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mmu_circAtp2b1_938_2

Basic information of circular RNA
PanCircBase ID:

mmu_circAtp2b1_938_2

mm39_Chr. Position ID:

chr10|98832629|98839240|+

Gene name:

Atp2b1

Transcript:

ENSMUST00000020107.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

9,10,11,12

Exon/intron offsets:

0,2971,4520,6373

Genomic length:

6611

Exon/intron sizes in nt:

2,15,24,32,42,238

Flanking exon/introns:

chr10:98830669-98832629|chr10:98839240-98845265

Splice length:

938

Other database IDs:

circAtlas: mmu-Atp2b1_0074

Human Ortholog IDs:
Mature spliced Sequence:

GTCTGCTGATGTCTGCCATCACAGTTATCATCCTAGTGTTGTATTTTGTGATCGATACCTTCTGGGTTCAGAAAAGACCATGGCTTGCAGAGTGCACACCGATCTACATCCAGTACTTCGTGAAGTTCTTCATTATTGGAGTCACAGTTCTAGTGGTCGCCGTGCCGGAAGGTCTTCCGCTGGCAGTCACCATCTCACTGGCTTACTCAGTCAAGAAAATGATGAAGGATAATAACTTAGTGAGACATCTGGATGCTTGTGAGACCATGGGGAATGCTACAGCTATCTGTTCAGATAAAACAGGAACCCTGACGATGAACAGGATGACGGTTGTTCAAGCTTACATAAATGAAAAGCATTATAAAAAGGTTCCGGAACCAGAAGCCATCCCACCAAATATCCTGTCCTACCTGGTAACGGGGATTTCTGTGAATTGTGCTTATACGTCAAAAATATTGCCACCGGAGAAAGAGGGTGGATTACCCCGCCATGTGGGTAACAAAACAGAGTGTGCCTTGTTGGGGTTTCTCTTGGATTTAAAACGGGATTATCAAGATGTTAGAAATGAAATACCAGAGGAAGCACTGTACAAAGTCTATACCTTCAATTCTGTTAGGAAGTCCATGAGCACAGTCCTGAAAAACTCAGATGGAAGTTTCCGCATCTTTAGCAAGGGTGCCTCCGAGATCATTCTGAAAAAGTGTTTCAAAATCCTGAGTGCTAATGGCGAGGCAAAAGTATTCCGACCCAGAGACCGCGATGACATTGTGAAAACTGTGATCGAGCCCATGGCATCAGAAGGCCTGAGGACCATATGCCTAGCGTTCAGAGACTTCCCAGCGGGGGAGCCAGAACCAGAGTGGGATAATGAGAATGATGTCGTCACCGGCCTTACGTGTATCGCGGTTGTGGGGATTGAAGATCCTGTGAGGCCTGAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GTCACCGGCCTTACGTGTAT

59.83

CACTCTGCAAGCCATGGTCT

60.32

151

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GTCACCGGCCTTACGTGTAT

59.83

ACTCTGCAAGCCATGGTCTT

59.6

150

PCR template sequence:

AGCGGGGGAGCCAGAACCAGAGTGGGATAATGAGAATGATGTCGTCACCGGCCTTACGTGTATCGCGGTTGTGGGGATTGAAGATCCTGTGAGGCCTGAGGTCTGCTGATGTCTGCCATCACAGTTATCATCCTAGTGTTGTATTTTGTGATCGATACCTTCTGGGTTCAGAAAAGACCATGGCTTGCAGAGTGCACACC

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-335-3p(2), mmu-miR-124-3p(1), mmu-miR-135a-5p(1), mmu-miR-5099(1), mmu-miR-3470b(1), mmu-miR-350-3p(1)

siRNAs for circular RNA silencing
Junction sequence

TGTGAGGCCTGAGGTCTGCTGATGTC

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCATP2B1_938_2_ORF_1

1.1014

0.199518609

0.987297088

939

ORF sequence:

ATGTCTGCCATCACAGTTATCATCCTAGTGTTGTATTTTGTGATCGATACCTTCTGGGTTCAGAAAAGACCATGGCTTGCAGAGTGCACACCGATCTACATCCAGTACTTCGTGAAGTTCTTCATTATTGGAGTCACAGTTCTAGTGGTCGCCGTGCCGGAAGGTCTTCCGCTGGCAGTCACCATCTCACTGGCTTACTCAGTCAAGAAAATGATGAAGGATAATAACTTAGTGAGACATCTGGATGCTTGTGAGACCATGGGGAATGCTACAGCTATCTGTTCAGATAAAACAGGAACCCTGACGATGAACAGGATGACGGTTGTTCAAGCTTACATAAATGAAAAGCATTATAAAAAGGTTCCGGAACCAGAAGCCATCCCACCAAATATCCTGTCCTACCTGGTAACGGGGATTTCTGTGAATTGTGCTTATACGTCAAAAATATTGCCACCGGAGAAAGAGGGTGGATTACCCCGCCATGTGGGTAACAAAACAGAGTGTGCCTTGTTGGGGTTTCTCTTGGATTTAAAACGGGATTATCAAGATGTTAGAAATGAAATACCAGAGGAAGCACTGTACAAAGTCTATACCTTCAATTCTGTTAGGAAGTCCATGAGCACAGTCCTGAAAAACTCAGATGGAAGTTTCCGCATCTTTAGCAAGGGTGCCTCCGAGATCATTCTGAAAAAGTGTTTCAAAATCCTGAGTGCTAATGGCGAGGCAAAAGTATTCCGACCCAGAGACCGCGATGACATTGTGAAAACTGTGATCGAGCCCATGGCATCAGAAGGCCTGAGGACCATATGCCTAGCGTTCAGAGACTTCCCAGCGGGGGAGCCAGAACCAGAGTGGGATAATGAGAATGATGTCGTCACCGGCCTTACGTGTATCGCGGTTGTGGGGATTGAAGATCCTGTGAGGCCTGAGGTCTGCTGA

Peptide sequence:

MSAITVIILVLYFVIDTFWVQKRPWLAECTPIYIQYFVKFFIIGVTVLVVAVPEGLPLAVTISLAYSVKKMMKDNNLVRHLDACETMGNATAICSDKTGTLTMNRMTVVQAYINEKHYKKVPEPEAIPPNILSYLVTGISVNCAYTSKILPPEKEGGLPRHVGNKTECALLGFLLDLKRDYQDVRNEIPEEALYKVYTFNSVRKSMSTVLKNSDGSFRIFSKGASEIILKKCFKILSANGEAKVFRPRDRDDIVKTVIEPMASEGLRTICLAFRDFPAGEPEPEWDNENDVVTGLTCIAVVGIEDPVRPEVC

IRESfinder result

IRESfinder score

0.476393175

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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