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mmu_circAatf_784

Basic information of circular RNA
PanCircBase ID:

mmu_circAatf_784

mm39_Chr. Position ID:

chr11|84333391|84363992|-

Gene name:

Aatf

Transcript:

ENSMUST00000018841.3

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

7

Exon/intron indexes:

12,11,10,9,8,7,6

Exon/intron offsets:

0,3061,6554,24895,27998,28522,30486

Genomic length:

30601

Exon/intron sizes in nt:

72,81,68,84,165,199,115

Flanking exon/introns:

chr11:84313845-84333391|chr11:84363992-84400484

Splice length:

784

Other database IDs:

circBase: mmu_circ_0003472, CIRCpedia: MMU_CIRCpedia_31677, circAtlas: mmu-Aatf_0003

circBase: hsa_circ_0043209, circAtlas: hsa-AATF_0003

Human Ortholog IDs:
Mature spliced Sequence:

GTCACAAAGCACTTAAAGCCTTGTTAAGGTCATTGGTGGATCTTCAGGAAGAGTTGCTTTTCCAGTACCCAGACACGAGACATATAGTAAATGGGGCGAAACCCAATACAGAGAGTGAGGAGATTTCCAGTGAAGATGATGAGCTAGTGGGAGAGAAGAAGAAACAACGAAAGGCCCCACCCAAGAGGAAGCTAGAGATGGAGGACTATCCCAGCTTCATGGCAAAGCGCTTTGCTGACTTCACCATCTATAGGAATCACACACTACAGAAATGGCATGATAAAACCAAGCTTGCTTCTGGAAAACTGGGCAAGGGTTTTGGTGCCTTCGAACGCTCGATCTTGACTCAGATCGATCATATCATGATGGACAAAGAAAGATTGCTTCGGAGGACACAGACCAAGCGCTCTGCCTACCGAGTTCTTGGCAAACCGGAGCCAGTCCCTGAGCCTGTTGCAGAGACCTTGCCAGGAGAACCAGAGACGCTTCCTCAGGGCCCTGCCAATGCCCACCTGAGGGACTTGGATGAGGAGATATTTGATGATGATGACTTTTACCACCAGCTCCTTCGAGAACTCATAGAGCGGAAAACCAGCTCTTTGGATCCAAATGATCAGGTGGCCATGGGAAGGCAGTGGCTTGCAATCCAGAAACTACGAAGCAAAATCCGCAAGAAGGTAGATAGAAAAGCCAGCAAAGGAAGGAAACTTCGGTTCCATGTCCTTAGCAAGCTCCTGAGTTTCATGGCACCTATTGACCACACCGCAATGAGTGATGATGCCAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TCCATGTCCTTAGCAAGCTCC

59.79

TCTCGTGTCTGGGTACTGGA

59.6

150

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CCATGTCCTTAGCAAGCTCCT

59.79

TCTCGTGTCTGGGTACTGGA

59.6

149

PCR template sequence:

GAAAAGCCAGCAAAGGAAGGAAACTTCGGTTCCATGTCCTTAGCAAGCTCCTGAGTTTCATGGCACCTATTGACCACACCGCAATGAGTGATGATGCCAGGTCACAAAGCACTTAAAGCCTTGTTAAGGTCATTGGTGGATCTTCAGGAAGAGTTGCTTTTCCAGTACCCAGACACGAGACATATAGTAAATGGGGCGAA

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-149-5p(2), mmu-miR-127-5p(2), mmu-miR-138-5p(1), mmu-miR-214-3p(1), mmu-miR-433-3p(1), mmu-miR-351-5p(1), mmu-miR-484(1), mmu-miR-1199-5p(1)

siRNAs for circular RNA silencing
Junction sequence

GTGATGATGCCAGGTCACAAAGCACT

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAATF_784_ORF_1

1.1149

0.33461589

0.979707216

792

ORF sequence:

ATGATGCCAGGTCACAAAGCACTTAAAGCCTTGTTAAGGTCATTGGTGGATCTTCAGGAAGAGTTGCTTTTCCAGTACCCAGACACGAGACATATAGTAAATGGGGCGAAACCCAATACAGAGAGTGAGGAGATTTCCAGTGAAGATGATGAGCTAGTGGGAGAGAAGAAGAAACAACGAAAGGCCCCACCCAAGAGGAAGCTAGAGATGGAGGACTATCCCAGCTTCATGGCAAAGCGCTTTGCTGACTTCACCATCTATAGGAATCACACACTACAGAAATGGCATGATAAAACCAAGCTTGCTTCTGGAAAACTGGGCAAGGGTTTTGGTGCCTTCGAACGCTCGATCTTGACTCAGATCGATCATATCATGATGGACAAAGAAAGATTGCTTCGGAGGACACAGACCAAGCGCTCTGCCTACCGAGTTCTTGGCAAACCGGAGCCAGTCCCTGAGCCTGTTGCAGAGACCTTGCCAGGAGAACCAGAGACGCTTCCTCAGGGCCCTGCCAATGCCCACCTGAGGGACTTGGATGAGGAGATATTTGATGATGATGACTTTTACCACCAGCTCCTTCGAGAACTCATAGAGCGGAAAACCAGCTCTTTGGATCCAAATGATCAGGTGGCCATGGGAAGGCAGTGGCTTGCAATCCAGAAACTACGAAGCAAAATCCGCAAGAAGGTAGATAGAAAAGCCAGCAAAGGAAGGAAACTTCGGTTCCATGTCCTTAGCAAGCTCCTGAGTTTCATGGCACCTATTGACCACACCGCAATGAGTGATGATGCC

Peptide sequence:

MMPGHKALKALLRSLVDLQEELLFQYPDTRHIVNGAKPNTESEEISSEDDELVGEKKKQRKAPPKRKLEMEDYPSFMAKRFADFTIYRNHTLQKWHDKTKLASGKLGKGFGAFERSILTQIDHIMMDKERLLRRTQTKRSAYRVLGKPEPVPEPVAETLPGEPETLPQGPANAHLRDLDEEIFDDDDFYHQLLRELIERKTSSLDPNDQVAMGRQWLAIQKLRSKIRKKVDRKASKGRKLRFHVLSKLLSFMAPIDHTAMSDDA

IRESfinder result

IRESfinder score

0.311571435

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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