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mmu_circAgl_559

Basic information of circular RNA
PanCircBase ID:

mmu_circAgl_559

mm39_Chr. Position ID:

chr3|116544046|116548657|-

Gene name:

Agl

Transcript:

ENSMUST00000040603.14

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

31,30,29,28

Exon/intron offsets:

0,1587,2853,4475

Genomic length:

4611

Exon/intron sizes in nt:

98,212,113,136

Flanking exon/introns:

chr3:116540353-116544046|chr3:116548657-116551887

Splice length:

559

Other database IDs:

circAtlas: mmu-Agl_0009

Human Ortholog IDs:
Mature spliced Sequence:

GTTTCAACATAACTGCGGGGATTGATGAAGAAACAGGATTTGTTTATGGAGGAAATCGCTTCAACTGTGGCACGTGGATGGATAAAATGGGAGAGAGTGACCGAGCTAGGAACAGAGGGATCCCAGCCACTCCAAGAGATGGGTCTGCTGTGGAAATCGTGGGCTTGTGTAAATCTGCTGTTCGTTGGTTGCTGGAATTGTCTAAGAAAAATATCTTTCCTTATCATGAAGTCAGAGTAAAAAGACATGGAAAGGTTGTGGCAGTCTCGTACGATGAGTGGAACAGAAAAATACAAAACAATTTCGAAAAGCTGTTTCATGTTTCCGAAGACCCTTCAGATCCTAACGAGAAGCATCCGAACCTGGTTCACAAACGCGGCATCTACAAGGACAGCTATGGTGCGTCGAGTCCTTGGTGTGACTATCAGCTCAGGCCCAACTTCACCATAGCAATGGTCGTGGCCCCTGAACTCTTTACTGCTGAGAAGGCTTGGAAGGCTTTGGAAATTGCAGAAAAAAAATTGCTTGGTCCCCTTGGCATGAAAACTTTAGACCCAGA

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TGCTGAGAAGGCTTGGAAGG

59.96

TATCCATCCACGTGCCACAG

59.82

165

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TGCTGAGAAGGCTTGGAAGG

59.96

ATCCACGTGCCACAGTTGAA

60.18

160

PCR template sequence:

TGGCCCCTGAACTCTTTACTGCTGAGAAGGCTTGGAAGGCTTTGGAAATTGCAGAAAAAAAATTGCTTGGTCCCCTTGGCATGAAAACTTTAGACCCAGAGTTTCAACATAACTGCGGGGATTGATGAAGAAACAGGATTTGTTTATGGAGGAAATCGCTTCAACTGTGGCACGTGGATGGATAAAATGGGAGAGAGTGA

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

2

Interacting miRNAs (#binding sites)

mmu-miR-384-3p(1), mmu-miR-7a-1-3p(1)

siRNAs for circular RNA silencing
Junction sequence

CTTTAGACCCAGAGTTTCAACATAAC

siRNA sets

GTTATGTTGAAACTCTGGG, TATGTTGAAACTCTGGGTC, TTATGTTGAAACTCTGGGT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAGL_559_ORF_1

0.9695

0.130797293

0.67417487

507

ORF sequence:

ATGGATAAAATGGGAGAGAGTGACCGAGCTAGGAACAGAGGGATCCCAGCCACTCCAAGAGATGGGTCTGCTGTGGAAATCGTGGGCTTGTGTAAATCTGCTGTTCGTTGGTTGCTGGAATTGTCTAAGAAAAATATCTTTCCTTATCATGAAGTCAGAGTAAAAAGACATGGAAAGGTTGTGGCAGTCTCGTACGATGAGTGGAACAGAAAAATACAAAACAATTTCGAAAAGCTGTTTCATGTTTCCGAAGACCCTTCAGATCCTAACGAGAAGCATCCGAACCTGGTTCACAAACGCGGCATCTACAAGGACAGCTATGGTGCGTCGAGTCCTTGGTGTGACTATCAGCTCAGGCCCAACTTCACCATAGCAATGGTCGTGGCCCCTGAACTCTTTACTGCTGAGAAGGCTTGGAAGGCTTTGGAAATTGCAGAAAAAAAATTGCTTGGTCCCCTTGGCATGAAAACTTTAGACCCAGAGTTTCAACATAACTGCGGGGATTGA

Peptide sequence:

MDKMGESDRARNRGIPATPRDGSAVEIVGLCKSAVRWLLELSKKNIFPYHEVRVKRHGKVVAVSYDEWNRKIQNNFEKLFHVSEDPSDPNEKHPNLVHKRGIYKDSYGASSPWCDYQLRPNFTIAMVVAPELFTAEKAWKALEIAEKKLLGPLGMKTLDPEFQHNCGD

IRESfinder result

IRESfinder score

0.639588916

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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