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mmu_circAgtpbp1_896

Basic information of circular RNA
PanCircBase ID:

mmu_circAgtpbp1_896

mm39_Chr. Position ID:

chr13|59655772|59679017|-

Gene name:

Agtpbp1

Transcript:

ENSMUST00000022040.14

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

7

Exon/intron indexes:

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

Exon/intron offsets:

0,4365,6128,9694,17187,20428,23098

Genomic length:

23245

Exon/intron sizes in nt:

9,81,78,20,93,89,41,32,000

Flanking exon/introns:

chr13:59652124-59655772|chr13:59679017-59679826

Splice length:

896

Other database IDs:

circAtlas: mmu-Agtpbp1_0093

Human Ortholog IDs:
Mature spliced Sequence:

GTGGGGGTCGAAGAGCGAGTTTCTTAGTTGCCAAAGGTGGTTCACAAATACTGTTGCAACTGCTTATGAATGCCAGCAAAGACTCTCCTCCACATGAGGAGGTGATGGTGCAGACTCACTCCATTCTTGCCAAGATTGGGCCAAAAGATAAGAAATTTGGAGTGAAAGCTCGAGTTAACGGGGCACTGACTGTGACTCTGAACTTGGTAAAGCAGCACTTTCAGAACTACCGCTTGGTTCTTCCTTGTCTTCAGCTCTTGCGAGTCTATTCTACCAACTCTGTGAACTCAGTATCTTTAGGTAAAAATGGAGTTGTGGAGTTGATGTTTAAAATCATTGGGCCATTCAGTAAGAAGAATTCGGGTCTCATGAAGGTTGCTTTAGACACTCTTGCTGCATTGCTAAAATCAAAGACAAACGCCAGGAGAGCGGTGGACAGAGGGTACGTTCAAGTGCTTCTAACCATCTATGTAGATTGGCACCGGCATGATAATCGGCATAGAAACATGCTCATTCGGAAGGGGATTCTACAGAGCTTAAAAAGTGTCACGAACATCAAGTTGGGCAGAAAAGCATTTATTGATGCGAATGGGATGAAAATTCTGTATAACACTTCTCAAGAGTGCTTGGCGGTCAGGACTCTTGATCCTCTTGTCAACACATCCAGTCTGATAATGAGAAAATGCTTCCCCAAAAACCGCCTTCCGCTCCCCACCATTAAAAGTTCTTTCCACTTCCAATTGCCAATTATCCCTGTGACTGGACCTGTGGCCCAGCTCTACAGCTTGCCGCCTGAAGTGGACGATGTGGTGGACGAGAGTGACGACAACGACGACATTGATTTAGAAGTGGAAAATGAACTCGAGAATGAAGATGACCTAGATCAGAGTTTTAAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AGAGTGACGACAACGACGAC

60.04

GAGGAGAGTCTTTGCTGGCA

59.68

170

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

ACGAGAGTGACGACAACGAC

60.04

GAGGAGAGTCTTTGCTGGCA

59.68

173

PCR template sequence:

AGTGGACGATGTGGTGGACGAGAGTGACGACAACGACGACATTGATTTAGAAGTGGAAAATGAACTCGAGAATGAAGATGACCTAGATCAGAGTTTTAAGGTGGGGGTCGAAGAGCGAGTTTCTTAGTTGCCAAAGGTGGTTCACAAATACTGTTGCAACTGCTTATGAATGCCAGCAAAGACTCTCCTCCACATGAGGA

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

10

Interacting miRNAs (#binding sites)

mmu-miR-182-5p(3), mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-205-5p(1), mmu-miR-106b-5p(1), mmu-miR-335-5p(1), mmu-miR-136-5p(1)

siRNAs for circular RNA silencing
Junction sequence

TCAGAGTTTTAAGGTGGGGGTCGAAG

siRNA sets

GACCCCCACCTTAAAACTC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAGTPBP1_896_ORF_1

1.1767

0.197175096

0.980179831

858

ORF sequence:

ATGAATGCCAGCAAAGACTCTCCTCCACATGAGGAGGTGATGGTGCAGACTCACTCCATTCTTGCCAAGATTGGGCCAAAAGATAAGAAATTTGGAGTGAAAGCTCGAGTTAACGGGGCACTGACTGTGACTCTGAACTTGGTAAAGCAGCACTTTCAGAACTACCGCTTGGTTCTTCCTTGTCTTCAGCTCTTGCGAGTCTATTCTACCAACTCTGTGAACTCAGTATCTTTAGGTAAAAATGGAGTTGTGGAGTTGATGTTTAAAATCATTGGGCCATTCAGTAAGAAGAATTCGGGTCTCATGAAGGTTGCTTTAGACACTCTTGCTGCATTGCTAAAATCAAAGACAAACGCCAGGAGAGCGGTGGACAGAGGGTACGTTCAAGTGCTTCTAACCATCTATGTAGATTGGCACCGGCATGATAATCGGCATAGAAACATGCTCATTCGGAAGGGGATTCTACAGAGCTTAAAAAGTGTCACGAACATCAAGTTGGGCAGAAAAGCATTTATTGATGCGAATGGGATGAAAATTCTGTATAACACTTCTCAAGAGTGCTTGGCGGTCAGGACTCTTGATCCTCTTGTCAACACATCCAGTCTGATAATGAGAAAATGCTTCCCCAAAAACCGCCTTCCGCTCCCCACCATTAAAAGTTCTTTCCACTTCCAATTGCCAATTATCCCTGTGACTGGACCTGTGGCCCAGCTCTACAGCTTGCCGCCTGAAGTGGACGATGTGGTGGACGAGAGTGACGACAACGACGACATTGATTTAGAAGTGGAAAATGAACTCGAGAATGAAGATGACCTAGATCAGAGTTTTAAGGTGGGGGTCGAAGAGCGAGTTTCTTAG

Peptide sequence:

MNASKDSPPHEEVMVQTHSILAKIGPKDKKFGVKARVNGALTVTLNLVKQHFQNYRLVLPCLQLLRVYSTNSVNSVSLGKNGVVELMFKIIGPFSKKNSGLMKVALDTLAALLKSKTNARRAVDRGYVQVLLTIYVDWHRHDNRHRNMLIRKGILQSLKSVTNIKLGRKAFIDANGMKILYNTSQECLAVRTLDPLVNTSSLIMRKCFPKNRLPLPTIKSSFHFQLPIIPVTGPVAQLYSLPPEVDDVVDESDDNDDIDLEVENELENEDDLDQSFKVGVEERVS

IRESfinder result

IRESfinder score

0.628581282

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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