACTATACTGTGGTCCCTCTGCATCCTTACAAGGCCTATCACTTCCAGGTAGAAGCCTGCACCTCCCAAGGGTGCTCTAAGTCACCATCGTCTGAGACTGTGTGGACACTCCCAGGAAATCCAGAAGGCATCCCAAGCCCACAGTTGTTCCCATACACTCCAACATCAATCATAGTAACTTGGCAACCCTCGGCACACCTGGATCTCTTGGTTGAGAACGTTACAATCGAGAGACGAGTCAAAGGGAAAAAGGAAGTTAGGAACCTGGTGACCCTGGCAAGAAGTCAAGCCATGAAGTTTATTGATAATGATCCTGCCCTCCGCCCTTGGACACGCTATGAATACCGGGTTCTGGGGAGCACTCTTGATGGGGGCACAAACAGCAGTGCTTGGGTAGAAGTGACCACAAGACCCTGTCGGCCTTCCGGAGTACAGCCACCCACAGTGCGTGTGCTGGCACCAGATACAGTCGAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CACAAACAGCAGTGCTTGGG

60.25

TACACTGTGAACGGCTGGAG

59.68

166

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GTGACCACAAGACCCTGTCG

60.6

GTGGCAACCAACCGAAACTC

59.97

162

PCR template sequence:

CACAAACAGCAGTGCTTGGGTAGAAGTGACCACAAGACCCTGTCGGCCTTCCGGAGTACAGCCACCCACAGTGCGTGTGCTGGCACCAGATACAGTCGAGATTATTCCCCATTCCTTCTGCATCGTTAAGCTACGAAGTGACTGGTCTCCAGCCGTTCACAGTGTATGAGTTTCGGTTGGTTGCCACCAATGGCTTTGGC

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

12

Interacting miRNAs (#binding sites)

mmu-miR-23b-3p(1), mmu-miR-32-5p(1), mmu-miR-135a-5p(1), mmu-miR-92a-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-23a-3p(1), mmu-miR-25-3p(1), mmu-miR-676-3p(1), mmu-miR-342-5p(1), mmu-miR-697(1), mmu-miR-574-5p(1)

siRNAs for circular RNA silencing
Junction sequence

AGATACAGTCGAGATTATTCCCCATT

siRNA sets

AATAATCTCGACTGTATCT, GAATAATCTCGACTGTATC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCUSH2A_772_1_ORF_1

0.842

0.144517435

0.883904381

714

ORF sequence:

ATGACTACAGAGGACAAGCCTGGACCTATAGATGCTCCAATTCTTATCAATGTGAAAGCTAGGATGTTGTCGGTCATCTGGAGGCAGCCTGCAAAGTGCAATGGGGCCATTACCCATTATAACATCTACCTGCATGGCCGTCTCTACTTAACAGTCTCTGGACGAGTCACTAACTATACTGTGGTCCCTCTGCATCCTTACAAGGCCTATCACTTCCAGGTAGAAGCCTGCACCTCCCAAGGGTGCTCTAAGTCACCATCGTCTGAGACTGTGTGGACACTCCCAGGAAATCCAGAAGGCATCCCAAGCCCACAGTTGTTCCCATACACTCCAACATCAATCATAGTAACTTGGCAACCCTCGGCACACCTGGATCTCTTGGTTGAGAACGTTACAATCGAGAGACGAGTCAAAGGGAAAAAGGAAGTTAGGAACCTGGTGACCCTGGCAAGAAGTCAAGCCATGAAGTTTATTGATAATGATCCTGCCCTCCGCCCTTGGACACGCTATGAATACCGGGTTCTGGGGAGCACTCTTGATGGGGGCACAAACAGCAGTGCTTGGGTAGAAGTGACCACAAGACCCTGTCGGCCTTCCGGAGTACAGCCACCCACAGTGCGTGTGCTGGCACCAGATACAGTCGAGATTATTCCCCATTCCTTCTGCATCGTTAAGCTACGAAGTGACTGGTCTCCAGCCGTTCACAGTGTATGA

Peptide sequence:

MTTEDKPGPIDAPILINVKARMLSVIWRQPAKCNGAITHYNIYLHGRLYLTVSGRVTNYTVVPLHPYKAYHFQVEACTSQGCSKSPSSETVWTLPGNPEGIPSPQLFPYTPTSIIVTWQPSAHLDLLVENVTIERRVKGKKEVRNLVTLARSQAMKFIDNDPALRPWTRYEYRVLGSTLDGGTNSSAWVEVTTRPCRPSGVQPPTVRVLAPDTVEIIPHSFCIVKLRSDWSPAVHSV

IRESfinder result

IRESfinder score

0.582030113

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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Institute of Life sciences, Bhubaneswar, India

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