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mmu_circAtxn2_1681
Basic information of circular RNA
PanCircBase ID:
mmu_circAtxn2_1681
mm39_Chr. Position ID:
chr5|121883785|121924467|+
Gene name:
Atxn2
Transcript:
ENSMUST00000051950.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
13
Exon/intron indexes:
2,3,4,5,6,7,8,9,10,11,12,13,14
Exon/intron offsets:
0,1687,2202,3356,26944,31647,32185,33695,35610,38134,39492,40036,40611
Genomic length:
40682
Exon/intron sizes in nt:
37,60,72,151,122,92,198,179,210,183,198,108,71
Flanking exon/introns:
chr5:121850339-121883785|chr5:121924467-121933000
Splice length:
1681
Other database IDs:
circAtlas: mmu-Atxn2_0010
circBase: hsa_circ_0028263, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_6687
Human Ortholog IDs:
Mature spliced Sequence:
AGGTCGGAACAGTAGCAAAGGACTGCCTCAGCCTACGATTTCTTTTGATGGAATCTATGCAAACGTGAGGATGGTTCATATACTTACGTCAGTTGTTGGATCGAAATGTGAAGTACAAGTGAAAAACGGAGGCATATATGAAGGAGTTTTTAAAACATACAGTCCTAAGTGTGACTTGGTACTTGATGCTGCACATGAGAAAAGTACAGAATCCAGTTCGGGGCCAAAACGTGAAGAAATAATGGAGAGTGTTTTGTTCAAATGCTCAGACTTCGTTGTGGTACAGTTTAAAGATACAGACTCCAGTTATGCACGGAGAGATGCTTTTACTGACTCTGCTCTCAGCGCAAAGGTGAATGGTGAGCACAAGGAGAAGGACCTGGAGCCCTGGGATGCAGGGGAGCTCACGGCCAGCGAGGAGCTGGAGCTGGAGAATGATGTGTCTAATGGATGGGACCCCAATGACATGTTTCGATATAATGAAGAGAATTATGGTGTGGTGTCCACATATGATAGCAGTTTATCTTCATATACGGTTCCTTTAGAAAGGGACAACTCAGAAGAATTTCTTAAACGGGAGGCAAGGGCAAACCAGTTAGCAGAAGAAATTGAATCCAGTGCTCAGTACAAAGCTCGTGTCGCCCTTGAGAATGATGACCGGAGTGAGGAAGAAAAATACACAGCAGTCCAGAGAAACTGCAGTGACCGGGAGGGGCATGGCCCCAACACTAGGGACAATAAATATATTCCTCCTGGACAAAGAAACAGAGAAGTCCTATCCTGGGGAAGTGGGAGACAGAGCTCACCACGGATGGGCCAGCCTGGGCCAGGCTCCATGCCGTCAAGAGCTGCTTCTCACACTTCAGATTTCAACCCGAACGCTGGCTCAGACCAAAGAGTAGTTAATGGAGGTGTTCCCTGGCCATCGCCTTGCCCATCTCCTTCCTCTCGCCCACCTTCTCGCTACCAGTCAGGTCCCAACTCTCTTCCACCTCGGGCAGCCACCCCTACACGGCCGCCCTCCAGGCCCCCCTCGAGGCCCTCCAGACCCCCGTCTCACCCCTCTGCTCATGGTTCTCCAGCTCCTGTCTCTACTATGCCTAAACGCATGTCTTCAGAAGGACCCCCAAGGATGTCTCCAAAGGCACAGCGCCACCCTCGGAATCACAGAGTCTCTGCTGGGAGAGGCTCCATGTCTAGTGGCCTAGAATTTGTATCCCACAATCCCCCAAGTGAAGCAGCTGCTCCTCCAGTGGCAAGGACCAGTCCTGCAGGGGGAACGTGGTCCTCAGTGGTCAGTGGGGTTCCAAGGTTATCTCCCAAAACTCACAGACCCAGGTCTCCCAGGCAGAGCAGCATTGGAAACTCTCCCAGCGGGCCTGTGCTTGCTTCTCCCCAAGCTGGCATCATCCCTGCAGAAGCCGTTTCCATGCCTGTTCCCGCCGCATCTCCGACTCCTGCCAGCCCTGCATCCAACAGAGCACTGACCCCATCTATTGAGGCAAAAGATTCCAGGCTTCAAGATCAGAGGCAGAACTCTCCTGCAGGGAGTAAAGAAAATGTTAAAGCAAGTGAAACATCACCTAGCTTTTCAAAAGCTGACAACAAAGGTATGTCACCAGTTGTTTCTGAACACAGAAAACAGATTGATGACTTAAAGAAGTTTAAGAATGATTTTAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGACAACAAAGGTATGTCACC
60.06
GAACCATCCTCACGTTTGCA
58.77
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGACAACAAAGGTATGTCACC
60.06
TGAACCATCCTCACGTTTGC
58.77
162
PCR template sequence:
ACCTAGCTTTTCAAAAGCTGACAACAAAGGTATGTCACCAGTTGTTTCTGAACACAGAAAACAGATTGATGACTTAAAGAAGTTTAAGAATGATTTTAGGAGGTCGGAACAGTAGCAAAGGACTGCCTCAGCCTACGATTTCTTTTGATGGAATCTATGCAAACGTGAGGATGGTTCATATACTTACGTCAGTTGTTGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-103-3p(1), mmu-miR-26a-5p(1), mmu-miR-324-5p(1), mmu-miR-136-5p(1), mmu-miR-153-3p(1), mmu-miR-107-3p(1), mmu-miR-207(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
GAATGATTTTAGGAGGTCGGAACAGT
siRNA sets
TTCCGACCTCCTAAAATCA, GTTCCGACCTCCTAAAATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATXN2_1681_ORF_1
0.9222
0.096993592
0.99987659
1692
ORF sequence:
ATGATTTTAGGAGGTCGGAACAGTAGCAAAGGACTGCCTCAGCCTACGATTTCTTTTGATGGAATCTATGCAAACGTGAGGATGGTTCATATACTTACGTCAGTTGTTGGATCGAAATGTGAAGTACAAGTGAAAAACGGAGGCATATATGAAGGAGTTTTTAAAACATACAGTCCTAAGTGTGACTTGGTACTTGATGCTGCACATGAGAAAAGTACAGAATCCAGTTCGGGGCCAAAACGTGAAGAAATAATGGAGAGTGTTTTGTTCAAATGCTCAGACTTCGTTGTGGTACAGTTTAAAGATACAGACTCCAGTTATGCACGGAGAGATGCTTTTACTGACTCTGCTCTCAGCGCAAAGGTGAATGGTGAGCACAAGGAGAAGGACCTGGAGCCCTGGGATGCAGGGGAGCTCACGGCCAGCGAGGAGCTGGAGCTGGAGAATGATGTGTCTAATGGATGGGACCCCAATGACATGTTTCGATATAATGAAGAGAATTATGGTGTGGTGTCCACATATGATAGCAGTTTATCTTCATATACGGTTCCTTTAGAAAGGGACAACTCAGAAGAATTTCTTAAACGGGAGGCAAGGGCAAACCAGTTAGCAGAAGAAATTGAATCCAGTGCTCAGTACAAAGCTCGTGTCGCCCTTGAGAATGATGACCGGAGTGAGGAAGAAAAATACACAGCAGTCCAGAGAAACTGCAGTGACCGGGAGGGGCATGGCCCCAACACTAGGGACAATAAATATATTCCTCCTGGACAAAGAAACAGAGAAGTCCTATCCTGGGGAAGTGGGAGACAGAGCTCACCACGGATGGGCCAGCCTGGGCCAGGCTCCATGCCGTCAAGAGCTGCTTCTCACACTTCAGATTTCAACCCGAACGCTGGCTCAGACCAAAGAGTAGTTAATGGAGGTGTTCCCTGGCCATCGCCTTGCCCATCTCCTTCCTCTCGCCCACCTTCTCGCTACCAGTCAGGTCCCAACTCTCTTCCACCTCGGGCAGCCACCCCTACACGGCCGCCCTCCAGGCCCCCCTCGAGGCCCTCCAGACCCCCGTCTCACCCCTCTGCTCATGGTTCTCCAGCTCCTGTCTCTACTATGCCTAAACGCATGTCTTCAGAAGGACCCCCAAGGATGTCTCCAAAGGCACAGCGCCACCCTCGGAATCACAGAGTCTCTGCTGGGAGAGGCTCCATGTCTAGTGGCCTAGAATTTGTATCCCACAATCCCCCAAGTGAAGCAGCTGCTCCTCCAGTGGCAAGGACCAGTCCTGCAGGGGGAACGTGGTCCTCAGTGGTCAGTGGGGTTCCAAGGTTATCTCCCAAAACTCACAGACCCAGGTCTCCCAGGCAGAGCAGCATTGGAAACTCTCCCAGCGGGCCTGTGCTTGCTTCTCCCCAAGCTGGCATCATCCCTGCAGAAGCCGTTTCCATGCCTGTTCCCGCCGCATCTCCGACTCCTGCCAGCCCTGCATCCAACAGAGCACTGACCCCATCTATTGAGGCAAAAGATTCCAGGCTTCAAGATCAGAGGCAGAACTCTCCTGCAGGGAGTAAAGAAAATGTTAAAGCAAGTGAAACATCACCTAGCTTTTCAAAAGCTGACAACAAAGGTATGTCACCAGTTGTTTCTGAACACAGAAAACAGATTGATGACTTAAAGAAGTTTAAGAATGATTTTAGG
Peptide sequence:
MILGGRNSSKGLPQPTISFDGIYANVRMVHILTSVVGSKCEVQVKNGGIYEGVFKTYSPKCDLVLDAAHEKSTESSSGPKREEIMESVLFKCSDFVVVQFKDTDSSYARRDAFTDSALSAKVNGEHKEKDLEPWDAGELTASEELELENDVSNGWDPNDMFRYNEENYGVVSTYDSSLSSYTVPLERDNSEEFLKREARANQLAEEIESSAQYKARVALENDDRSEEEKYTAVQRNCSDREGHGPNTRDNKYIPPGQRNREVLSWGSGRQSSPRMGQPGPGSMPSRAASHTSDFNPNAGSDQRVVNGGVPWPSPCPSPSSRPPSRYQSGPNSLPPRAATPTRPPSRPPSRPSRPPSHPSAHGSPAPVSTMPKRMSSEGPPRMSPKAQRHPRNHRVSAGRGSMSSGLEFVSHNPPSEAAAPPVARTSPAGGTWSSVVSGVPRLSPKTHRPRSPRQSSIGNSPSGPVLASPQAGIIPAEAVSMPVPAASPTPASPASNRALTPSIEAKDSRLQDQRQNSPAGSKENVKASETSPSFSKADNKGMSPVVSEHRKQIDDLKKFKNDFR
IRESfinder result
IRESfinder score
0.49019325
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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