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mmu_circSmc5_929

Basic information of circular RNA
PanCircBase ID:

mmu_circSmc5_929

mm39_Chr. Position ID:

chr19|23221218|23241130|-

Gene name:

Smc5

Transcript:

ENSMUST00000087556.7

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

6

Exon/intron indexes:

9,8,7,6,5,4

Exon/intron offsets:

0,10822,13633,15792,17478,19749

Genomic length:

19912

Exon/intron sizes in nt:

25,67,21,62,14,11,35,100

Flanking exon/introns:

chr19:23220154-23221218|chr19:23241130-23243029

Splice length:

929

Other database IDs:

circAtlas: mmu-Smc5_0017

Human Ortholog IDs:
Mature spliced Sequence:

GTTCAGGACTTCTGGAAATCTTATAATCACCCGCGAGATTGATGTGATAAAAAATCAGTCCTTTTGGTTCATCAACAAAAAGCCTGTAACCCAGAAGATAGTGGAAGAACAGGTTGCAGCCTTAAACATCCAAGTGGGCAATCTGTGCCAGTTCTTGCCTCAGGACAAAGTTGGGGAATTTGCTAAACTCAGCAAAATTGAACTCCTTGAAGCTACTGAGAAGTCAGTTGGTCCTCCAGAGATGCACAGATACCACTGTGAACTCAAAAACTTCAGGGAGAAGGAGAAGCAGCTAGAGACCTCTTGCAAAGAGAAAACTGAATACCTAGAGAAAATGGTTCAGAGAAATGAAAGGTACAAACAAGATGTGGAAAGATTCTATGAACGAAAACGACATTTAGATTTAATTGAGATGCTTGAGGCCAAAAGACCATGGGTGGAATATGAGAATGTACGTCAGGAATATGAAGGTGTGAAACTAATTCGTGACCGAGTGAAGGAAGAGGTCAGGAAACTTAAAGAAGGGCAGATTCCTATGACACGGCGGATTGAGGAGATTGACCGGCAGCGTCACACTTTGGAAGTTCGAATCAAAGAAAAGTCAACCGATATTAAGGAAGCATCTCAGAAATGCAAGCAAAGGCAAGACTTGATTGAACGGAAGGACAGACAGATTAAGGAACTTCAGCAGGCATTAACAGTCAAGCAGAATGAAGAGCTGGACCGGCAGAAGAGAATAAGTAACACCCGCAAGATGATAGAGGATCTGCAGAGTGAGCTCAAGACTGCGGAAAACTGCGAGAACCTTCAGCCTCAGATCGACACCGTCACAAATGATCTGAGGCGTGTGCAGGAGGAGAAAGCCTTATGTGAAGGCGAGATCATTGATAAACAGCGAGAAAAGGAAATGCTGGAGAAGCAGAGACGGA

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AATGATCTGAGGCGTGTGCA

60.04

CACATCAATCTCGCGGGTGA

60.46

143

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

AATGATCTGAGGCGTGTGCA

60.04

TCACATCAATCTCGCGGGTG

60.46

144

PCR template sequence:

ACAAATGATCTGAGGCGTGTGCAGGAGGAGAAAGCCTTATGTGAAGGCGAGATCATTGATAAACAGCGAGAAAAGGAAATGCTGGAGAAGCAGAGACGGAGTTCAGGACTTCTGGAAATCTTATAATCACCCGCGAGATTGATGTGATAAAAAATCAGTCCTTTTGGTTCATCAACAAAAAGCCTGTAACCCAGAAGATA

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-207(3), mmu-miR-5101(2), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-31-5p(1), mmu-miR-370-3p(1), mmu-miR-3470b(1), mmu-miR-670-5p(1)

siRNAs for circular RNA silencing
Junction sequence

AAGCAGAGACGGAGTTCAGGACTTCT

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCSMC5_929_ORF_1

1.2551

0.356880801

0.974891108

714

ORF sequence:

ATGCACAGATACCACTGTGAACTCAAAAACTTCAGGGAGAAGGAGAAGCAGCTAGAGACCTCTTGCAAAGAGAAAACTGAATACCTAGAGAAAATGGTTCAGAGAAATGAAAGGTACAAACAAGATGTGGAAAGATTCTATGAACGAAAACGACATTTAGATTTAATTGAGATGCTTGAGGCCAAAAGACCATGGGTGGAATATGAGAATGTACGTCAGGAATATGAAGGTGTGAAACTAATTCGTGACCGAGTGAAGGAAGAGGTCAGGAAACTTAAAGAAGGGCAGATTCCTATGACACGGCGGATTGAGGAGATTGACCGGCAGCGTCACACTTTGGAAGTTCGAATCAAAGAAAAGTCAACCGATATTAAGGAAGCATCTCAGAAATGCAAGCAAAGGCAAGACTTGATTGAACGGAAGGACAGACAGATTAAGGAACTTCAGCAGGCATTAACAGTCAAGCAGAATGAAGAGCTGGACCGGCAGAAGAGAATAAGTAACACCCGCAAGATGATAGAGGATCTGCAGAGTGAGCTCAAGACTGCGGAAAACTGCGAGAACCTTCAGCCTCAGATCGACACCGTCACAAATGATCTGAGGCGTGTGCAGGAGGAGAAAGCCTTATGTGAAGGCGAGATCATTGATAAACAGCGAGAAAAGGAAATGCTGGAGAAGCAGAGACGGAGTTCAGGACTTCTGGAAATCTTATAA

Peptide sequence:

MHRYHCELKNFREKEKQLETSCKEKTEYLEKMVQRNERYKQDVERFYERKRHLDLIEMLEAKRPWVEYENVRQEYEGVKLIRDRVKEEVRKLKEGQIPMTRRIEEIDRQRHTLEVRIKEKSTDIKEASQKCKQRQDLIERKDRQIKELQQALTVKQNEELDRQKRISNTRKMIEDLQSELKTAENCENLQPQIDTVTNDLRRVQEEKALCEGEIIDKQREKEMLEKQRRSSGLLEIL

IRESfinder result

IRESfinder score

0.498082453

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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