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mmu_circCcdc57_1096

Basic information of circular RNA
PanCircBase ID:

mmu_circCcdc57_1096

mm39_Chr. Position ID:

chr11|120769703|120788793|-

Gene name:

Ccdc57

Transcript:

ENSMUST00000056781.5

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

7

Exon/intron indexes:

14,13,12,11,10,9,8

Exon/intron offsets:

0,2937,6355,6972,15721,16379,18931

Genomic length:

19090

Exon/intron sizes in nt:

17,11,01,15,32,14,13,50,00,000

Flanking exon/introns:

chr11:120764625-120769703|chr11:120788793-120792700

Splice length:

1096

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

ATTTCGTGAAGATGCGGCAGCTCTGAAAGCTGCCTGGGACGCCCAGATCACGCAGATGTCCAAGGAGACTGTCTCCAAAGACTTTCAGATTCACACGCTGCAGGAAGAAGAGATGAAGCTCAAGGCACAGGTGGCCAGATTCCAACAGGACATAGACAGGTACAAGCAGCAGCTGTCCCTGGCAGTGGAGAGGGGACAGAGCCTGGAGCGTGAACAGGTACAGCTAGGCCTTGACTGGCAGCGTCGCTGCGATGATATTGAACGAGACCAGATCCAGAAATCGGAGACTTTGATCGAAGGGCTGACCAAGGCCAGGGATCAGGTCGCTGCTAAACTCCAGGAGACAGAGAAGGCACTGCGTCAGCAGGAGACTCTGCTGAAGGCTGTGTCACTGGAGCGAGACCAAGCTATGGAAACCCTACGTACACATGGGCTCCTTCCTGGACAGGAGGCACAGGTACCTCCTCAGCAGCATGAAGGAGAAATAAGGGCAGATTCTCCATCTACTGAGATCCAGAGGCTACAGGAACAGAATGCAGGTCTGCGGAACGCTGTTTCACAGATGAGGAGAGAGATGGAGATGCTGAGCGGTCATCTCCCCCCTGCCCAGCCAGAAGAGTGTTCAAATGCAGACCCTGATCCCAAGGCTGGAGGAGACTCCACCCCTCCAGATTATGTTCTGACCCTTGAAGCAGAAATGCAAAATCTAAAGCATAAACTTAAGGCATTGGAGGAACAACTACAAAGCACAGAAGAGCCAGTGAAGACGTCCGTGGCCACTGCTGATCCACACCATGGTGTCCACAGCTCTGCAGCAGCAGCTGACGCAGCTCTGGCAGACCAGACATCCACTGCATTAGCACTCAGAAAACTTGGAGACAGAGTGCACCTCTTGAACTTGCTGGTGACACAGCTCAAAAGGAAGCTGCGGCAGAAGCCCCGGGAGCTGGTCCCTGTCCAACACGAGGTCCCCAGTGAGGTGGACCAGGTGCACCTGGAGGTTTTGGAGCTGCAGAAGCAGGTGGCTGAGTTAAGGAAGCATCTCAAGGTGACACCCCAGGGAGAGCCTTCATCCAGGGAGCAGTTACAGAGACAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GGAGGTTTTGGAGCTGCAGA

60.25

TGGACATCTGCGTGATCTGG

59.82

162

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GGAGGTTTTGGAGCTGCAGA

60.25

CTCCTTGGACATCTGCGTGA

59.75

167

PCR template sequence:

GGAGGTTTTGGAGCTGCAGAAGCAGGTGGCTGAGTTAAGGAAGCATCTCAAGGTGACACCCCAGGGAGAGCCTTCATCCAGGGAGCAGTTACAGAGACAGATTTCGTGAAGATGCGGCAGCTCTGAAAGCTGCCTGGGACGCCCAGATCACGCAGATGTCCAAGGAGACTGTCTCCAAAGACTTTCAGATTCACACGCTG

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

8

Interacting miRNAs (#binding sites)

mmu-miR-370-3p(2), mmu-miR-18a-5p(1), mmu-miR-143-3p(1), mmu-miR-324-3p(1), mmu-miR-680(1), mmu-miR-532-5p(1), mmu-miR-484(1), mmu-miR-3470b(1)

siRNAs for circular RNA silencing
Junction sequence

GTTACAGAGACAGATTTCGTGAAGAT

siRNA sets

CTTCACGAAATCTGTCTCT, ATCTTCACGAAATCTGTCT, TTCACGAAATCTGTCTCTG

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCCCDC57_1096_ORF_1

1.2674

0.346813275

0.997665687

1050

ORF sequence:

ATGTCCAAGGAGACTGTCTCCAAAGACTTTCAGATTCACACGCTGCAGGAAGAAGAGATGAAGCTCAAGGCACAGGTGGCCAGATTCCAACAGGACATAGACAGGTACAAGCAGCAGCTGTCCCTGGCAGTGGAGAGGGGACAGAGCCTGGAGCGTGAACAGGTACAGCTAGGCCTTGACTGGCAGCGTCGCTGCGATGATATTGAACGAGACCAGATCCAGAAATCGGAGACTTTGATCGAAGGGCTGACCAAGGCCAGGGATCAGGTCGCTGCTAAACTCCAGGAGACAGAGAAGGCACTGCGTCAGCAGGAGACTCTGCTGAAGGCTGTGTCACTGGAGCGAGACCAAGCTATGGAAACCCTACGTACACATGGGCTCCTTCCTGGACAGGAGGCACAGGTACCTCCTCAGCAGCATGAAGGAGAAATAAGGGCAGATTCTCCATCTACTGAGATCCAGAGGCTACAGGAACAGAATGCAGGTCTGCGGAACGCTGTTTCACAGATGAGGAGAGAGATGGAGATGCTGAGCGGTCATCTCCCCCCTGCCCAGCCAGAAGAGTGTTCAAATGCAGACCCTGATCCCAAGGCTGGAGGAGACTCCACCCCTCCAGATTATGTTCTGACCCTTGAAGCAGAAATGCAAAATCTAAAGCATAAACTTAAGGCATTGGAGGAACAACTACAAAGCACAGAAGAGCCAGTGAAGACGTCCGTGGCCACTGCTGATCCACACCATGGTGTCCACAGCTCTGCAGCAGCAGCTGACGCAGCTCTGGCAGACCAGACATCCACTGCATTAGCACTCAGAAAACTTGGAGACAGAGTGCACCTCTTGAACTTGCTGGTGACACAGCTCAAAAGGAAGCTGCGGCAGAAGCCCCGGGAGCTGGTCCCTGTCCAACACGAGGTCCCCAGTGAGGTGGACCAGGTGCACCTGGAGGTTTTGGAGCTGCAGAAGCAGGTGGCTGAGTTAAGGAAGCATCTCAAGGTGACACCCCAGGGAGAGCCTTCATCCAGGGAGCAGTTACAGAGACAGATTTCGTGA

Peptide sequence:

MSKETVSKDFQIHTLQEEEMKLKAQVARFQQDIDRYKQQLSLAVERGQSLEREQVQLGLDWQRRCDDIERDQIQKSETLIEGLTKARDQVAAKLQETEKALRQQETLLKAVSLERDQAMETLRTHGLLPGQEAQVPPQQHEGEIRADSPSTEIQRLQEQNAGLRNAVSQMRREMEMLSGHLPPAQPEECSNADPDPKAGGDSTPPDYVLTLEAEMQNLKHKLKALEEQLQSTEEPVKTSVATADPHHGVHSSAAAADAALADQTSTALALRKLGDRVHLLNLLVTQLKRKLRQKPRELVPVQHEVPSEVDQVHLEVLELQKQVAELRKHLKVTPQGEPSSREQLQRQIS

IRESfinder result

IRESfinder score

0.391361507

IRES/non IRES

non-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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