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mmu_circAgap1_631

Basic information of circular RNA
PanCircBase ID:

mmu_circAgap1_631

mm39_Chr. Position ID:

chr1|89716884|89770965|+

Gene name:

Agap1

Transcript:

ENSMUST00000027521.15

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

13,14,15,16

Exon/intron offsets:

0,45271,48549,53858

Genomic length:

54081

Exon/intron sizes in nt:

16,21,55,91,223

Flanking exon/introns:

chr1:89694186-89716884|chr1:89770965-89815227

Splice length:

631

Other database IDs:

CIRCpedia: MMU_CIRCpedia_33532, circAtlas: mmu-Agap1_0032

circBase: hsa_circ_0058812, circAtlas: hsa-AGAP1_0032, CIRCpedia: HSA_CIRCpedia_40127

Human Ortholog IDs:
Mature spliced Sequence:

ACACGGGGCTGGGTGACTCGGTGTGTTCCAGCCCAAGTATCTCCAGCAGCACCAGCCCCAAGCTCGACCCACCCCCCTCCCCCCACGCCAACAGAAAGAAGCACCGGAGGAAGAAAAGTACCAGCAACTTCAAGGCTGACGGGCTCTCAGGCACTGCTGAAGAGCAAGAAGAAAACTTGGAGTTTATCATTGTGTCCCTCACTGGCCAGACGTGGCACTTTGAAGCCACCACATACGAGGAGCGAGACGCATGGGTCCAAGCCATCGAGAGCCAGATCCTCGCCAGCCTGCAGTCGTGCGAGAGCAGCAAGAATAAGTCCCGACTAACCAGCCAGAGCGAAGCCATGGCCCTGCAGTCCATCCGTAACATGAGAGGGAACTCGCACTGCGTGGACTGTGACACCCAAAACCCTAACTGGGCCAGTTTGAACTTGGGAGCCCTCATGTGTATCGAGTGCTCGGGGATCCACCGGAATCTCGGCACCCACCTCTCTCGGGTCAGATCGCTAGACCTGGACGACTGGCCCATGGAGCTGATCAAGGTGATGTCATCCATCGGGAATGAGCTGGCCAACAGCGTGTGGGAAGAGGGCAGCCAGGGACGGACAAAGCCCTCACTGGACTCCACCAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AACAGCGTGTGGGAAGAGG

59.93

TTCTTTCTGTTGGCGTGGGG

60.82

159

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CCAACAGCGTGTGGGAAGA

60.23

TTCTTTCTGTTGGCGTGGGG

60.82

161

PCR template sequence:

AGCTGATCAAGGTGATGTCATCCATCGGGAATGAGCTGGCCAACAGCGTGTGGGAAGAGGGCAGCCAGGGACGGACAAAGCCCTCACTGGACTCCACCAGACACGGGGCTGGGTGACTCGGTGTGTTCCAGCCCAAGTATCTCCAGCAGCACCAGCCCCAAGCTCGACCCACCCCCCTCCCCCCACGCCAACAGAAAGAA

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

7

Interacting miRNAs (#binding sites)

mmu-miR-93-5p(1), mmu-miR-138-5p(1), mmu-miR-149-5p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-188-3p(1), mmu-miR-193b-3p(1)

siRNAs for circular RNA silencing
Junction sequence

TGGACTCCACCAGACACGGGGCTGGG

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAGAP1_631_ORF_1

1.0369

0.393332144

0.96470299

699

ORF sequence:

ATGAGCTGGCCAACAGCGTGTGGGAAGAGGGCAGCCAGGGACGGACAAAGCCCTCACTGGACTCCACCAGACACGGGGCTGGGTGACTCGGTGTGTTCCAGCCCAAGTATCTCCAGCAGCACCAGCCCCAAGCTCGACCCACCCCCCTCCCCCCACGCCAACAGAAAGAAGCACCGGAGGAAGAAAAGTACCAGCAACTTCAAGGCTGACGGGCTCTCAGGCACTGCTGAAGAGCAAGAAGAAAACTTGGAGTTTATCATTGTGTCCCTCACTGGCCAGACGTGGCACTTTGAAGCCACCACATACGAGGAGCGAGACGCATGGGTCCAAGCCATCGAGAGCCAGATCCTCGCCAGCCTGCAGTCGTGCGAGAGCAGCAAGAATAAGTCCCGACTAACCAGCCAGAGCGAAGCCATGGCCCTGCAGTCCATCCGTAACATGAGAGGGAACTCGCACTGCGTGGACTGTGACACCCAAAACCCTAACTGGGCCAGTTTGAACTTGGGAGCCCTCATGTGTATCGAGTGCTCGGGGATCCACCGGAATCTCGGCACCCACCTCTCTCGGGTCAGATCGCTAGACCTGGACGACTGGCCCATGGAGCTGATCAAGGTGATGTCATCCATCGGGAATGAGCTGGCCAACAGCGTGTGGGAAGAGGGCAGCCAGGGACGGACAAAGCCCTCACTGGACTCCACC

Peptide sequence:

MSWPTACGKRAARDGQSPHWTPPDTGLGDSVCSSPSISSSTSPKLDPPPSPHANRKKHRRKKSTSNFKADGLSGTAEEQEENLEFIIVSLTGQTWHFEATTYEERDAWVQAIESQILASLQSCESSKNKSRLTSQSEAMALQSIRNMRGNSHCVDCDTQNPNWASLNLGALMCIECSGIHRNLGTHLSRVRSLDLDDWPMELIKVMSSIGNELANSVWEEGSQGRTKPSLDST

IRESfinder result

IRESfinder score

0.368201304

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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