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mmu_circAtad2_509

Basic information of circular RNA
PanCircBase ID:

mmu_circAtad2_509

mm39_Chr. Position ID:

chr15|57967826|57970307|-

Gene name:

Atad2

Transcript:

ENSMUST00000038194.5

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

3

Exon/intron indexes:

20,19,18

Exon/intron offsets:

0,1046,2294

Genomic length:

2481

Exon/intron sizes in nt:

136,186,187

Flanking exon/introns:

chr15:57966790-57967826|chr15:57970307-57971476

Splice length:

509

Other database IDs:

CIRCpedia: MMU_CIRCpedia_36795, circAtlas: mmu-Atad2_0004

circAtlas: hsa-ATAD2_0025

Human Ortholog IDs:
Mature spliced Sequence:

AAATGCCTGTTACCAGCCTATGTCTTTTCGACCAAGACTATTGATAGTGGGAGAACCAGGATTTGGACAGAGTTCTCACTTGGCACCAGCTGTCATCCATGCTTTGGAAAAATTTACTGTATATACATTAGACATTCCTGTTCTTTTTGGCATCAGTACAACATCTCCTGAAGAGGCATGTTCCCAAATGATTCGTGAAGCTAAGAGAACAGCACCCAGCATAGTCTATGTCCCACATATCCATTTGTGGTGGGAAATAGTTGGACCGACACTCAAAGCCACATTTACAACATTATTACAGACTATACCTTCATTTGCTCCAGTTTTATTACTTGCAACTTCTGAGAAACCATACTCAGCTTTGCCGGAAGAGGTACAAGAATTGTTTACCCATGATTATGGAGAAATTTTTAATGTACAGTTACCAGATAAAGAAGAACGAACCAAATTTTTTGAAGACTTAATTTTAAAACAAGCTTCAAAGCCTCCTGTGTCACAAAAGAAAGCAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ACCAGATAAAGAAGAACGAACCA

57.78

CAGCTGGTGCCAAGTGAGAA

60.54

178

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

ACCAGATAAAGAAGAACGAACCA

57.78

GCTGGTGCCAAGTGAGAACT

60.54

176

PCR template sequence:

TTTAATGTACAGTTACCAGATAAAGAAGAACGAACCAAATTTTTTGAAGACTTAATTTTAAAACAAGCTTCAAAGCCTCCTGTGTCACAAAAGAAAGCAGAAATGCCTGTTACCAGCCTATGTCTTTTCGACCAAGACTATTGATAGTGGGAGAACCAGGATTTGGACAGAGTTCTCACTTGGCACCAGCTGTCATCCAT

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

6

Interacting miRNAs (#binding sites)

mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-miR-30e-5p(1), mmu-miR-320-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-190b-5p(1)

siRNAs for circular RNA silencing
Junction sequence

CAAAAGAAAGCAGAAATGCCTGTTAC

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCATAD2_509_ORF_1

0.9536

-0.126227307

0.461051262

534

ORF sequence:

ATGTCTTTTCGACCAAGACTATTGATAGTGGGAGAACCAGGATTTGGACAGAGTTCTCACTTGGCACCAGCTGTCATCCATGCTTTGGAAAAATTTACTGTATATACATTAGACATTCCTGTTCTTTTTGGCATCAGTACAACATCTCCTGAAGAGGCATGTTCCCAAATGATTCGTGAAGCTAAGAGAACAGCACCCAGCATAGTCTATGTCCCACATATCCATTTGTGGTGGGAAATAGTTGGACCGACACTCAAAGCCACATTTACAACATTATTACAGACTATACCTTCATTTGCTCCAGTTTTATTACTTGCAACTTCTGAGAAACCATACTCAGCTTTGCCGGAAGAGGTACAAGAATTGTTTACCCATGATTATGGAGAAATTTTTAATGTACAGTTACCAGATAAAGAAGAACGAACCAAATTTTTTGAAGACTTAATTTTAAAACAAGCTTCAAAGCCTCCTGTGTCACAAAAGAAAGCAGAAATGCCTGTTACCAGCCTATGTCTTTTCGACCAAGACTATTGA

Peptide sequence:

MSFRPRLLIVGEPGFGQSSHLAPAVIHALEKFTVYTLDIPVLFGISTTSPEEACSQMIREAKRTAPSIVYVPHIHLWWEIVGPTLKATFTTLLQTIPSFAPVLLLATSEKPYSALPEEVQELFTHDYGEIFNVQLPDKEERTKFFEDLILKQASKPPVSQKKAEMPVTSLCLFDQDY

IRESfinder result

IRESfinder score

0.839084431

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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