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mmu_circXrn2_1557
Basic information of circular RNA
PanCircBase ID:
mmu_circXrn2_1557
mm39_Chr. Position ID:
chr2|146876773|146916946|+
Gene name:
Xrn2
Transcript:
ENSMUST00000028921.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
16
Exon/intron indexes:
14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29
Exon/intron offsets:
0,1810,3315,5962,7134,7320,8006,12781,14438,15129,16859,26395,26552,28379,33938,40031
Genomic length:
40173
Exon/intron sizes in nt:
45,13,21,19,13,61,08,90,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr2:146871896-146876773|chr2:146916946-146919402
Splice length:
1557
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GACAGTTTTAGAAGACGACAGAAAGAAAAAAGAAAGAGGATGAAGAGAGATCAACCAGCTTTTACTCCTAGTGGAATATTAACACCTCATGCCTTGGGTTCAAGAAATTCACCAGGTTGTCAAGTAGCCAGTAATCCAAGACAAGCAGCCTATGAAATGAGGATGCAGAGAAACTCTAGTCCTTCAATATCTCCTAATACAAGTTTTGCATCTGATGGCTCCCCATCTCCACTAGGAGGAATTAAGAGAAAAGCAGAAGACAGTGACAGTGAGCCAGAGCCAGAGGATAACGTCAGGTTATGGGAAGCTGGTTGGAAGCAACGATACTACAAGAACAAATTTGATGTAGATGCAGCTGATGAGAAATTCCGACGTAAGGTTGTTCAGTCCTACGTTGAAGGACTGTGCTGGGTTCTTCGCTATTATTACCAGGGCTGTGCTTCCTGGAAGTGGTATTATCCATTCCATTATGCACCATTTGCCTCAGACTTTGAAGGTATTGCAGACATGTCCTCTGAATTTGAAAAGGGCACAAAACCGTTTAAGCCACTGGAACAACTAATGGGGGTTTTCCCAGCTGCAAGTGGTAACTTTCTACCTCCAACATGGCGGAAGCTCATGAGTGACCCTGATTCCAGTATAATTGACTTCTATCCTGAAGATTTTGCTATTGATTTGAATGGGAAGAAATATGCATGGCAAGGTGTTGCTCTATTGCCATTTGTGGATGAGCGAAGGCTGCGAGCGGCTCTAGAAGAGGTGTACCCAGACCTCACTCCAGAAGAGAACAGGAGAAATAGTCTTGGAGGTGATGTTTTGTTTGTGGGAAAACTTCATCCACTACGCGACTTCATTTTAGAGCTGTATCAGACGGGTTCCACAGAGCCAGTTGATGTGCCACCTGAATTGTGTCACGGGATTCAAGGGACGTTTTCTTTGGATGAAGAAGCCATTCTTCCAGACCAAACAGTATGTTCCCCTGTGCCCATGTTGCGGGACCTGACACAGAACACTGCAGTCAGTATTAATTTTAAAGATCCACAGTTTGCTGAAGATTATGTTTTTAAAGCTGCAATGCTTCCAGGAGCAAGAAAGCCAGCAACAGTTCTGAAACCTGGTGACTGGGAAAAATCCAGCAATGGGCGGCAATGGAAACCTCAGCTTGGCTTTAACCGGGACCGGCGGCCTGTTCACCTGGACCAGGCAGCCTTTAGAACTTTAGGCCATGTTACACCAAGAGGCTCGGGGACGAGTGTTTATACGAACACTGCACTACCACCTGCCAATTACCAGGGGAACAATTACAGGCCACTGCTGAGAGGTCAAGCTCAGATCCCAAAACTTATGTCAAATATGAGGCCCCAAGATTCCTGGCGAGGCCCTCCTCCTCTTTTCCAGCAGCATAGATTTGAGAGAAGTGTTGGAGCTGAACCTCTACTGCCATGGAACCGGATGATCCAAAACCAAAATGCAGCCTTTCAGCCAAATCAGTACCAGATGCTAGGAGGACCTGGAGGCTATCCACCCAGACGTGACGATCACCGAGGAGGGAGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTATCCACCCAGACGTGACG
59.9
AACCCAAGGCATGAGGTGTT
59.81
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCTAGGAGGACCTGGAGG
60.11
AACCCAAGGCATGAGGTGTT
59.81
160
PCR template sequence:
CCAAAACCAAAATGCAGCCTTTCAGCCAAATCAGTACCAGATGCTAGGAGGACCTGGAGGCTATCCACCCAGACGTGACGATCACCGAGGAGGGAGACAGGACAGTTTTAGAAGACGACAGAAAGAAAAAAGAAAGAGGATGAAGAGAGATCAACCAGCTTTTACTCCTAGTGGAATATTAACACCTCATGCCTTGGGTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-149-5p(2), mmu-let-7a-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-135a-5p(1), mmu-miR-200c-3p(1), mmu-let-7c-5p(1), mmu-miR-320-3p(1), mmu-let-7d-5p(1), mmu-miR-382-5p(1), mmu-miR-98-5p(1), mmu-miR-188-3p(1), mmu-miR-670-5p(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGGAGGGAGACAGGACAGTTTTAGAA
siRNA sets
AACTGTCCTGTCTCCCTCC, CTAAAACTGTCCTGTCTCC, AAACTGTCCTGTCTCCCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCXRN2_1557_ORF_1
1.0099
0.082656684
0.999999995
3075
ORF sequence:
ATGAAGAGAGATCAACCAGCTTTTACTCCTAGTGGAATATTAACACCTCATGCCTTGGGTTCAAGAAATTCACCAGGTTGTCAAGTAGCCAGTAATCCAAGACAAGCAGCCTATGAAATGAGGATGCAGAGAAACTCTAGTCCTTCAATATCTCCTAATACAAGTTTTGCATCTGATGGCTCCCCATCTCCACTAGGAGGAATTAAGAGAAAAGCAGAAGACAGTGACAGTGAGCCAGAGCCAGAGGATAACGTCAGGTTATGGGAAGCTGGTTGGAAGCAACGATACTACAAGAACAAATTTGATGTAGATGCAGCTGATGAGAAATTCCGACGTAAGGTTGTTCAGTCCTACGTTGAAGGACTGTGCTGGGTTCTTCGCTATTATTACCAGGGCTGTGCTTCCTGGAAGTGGTATTATCCATTCCATTATGCACCATTTGCCTCAGACTTTGAAGGTATTGCAGACATGTCCTCTGAATTTGAAAAGGGCACAAAACCGTTTAAGCCACTGGAACAACTAATGGGGGTTTTCCCAGCTGCAAGTGGTAACTTTCTACCTCCAACATGGCGGAAGCTCATGAGTGACCCTGATTCCAGTATAATTGACTTCTATCCTGAAGATTTTGCTATTGATTTGAATGGGAAGAAATATGCATGGCAAGGTGTTGCTCTATTGCCATTTGTGGATGAGCGAAGGCTGCGAGCGGCTCTAGAAGAGGTGTACCCAGACCTCACTCCAGAAGAGAACAGGAGAAATAGTCTTGGAGGTGATGTTTTGTTTGTGGGAAAACTTCATCCACTACGCGACTTCATTTTAGAGCTGTATCAGACGGGTTCCACAGAGCCAGTTGATGTGCCACCTGAATTGTGTCACGGGATTCAAGGGACGTTTTCTTTGGATGAAGAAGCCATTCTTCCAGACCAAACAGTATGTTCCCCTGTGCCCATGTTGCGGGACCTGACACAGAACACTGCAGTCAGTATTAATTTTAAAGATCCACAGTTTGCTGAAGATTATGTTTTTAAAGCTGCAATGCTTCCAGGAGCAAGAAAGCCAGCAACAGTTCTGAAACCTGGTGACTGGGAAAAATCCAGCAATGGGCGGCAATGGAAACCTCAGCTTGGCTTTAACCGGGACCGGCGGCCTGTTCACCTGGACCAGGCAGCCTTTAGAACTTTAGGCCATGTTACACCAAGAGGCTCGGGGACGAGTGTTTATACGAACACTGCACTACCACCTGCCAATTACCAGGGGAACAATTACAGGCCACTGCTGAGAGGTCAAGCTCAGATCCCAAAACTTATGTCAAATATGAGGCCCCAAGATTCCTGGCGAGGCCCTCCTCCTCTTTTCCAGCAGCATAGATTTGAGAGAAGTGTTGGAGCTGAACCTCTACTGCCATGGAACCGGATGATCCAAAACCAAAATGCAGCCTTTCAGCCAAATCAGTACCAGATGCTAGGAGGACCTGGAGGCTATCCACCCAGACGTGACGATCACCGAGGAGGGAGACAGGACAGTTTTAGAAGACGACAGAAAGAAAAAAGAAAGAGGATGAAGAGAGATCAACCAGCTTTTACTCCTAGTGGAATATTAACACCTCATGCCTTGGGTTCAAGAAATTCACCAGGTTGTCAAGTAGCCAGTAATCCAAGACAAGCAGCCTATGAAATGAGGATGCAGAGAAACTCTAGTCCTTCAATATCTCCTAATACAAGTTTTGCATCTGATGGCTCCCCATCTCCACTAGGAGGAATTAAGAGAAAAGCAGAAGACAGTGACAGTGAGCCAGAGCCAGAGGATAACGTCAGGTTATGGGAAGCTGGTTGGAAGCAACGATACTACAAGAACAAATTTGATGTAGATGCAGCTGATGAGAAATTCCGACGTAAGGTTGTTCAGTCCTACGTTGAAGGACTGTGCTGGGTTCTTCGCTATTATTACCAGGGCTGTGCTTCCTGGAAGTGGTATTATCCATTCCATTATGCACCATTTGCCTCAGACTTTGAAGGTATTGCAGACATGTCCTCTGAATTTGAAAAGGGCACAAAACCGTTTAAGCCACTGGAACAACTAATGGGGGTTTTCCCAGCTGCAAGTGGTAACTTTCTACCTCCAACATGGCGGAAGCTCATGAGTGACCCTGATTCCAGTATAATTGACTTCTATCCTGAAGATTTTGCTATTGATTTGAATGGGAAGAAATATGCATGGCAAGGTGTTGCTCTATTGCCATTTGTGGATGAGCGAAGGCTGCGAGCGGCTCTAGAAGAGGTGTACCCAGACCTCACTCCAGAAGAGAACAGGAGAAATAGTCTTGGAGGTGATGTTTTGTTTGTGGGAAAACTTCATCCACTACGCGACTTCATTTTAGAGCTGTATCAGACGGGTTCCACAGAGCCAGTTGATGTGCCACCTGAATTGTGTCACGGGATTCAAGGGACGTTTTCTTTGGATGAAGAAGCCATTCTTCCAGACCAAACAGTATGTTCCCCTGTGCCCATGTTGCGGGACCTGACACAGAACACTGCAGTCAGTATTAATTTTAAAGATCCACAGTTTGCTGAAGATTATGTTTTTAAAGCTGCAATGCTTCCAGGAGCAAGAAAGCCAGCAACAGTTCTGAAACCTGGTGACTGGGAAAAATCCAGCAATGGGCGGCAATGGAAACCTCAGCTTGGCTTTAACCGGGACCGGCGGCCTGTTCACCTGGACCAGGCAGCCTTTAGAACTTTAGGCCATGTTACACCAAGAGGCTCGGGGACGAGTGTTTATACGAACACTGCACTACCACCTGCCAATTACCAGGGGAACAATTACAGGCCACTGCTGAGAGGTCAAGCTCAGATCCCAAAACTTATGTCAAATATGAGGCCCCAAGATTCCTGGCGAGGCCCTCCTCCTCTTTTCCAGCAGCATAGATTTGAGAGAAGTGTTGGAGCTGAACCTCTACTGCCATGGAACCGGATGATCCAAAACCAAAATGCAGCCTTTCAGCCAAATCAGTACCAGATGCTAGGAGGACCTGGAGGCTATCCACCCAGACGTGACGATCACCGAGGAGGGAGACAG
Peptide sequence:
MKRDQPAFTPSGILTPHALGSRNSPGCQVASNPRQAAYEMRMQRNSSPSISPNTSFASDGSPSPLGGIKRKAEDSDSEPEPEDNVRLWEAGWKQRYYKNKFDVDAADEKFRRKVVQSYVEGLCWVLRYYYQGCASWKWYYPFHYAPFASDFEGIADMSSEFEKGTKPFKPLEQLMGVFPAASGNFLPPTWRKLMSDPDSSIIDFYPEDFAIDLNGKKYAWQGVALLPFVDERRLRAALEEVYPDLTPEENRRNSLGGDVLFVGKLHPLRDFILELYQTGSTEPVDVPPELCHGIQGTFSLDEEAILPDQTVCSPVPMLRDLTQNTAVSINFKDPQFAEDYVFKAAMLPGARKPATVLKPGDWEKSSNGRQWKPQLGFNRDRRPVHLDQAAFRTLGHVTPRGSGTSVYTNTALPPANYQGNNYRPLLRGQAQIPKLMSNMRPQDSWRGPPPLFQQHRFERSVGAEPLLPWNRMIQNQNAAFQPNQYQMLGGPGGYPPRRDDHRGGRQDSFRRRQKEKRKRMKRDQPAFTPSGILTPHALGSRNSPGCQVASNPRQAAYEMRMQRNSSPSISPNTSFASDGSPSPLGGIKRKAEDSDSEPEPEDNVRLWEAGWKQRYYKNKFDVDAADEKFRRKVVQSYVEGLCWVLRYYYQGCASWKWYYPFHYAPFASDFEGIADMSSEFEKGTKPFKPLEQLMGVFPAASGNFLPPTWRKLMSDPDSSIIDFYPEDFAIDLNGKKYAWQGVALLPFVDERRLRAALEEVYPDLTPEENRRNSLGGDVLFVGKLHPLRDFILELYQTGSTEPVDVPPELCHGIQGTFSLDEEAILPDQTVCSPVPMLRDLTQNTAVSINFKDPQFAEDYVFKAAMLPGARKPATVLKPGDWEKSSNGRQWKPQLGFNRDRRPVHLDQAAFRTLGHVTPRGSGTSVYTNTALPPANYQGNNYRPLLRGQAQIPKLMSNMRPQDSWRGPPPLFQQHRFERSVGAEPLLPWNRMIQNQNAAFQPNQYQMLGGPGGYPPRRDDHRGGRQ
IRESfinder result
IRESfinder score
0.564863816
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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