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mmu_circXrn2_983
Basic information of circular RNA
PanCircBase ID:
mmu_circXrn2_983
mm39_Chr. Position ID:
chr2|146868300|146878715|+
Gene name:
Xrn2
Transcript:
ENSMUST00000028921.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
5,6,7,8,9,10,11,12,13,14,15
Exon/intron offsets:
0,134,926,1214,1712,2957,3114,3346,3488,8473,10283
Genomic length:
10415
Exon/intron sizes in nt:
5,99,07,35,11,58,75,13,00,00,00,00,000
Flanking exon/introns:
chr2:146867226-146868300|chr2:146878715-146880088
Splice length:
983
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_348142
Human Ortholog IDs:
Mature spliced Sequence:
GTGGCTTTCTTCCTCCAGAAGAAATAAAAGAAAGATTTGACAGCAACTGTATTACCCCAGGAACTGAGTTCATGGACAATCTTGCTAAATGCCTTCGCTATTACATAGCTGATCGTTTAAATAATGACCCTGGGTGGAAAAATTTGACAGTTATATTATCTGATGCTAGTGCACCTGGTGAAGGAGAACACAAAATCATGGATTACATTAGAAGACAAAGAGCCCAGCCTAACCATGACCCAAATACTCATCATTGTTTGTGTGGAGCTGATGCTGATCTAATTATGCTTGGTCTTGCTACACATGAACCTAACTTCACCATAATCAGAGAAGAATTCAAACCAAATAAACCTAAACCATGTGCTCTTTGTAATCAGTTTGGACACGAGGTCAAGGATTGTGAAGGTTTGCCAAGAGAAAAGAAGGGAAAGCATGATGAACTTGCAGATAGTCTTCCTTGTGCAGAAGGGGAGTTTATCTTCCTTCGGCTGAATGTCCTTCGAGAGTATCTGGAAAGAGAACTCACCATGGCCAGCTTACCATTCCCATTTGATGTGGAGAGGAGCATTGATGACTGGGTGTTCATGTGCTTCTTTGTGGGGAATGATTTCCTTCCTCACTTGCCATCACTAGAGATTAGGGAAGGTGCAATTGATCGTTTGGTTAACATATACAAAAACGTGGTACACAAAACTGGGGGTTACCTTACAGAAAGTGGTTATGTCAATCTGCAAAGAGTACAGATGATCATGTTAGCAGTTGGTGAAGTTGAGGATAGCATTTTTAAAAAGAGAAAAGATGATGAGGACAGTTTTAGAAGACGACAGAAAGAAAAAAGAAAGAGGATGAAGAGAGATCAACCAGCTTTTACTCCTAGTGGAATATTAACACCTCATGCCTTGGGTTCAAGAAATTCACCAGGTTGTCAAGTAGCCAGTAATCCAAGACAAGCAGCCTATGAAATGAGGATGCAGAGAAACTCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACACCTCATGCCTTGGGTT
59.81
CCATGAACTCAGTTCCTGGGG
60.34
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACACCTCATGCCTTGGGTT
59.81
CATGAACTCAGTTCCTGGGGT
59.65
171
PCR template sequence:
ATTAACACCTCATGCCTTGGGTTCAAGAAATTCACCAGGTTGTCAAGTAGCCAGTAATCCAAGACAAGCAGCCTATGAAATGAGGATGCAGAGAAACTCTGTGGCTTTCTTCCTCCAGAAGAAATAAAAGAAAGATTTGACAGCAACTGTATTACCCCAGGAACTGAGTTCATGGACAATCTTGCTAAATGCCTTCGCTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-32-5p(1), mmu-miR-7b-5p(1), mmu-miR-92a-3p(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-miR-363-3p(1), mmu-miR-511-3p(1), mmu-miR-362-5p(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCAGAGAAACTCTGTGGCTTTCTTCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCXRN2_983_ORF_1
0.9541
0.016444256
0.965396929
939
ORF sequence:
ATGGACAATCTTGCTAAATGCCTTCGCTATTACATAGCTGATCGTTTAAATAATGACCCTGGGTGGAAAAATTTGACAGTTATATTATCTGATGCTAGTGCACCTGGTGAAGGAGAACACAAAATCATGGATTACATTAGAAGACAAAGAGCCCAGCCTAACCATGACCCAAATACTCATCATTGTTTGTGTGGAGCTGATGCTGATCTAATTATGCTTGGTCTTGCTACACATGAACCTAACTTCACCATAATCAGAGAAGAATTCAAACCAAATAAACCTAAACCATGTGCTCTTTGTAATCAGTTTGGACACGAGGTCAAGGATTGTGAAGGTTTGCCAAGAGAAAAGAAGGGAAAGCATGATGAACTTGCAGATAGTCTTCCTTGTGCAGAAGGGGAGTTTATCTTCCTTCGGCTGAATGTCCTTCGAGAGTATCTGGAAAGAGAACTCACCATGGCCAGCTTACCATTCCCATTTGATGTGGAGAGGAGCATTGATGACTGGGTGTTCATGTGCTTCTTTGTGGGGAATGATTTCCTTCCTCACTTGCCATCACTAGAGATTAGGGAAGGTGCAATTGATCGTTTGGTTAACATATACAAAAACGTGGTACACAAAACTGGGGGTTACCTTACAGAAAGTGGTTATGTCAATCTGCAAAGAGTACAGATGATCATGTTAGCAGTTGGTGAAGTTGAGGATAGCATTTTTAAAAAGAGAAAAGATGATGAGGACAGTTTTAGAAGACGACAGAAAGAAAAAAGAAAGAGGATGAAGAGAGATCAACCAGCTTTTACTCCTAGTGGAATATTAACACCTCATGCCTTGGGTTCAAGAAATTCACCAGGTTGTCAAGTAGCCAGTAATCCAAGACAAGCAGCCTATGAAATGAGGATGCAGAGAAACTCTGTGGCTTTCTTCCTCCAGAAGAAATAA
Peptide sequence:
MDNLAKCLRYYIADRLNNDPGWKNLTVILSDASAPGEGEHKIMDYIRRQRAQPNHDPNTHHCLCGADADLIMLGLATHEPNFTIIREEFKPNKPKPCALCNQFGHEVKDCEGLPREKKGKHDELADSLPCAEGEFIFLRLNVLREYLERELTMASLPFPFDVERSIDDWVFMCFFVGNDFLPHLPSLEIREGAIDRLVNIYKNVVHKTGGYLTESGYVNLQRVQMIMLAVGEVEDSIFKKRKDDEDSFRRRQKEKRKRMKRDQPAFTPSGILTPHALGSRNSPGCQVASNPRQAAYEMRMQRNSVAFFLQKK
IRESfinder result
IRESfinder score
0.593987494
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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