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mmu_circXrn2_1828
Basic information of circular RNA
PanCircBase ID:
mmu_circXrn2_1828
mm39_Chr. Position ID:
chr2|146868300|146893689|+
Gene name:
Xrn2
Transcript:
ENSMUST00000028921.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
20
Exon/intron indexes:
5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24
Exon/intron offsets:
0,134,926,1214,1712,2957,3114,3346,3488,8473,10283,11788,14435,15607,15793,16479,21254,22911,23602,25332
Genomic length:
25389
Exon/intron sizes in nt:
59,90,73,51,158,75,134,58,108,45,132,119,136,108,90,73,84,98,80,57
Flanking exon/introns:
chr2:146867226-146868300|chr2:146893689-146903168
Splice length:
1828
Other database IDs:
circAtlas: mmu-Xrn2_0014
Human Ortholog IDs:
Mature spliced Sequence:
GTGGCTTTCTTCCTCCAGAAGAAATAAAAGAAAGATTTGACAGCAACTGTATTACCCCAGGAACTGAGTTCATGGACAATCTTGCTAAATGCCTTCGCTATTACATAGCTGATCGTTTAAATAATGACCCTGGGTGGAAAAATTTGACAGTTATATTATCTGATGCTAGTGCACCTGGTGAAGGAGAACACAAAATCATGGATTACATTAGAAGACAAAGAGCCCAGCCTAACCATGACCCAAATACTCATCATTGTTTGTGTGGAGCTGATGCTGATCTAATTATGCTTGGTCTTGCTACACATGAACCTAACTTCACCATAATCAGAGAAGAATTCAAACCAAATAAACCTAAACCATGTGCTCTTTGTAATCAGTTTGGACACGAGGTCAAGGATTGTGAAGGTTTGCCAAGAGAAAAGAAGGGAAAGCATGATGAACTTGCAGATAGTCTTCCTTGTGCAGAAGGGGAGTTTATCTTCCTTCGGCTGAATGTCCTTCGAGAGTATCTGGAAAGAGAACTCACCATGGCCAGCTTACCATTCCCATTTGATGTGGAGAGGAGCATTGATGACTGGGTGTTCATGTGCTTCTTTGTGGGGAATGATTTCCTTCCTCACTTGCCATCACTAGAGATTAGGGAAGGTGCAATTGATCGTTTGGTTAACATATACAAAAACGTGGTACACAAAACTGGGGGTTACCTTACAGAAAGTGGTTATGTCAATCTGCAAAGAGTACAGATGATCATGTTAGCAGTTGGTGAAGTTGAGGATAGCATTTTTAAAAAGAGAAAAGATGATGAGGACAGTTTTAGAAGACGACAGAAAGAAAAAAGAAAGAGGATGAAGAGAGATCAACCAGCTTTTACTCCTAGTGGAATATTAACACCTCATGCCTTGGGTTCAAGAAATTCACCAGGTTGTCAAGTAGCCAGTAATCCAAGACAAGCAGCCTATGAAATGAGGATGCAGAGAAACTCTAGTCCTTCAATATCTCCTAATACAAGTTTTGCATCTGATGGCTCCCCATCTCCACTAGGAGGAATTAAGAGAAAAGCAGAAGACAGTGACAGTGAGCCAGAGCCAGAGGATAACGTCAGGTTATGGGAAGCTGGTTGGAAGCAACGATACTACAAGAACAAATTTGATGTAGATGCAGCTGATGAGAAATTCCGACGTAAGGTTGTTCAGTCCTACGTTGAAGGACTGTGCTGGGTTCTTCGCTATTATTACCAGGGCTGTGCTTCCTGGAAGTGGTATTATCCATTCCATTATGCACCATTTGCCTCAGACTTTGAAGGTATTGCAGACATGTCCTCTGAATTTGAAAAGGGCACAAAACCGTTTAAGCCACTGGAACAACTAATGGGGGTTTTCCCAGCTGCAAGTGGTAACTTTCTACCTCCAACATGGCGGAAGCTCATGAGTGACCCTGATTCCAGTATAATTGACTTCTATCCTGAAGATTTTGCTATTGATTTGAATGGGAAGAAATATGCATGGCAAGGTGTTGCTCTATTGCCATTTGTGGATGAGCGAAGGCTGCGAGCGGCTCTAGAAGAGGTGTACCCAGACCTCACTCCAGAAGAGAACAGGAGAAATAGTCTTGGAGGTGATGTTTTGTTTGTGGGAAAACTTCATCCACTACGCGACTTCATTTTAGAGCTGTATCAGACGGGTTCCACAGAGCCAGTTGATGTGCCACCTGAATTGTGTCACGGGATTCAAGGGACGTTTTCTTTGGATGAAGAAGCCATTCTTCCAGACCAAACAGTATGTTCCCCTGTGCCCATGTTGCGGGACCTGACACAGAACACTGCAGTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCATTCTTCCAGACCAAACA
60.16
CCATGAACTCAGTTCCTGGGG
60.34
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCATTCTTCCAGACCAAACA
60.16
CATGAACTCAGTTCCTGGGGT
59.65
149
PCR template sequence:
AAGGGACGTTTTCTTTGGATGAAGAAGCCATTCTTCCAGACCAAACAGTATGTTCCCCTGTGCCCATGTTGCGGGACCTGACACAGAACACTGCAGTCAGGTGGCTTTCTTCCTCCAGAAGAAATAAAAGAAAGATTTGACAGCAACTGTATTACCCCAGGAACTGAGTTCATGGACAATCTTGCTAAATGCCTTCGCTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
22
Interacting miRNAs (#binding sites)
mmu-miR-149-5p(2), mmu-let-7a-5p(1), mmu-miR-32-5p(1), mmu-miR-7b-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-135a-5p(1), mmu-miR-92a-3p(1), mmu-let-7c-5p(1), mmu-miR-18a-5p(1), mmu-miR-7a-5p(1), mmu-miR-320-3p(1), mmu-miR-25-3p(1), mmu-miR-181b-5p(1), mmu-let-7d-5p(1), mmu-miR-363-3p(1), mmu-miR-382-5p(1), mmu-miR-511-3p(1), mmu-miR-362-5p(1), mmu-miR-98-5p(1), mmu-miR-188-3p(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACACTGCAGTCAGGTGGCTTTCTTCC
siRNA sets
AAGAAAGCCACCTGACTGC, AGAAAGCCACCTGACTGCA, GAAGAAAGCCACCTGACTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCXRN2_1828_ORF_1
0.9666
0.053513601
0.999935934
1797
ORF sequence:
ATGGACAATCTTGCTAAATGCCTTCGCTATTACATAGCTGATCGTTTAAATAATGACCCTGGGTGGAAAAATTTGACAGTTATATTATCTGATGCTAGTGCACCTGGTGAAGGAGAACACAAAATCATGGATTACATTAGAAGACAAAGAGCCCAGCCTAACCATGACCCAAATACTCATCATTGTTTGTGTGGAGCTGATGCTGATCTAATTATGCTTGGTCTTGCTACACATGAACCTAACTTCACCATAATCAGAGAAGAATTCAAACCAAATAAACCTAAACCATGTGCTCTTTGTAATCAGTTTGGACACGAGGTCAAGGATTGTGAAGGTTTGCCAAGAGAAAAGAAGGGAAAGCATGATGAACTTGCAGATAGTCTTCCTTGTGCAGAAGGGGAGTTTATCTTCCTTCGGCTGAATGTCCTTCGAGAGTATCTGGAAAGAGAACTCACCATGGCCAGCTTACCATTCCCATTTGATGTGGAGAGGAGCATTGATGACTGGGTGTTCATGTGCTTCTTTGTGGGGAATGATTTCCTTCCTCACTTGCCATCACTAGAGATTAGGGAAGGTGCAATTGATCGTTTGGTTAACATATACAAAAACGTGGTACACAAAACTGGGGGTTACCTTACAGAAAGTGGTTATGTCAATCTGCAAAGAGTACAGATGATCATGTTAGCAGTTGGTGAAGTTGAGGATAGCATTTTTAAAAAGAGAAAAGATGATGAGGACAGTTTTAGAAGACGACAGAAAGAAAAAAGAAAGAGGATGAAGAGAGATCAACCAGCTTTTACTCCTAGTGGAATATTAACACCTCATGCCTTGGGTTCAAGAAATTCACCAGGTTGTCAAGTAGCCAGTAATCCAAGACAAGCAGCCTATGAAATGAGGATGCAGAGAAACTCTAGTCCTTCAATATCTCCTAATACAAGTTTTGCATCTGATGGCTCCCCATCTCCACTAGGAGGAATTAAGAGAAAAGCAGAAGACAGTGACAGTGAGCCAGAGCCAGAGGATAACGTCAGGTTATGGGAAGCTGGTTGGAAGCAACGATACTACAAGAACAAATTTGATGTAGATGCAGCTGATGAGAAATTCCGACGTAAGGTTGTTCAGTCCTACGTTGAAGGACTGTGCTGGGTTCTTCGCTATTATTACCAGGGCTGTGCTTCCTGGAAGTGGTATTATCCATTCCATTATGCACCATTTGCCTCAGACTTTGAAGGTATTGCAGACATGTCCTCTGAATTTGAAAAGGGCACAAAACCGTTTAAGCCACTGGAACAACTAATGGGGGTTTTCCCAGCTGCAAGTGGTAACTTTCTACCTCCAACATGGCGGAAGCTCATGAGTGACCCTGATTCCAGTATAATTGACTTCTATCCTGAAGATTTTGCTATTGATTTGAATGGGAAGAAATATGCATGGCAAGGTGTTGCTCTATTGCCATTTGTGGATGAGCGAAGGCTGCGAGCGGCTCTAGAAGAGGTGTACCCAGACCTCACTCCAGAAGAGAACAGGAGAAATAGTCTTGGAGGTGATGTTTTGTTTGTGGGAAAACTTCATCCACTACGCGACTTCATTTTAGAGCTGTATCAGACGGGTTCCACAGAGCCAGTTGATGTGCCACCTGAATTGTGTCACGGGATTCAAGGGACGTTTTCTTTGGATGAAGAAGCCATTCTTCCAGACCAAACAGTATGTTCCCCTGTGCCCATGTTGCGGGACCTGACACAGAACACTGCAGTCAGGTGGCTTTCTTCCTCCAGAAGAAATAAAAGAAAGATTTGA
Peptide sequence:
MDNLAKCLRYYIADRLNNDPGWKNLTVILSDASAPGEGEHKIMDYIRRQRAQPNHDPNTHHCLCGADADLIMLGLATHEPNFTIIREEFKPNKPKPCALCNQFGHEVKDCEGLPREKKGKHDELADSLPCAEGEFIFLRLNVLREYLERELTMASLPFPFDVERSIDDWVFMCFFVGNDFLPHLPSLEIREGAIDRLVNIYKNVVHKTGGYLTESGYVNLQRVQMIMLAVGEVEDSIFKKRKDDEDSFRRRQKEKRKRMKRDQPAFTPSGILTPHALGSRNSPGCQVASNPRQAAYEMRMQRNSSPSISPNTSFASDGSPSPLGGIKRKAEDSDSEPEPEDNVRLWEAGWKQRYYKNKFDVDAADEKFRRKVVQSYVEGLCWVLRYYYQGCASWKWYYPFHYAPFASDFEGIADMSSEFEKGTKPFKPLEQLMGVFPAASGNFLPPTWRKLMSDPDSSIIDFYPEDFAIDLNGKKYAWQGVALLPFVDERRLRAALEEVYPDLTPEENRRNSLGGDVLFVGKLHPLRDFILELYQTGSTEPVDVPPELCHGIQGTFSLDEEAILPDQTVCSPVPMLRDLTQNTAVRWLSSSRRNKRKI
IRESfinder result
IRESfinder score
0.584617053
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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