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mmu_circSynrg_1539
Basic information of circular RNA
PanCircBase ID:
mmu_circSynrg_1539
mm39_Chr. Position ID:
chr11|83867905|83893061|+
Gene name:
Synrg
Transcript:
ENSMUST00000049714.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
3,4,5,6,7,8,9,10,11,12,13
Exon/intron offsets:
0,1840,4337,5116,9734,10833,12600,13615,17249,24778,25093
Genomic length:
25156
Exon/intron sizes in nt:
122,131,106,112,234,78,197,249,134,113,63
Flanking exon/introns:
chr11:83862418-83867905|chr11:83893061-83899443
Splice length:
1539
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CAGGCCTGATTCCAATGCAACAGCAAGGATTCCCTATGGTCTCTGTCATGCAGCCCAATATGCAAGGCATGATGGGAATGAATTACAGCTCTCAGATGTCCCAAGGACCGATTGCAATGCAGGCAGGAATACCAATGGGGCCAATGCCAGCAGCGGGTGTGCCTTTCCTGGGTCAGCCACCTTTCTTGAGCATGCGTCCTGCAGGCCCACAGTACACTCCAGACATGCAGAAGCAGTTTGCGGAAGAGCAACAAAAACGATTTGAACAACAACAAAAGCTCTTAGAAGAAGAAAGAAAAAGACGTCAGTTTGAAGAGCAAAAGCAAAAGCTCAGACTTCTCAGCAGCGTGAAGCCCAAGACAGGAGAGAAGAACAGAGACGATGCTTTGGAAGCCATAAAAGGAAACTTGGATGGGTTTTCCAGAGATGCTAAGATGCACCCCACTCCAGCATCACATCCAAAGAAACAAGGCCCTTCCTTGGAAGAGAAGCTCCTAGTGTCTTGTGATGTAAGTGCATCCGGGCAGGAACACATAAAATTAAACACTCCTGATGCTGGGCACAAAGCCATAGTCCCAGGATCCAGTAAGAACTGCCCTGGTTTAATGGCCCATAACAGGGGTGCTGTGGATGGATGTGTGAGTGGTCCCGCCAGTGCAGAGGCAGAAAAGACTTCAGATCAAACCCTGTCAAAGGAAGAGAGTGGTGTGGGCGTGTTTCCCTCTCAGGACCCTGCTCAGTCCAGAATGCCTCCTTGGATTTACAATGAGAGTTTGGTTCCAGATGCCTATAAGAAAATTTTAGAAACCACAATGACTCCAACTGGAATAGATACTGCTAAACTTTATCCCATTCTGATGTCATCTGGACTTCCCAGGGAAACTCTCGGACAGATATGGGCCTTAGCTAATCGAACCACACCTGGCAGGCTCACTAAGGAGGAGCTTTACACGGTTCTCGCCATGGTAGCAGTAACACAGAGGGGTGTTCCTGCCATGAGCCCTGATGCTTTGAGCCAGTTCCCTGCGGCTCCCATCCCTACCTTAAGCGGCTTTCCTATGACTCTGCCTACCCCAGTGAGCCAGCCAACGGCGATGCCCTCTGGCCCTACAGGCTCCATGCCCCTCACCCTTGGACAACCCATCATGGGTATCAACCTTGTTGGACCAGTGGGTGGAGCTGCAGCACCAACTTCCAGTGGCTTCATGCCAGCCTACCCATCAAACCAGGTGGGAAAGACAGAAGAAGATGACTTCCAGGATTTTCAAGATGCTTCGAAATCAGGATCCATCGATGATTCCTTCACTGACTTCCAAGAGATGCCTGCTTCCTCAAAAACCAGTAATTCCCAGCATGGAAACAGTGCTCCATCACTCTTGATCCCATTTCCTGGAACTAAAGCCTCCACAGACAAATACGCAGTGTTCAAAGGGATTTCCACTGACAAGCCCTCTGAAAACCCTGCTTCGTTTGGAGAGTCTGGTGATAAATACAGTGCTTTCAGGGAACTCGAGCAAACGACAGACAGTAAACCTTTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCTGCTTCGTTTGGAGAGT
59.96
GCATATTGGGCTGCATGACA
58.97
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCTGCTTCGTTTGGAGAGT
59.96
TGCATATTGGGCTGCATGAC
58.97
144
PCR template sequence:
ACTGACAAGCCCTCTGAAAACCCTGCTTCGTTTGGAGAGTCTGGTGATAAATACAGTGCTTTCAGGGAACTCGAGCAAACGACAGACAGTAAACCTTTAGCAGGCCTGATTCCAATGCAACAGCAAGGATTCCCTATGGTCTCTGTCATGCAGCCCAATATGCAAGGCATGATGGGAATGAATTACAGCTCTCAGATGTC
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-33-5p(2), mmu-miR-135a-5p(1), mmu-miR-122-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-342-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-342-3p(1), mmu-miR-1198-5p(1), mmu-miR-532-5p(1), mmu-miR-670-5p(1), mmu-miR-1904(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGTAAACCTTTAGCAGGCCTGATTCC
siRNA sets
GAATCAGGCCTGCTAAAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSYNRG_1539_ORF_1
0.9716
0.148566618
0.999999995
3063
ORF sequence:
ATGCAACAGCAAGGATTCCCTATGGTCTCTGTCATGCAGCCCAATATGCAAGGCATGATGGGAATGAATTACAGCTCTCAGATGTCCCAAGGACCGATTGCAATGCAGGCAGGAATACCAATGGGGCCAATGCCAGCAGCGGGTGTGCCTTTCCTGGGTCAGCCACCTTTCTTGAGCATGCGTCCTGCAGGCCCACAGTACACTCCAGACATGCAGAAGCAGTTTGCGGAAGAGCAACAAAAACGATTTGAACAACAACAAAAGCTCTTAGAAGAAGAAAGAAAAAGACGTCAGTTTGAAGAGCAAAAGCAAAAGCTCAGACTTCTCAGCAGCGTGAAGCCCAAGACAGGAGAGAAGAACAGAGACGATGCTTTGGAAGCCATAAAAGGAAACTTGGATGGGTTTTCCAGAGATGCTAAGATGCACCCCACTCCAGCATCACATCCAAAGAAACAAGGCCCTTCCTTGGAAGAGAAGCTCCTAGTGTCTTGTGATGTAAGTGCATCCGGGCAGGAACACATAAAATTAAACACTCCTGATGCTGGGCACAAAGCCATAGTCCCAGGATCCAGTAAGAACTGCCCTGGTTTAATGGCCCATAACAGGGGTGCTGTGGATGGATGTGTGAGTGGTCCCGCCAGTGCAGAGGCAGAAAAGACTTCAGATCAAACCCTGTCAAAGGAAGAGAGTGGTGTGGGCGTGTTTCCCTCTCAGGACCCTGCTCAGTCCAGAATGCCTCCTTGGATTTACAATGAGAGTTTGGTTCCAGATGCCTATAAGAAAATTTTAGAAACCACAATGACTCCAACTGGAATAGATACTGCTAAACTTTATCCCATTCTGATGTCATCTGGACTTCCCAGGGAAACTCTCGGACAGATATGGGCCTTAGCTAATCGAACCACACCTGGCAGGCTCACTAAGGAGGAGCTTTACACGGTTCTCGCCATGGTAGCAGTAACACAGAGGGGTGTTCCTGCCATGAGCCCTGATGCTTTGAGCCAGTTCCCTGCGGCTCCCATCCCTACCTTAAGCGGCTTTCCTATGACTCTGCCTACCCCAGTGAGCCAGCCAACGGCGATGCCCTCTGGCCCTACAGGCTCCATGCCCCTCACCCTTGGACAACCCATCATGGGTATCAACCTTGTTGGACCAGTGGGTGGAGCTGCAGCACCAACTTCCAGTGGCTTCATGCCAGCCTACCCATCAAACCAGGTGGGAAAGACAGAAGAAGATGACTTCCAGGATTTTCAAGATGCTTCGAAATCAGGATCCATCGATGATTCCTTCACTGACTTCCAAGAGATGCCTGCTTCCTCAAAAACCAGTAATTCCCAGCATGGAAACAGTGCTCCATCACTCTTGATCCCATTTCCTGGAACTAAAGCCTCCACAGACAAATACGCAGTGTTCAAAGGGATTTCCACTGACAAGCCCTCTGAAAACCCTGCTTCGTTTGGAGAGTCTGGTGATAAATACAGTGCTTTCAGGGAACTCGAGCAAACGACAGACAGTAAACCTTTAGCAGGCCTGATTCCAATGCAACAGCAAGGATTCCCTATGGTCTCTGTCATGCAGCCCAATATGCAAGGCATGATGGGAATGAATTACAGCTCTCAGATGTCCCAAGGACCGATTGCAATGCAGGCAGGAATACCAATGGGGCCAATGCCAGCAGCGGGTGTGCCTTTCCTGGGTCAGCCACCTTTCTTGAGCATGCGTCCTGCAGGCCCACAGTACACTCCAGACATGCAGAAGCAGTTTGCGGAAGAGCAACAAAAACGATTTGAACAACAACAAAAGCTCTTAGAAGAAGAAAGAAAAAGACGTCAGTTTGAAGAGCAAAAGCAAAAGCTCAGACTTCTCAGCAGCGTGAAGCCCAAGACAGGAGAGAAGAACAGAGACGATGCTTTGGAAGCCATAAAAGGAAACTTGGATGGGTTTTCCAGAGATGCTAAGATGCACCCCACTCCAGCATCACATCCAAAGAAACAAGGCCCTTCCTTGGAAGAGAAGCTCCTAGTGTCTTGTGATGTAAGTGCATCCGGGCAGGAACACATAAAATTAAACACTCCTGATGCTGGGCACAAAGCCATAGTCCCAGGATCCAGTAAGAACTGCCCTGGTTTAATGGCCCATAACAGGGGTGCTGTGGATGGATGTGTGAGTGGTCCCGCCAGTGCAGAGGCAGAAAAGACTTCAGATCAAACCCTGTCAAAGGAAGAGAGTGGTGTGGGCGTGTTTCCCTCTCAGGACCCTGCTCAGTCCAGAATGCCTCCTTGGATTTACAATGAGAGTTTGGTTCCAGATGCCTATAAGAAAATTTTAGAAACCACAATGACTCCAACTGGAATAGATACTGCTAAACTTTATCCCATTCTGATGTCATCTGGACTTCCCAGGGAAACTCTCGGACAGATATGGGCCTTAGCTAATCGAACCACACCTGGCAGGCTCACTAAGGAGGAGCTTTACACGGTTCTCGCCATGGTAGCAGTAACACAGAGGGGTGTTCCTGCCATGAGCCCTGATGCTTTGAGCCAGTTCCCTGCGGCTCCCATCCCTACCTTAAGCGGCTTTCCTATGACTCTGCCTACCCCAGTGAGCCAGCCAACGGCGATGCCCTCTGGCCCTACAGGCTCCATGCCCCTCACCCTTGGACAACCCATCATGGGTATCAACCTTGTTGGACCAGTGGGTGGAGCTGCAGCACCAACTTCCAGTGGCTTCATGCCAGCCTACCCATCAAACCAGGTGGGAAAGACAGAAGAAGATGACTTCCAGGATTTTCAAGATGCTTCGAAATCAGGATCCATCGATGATTCCTTCACTGACTTCCAAGAGATGCCTGCTTCCTCAAAAACCAGTAATTCCCAGCATGGAAACAGTGCTCCATCACTCTTGATCCCATTTCCTGGAACTAAAGCCTCCACAGACAAATACGCAGTGTTCAAAGGGATTTCCACTGACAAGCCCTCTGAAAACCCTGCTTCGTTTGGAGAGTCTGGTGATAAATACAGTGCTTTCAGGGAACTCGAGCAAACGACAGACAGTAAACCTTTA
Peptide sequence:
MQQQGFPMVSVMQPNMQGMMGMNYSSQMSQGPIAMQAGIPMGPMPAAGVPFLGQPPFLSMRPAGPQYTPDMQKQFAEEQQKRFEQQQKLLEEERKRRQFEEQKQKLRLLSSVKPKTGEKNRDDALEAIKGNLDGFSRDAKMHPTPASHPKKQGPSLEEKLLVSCDVSASGQEHIKLNTPDAGHKAIVPGSSKNCPGLMAHNRGAVDGCVSGPASAEAEKTSDQTLSKEESGVGVFPSQDPAQSRMPPWIYNESLVPDAYKKILETTMTPTGIDTAKLYPILMSSGLPRETLGQIWALANRTTPGRLTKEELYTVLAMVAVTQRGVPAMSPDALSQFPAAPIPTLSGFPMTLPTPVSQPTAMPSGPTGSMPLTLGQPIMGINLVGPVGGAAAPTSSGFMPAYPSNQVGKTEEDDFQDFQDASKSGSIDDSFTDFQEMPASSKTSNSQHGNSAPSLLIPFPGTKASTDKYAVFKGISTDKPSENPASFGESGDKYSAFRELEQTTDSKPLAGLIPMQQQGFPMVSVMQPNMQGMMGMNYSSQMSQGPIAMQAGIPMGPMPAAGVPFLGQPPFLSMRPAGPQYTPDMQKQFAEEQQKRFEQQQKLLEEERKRRQFEEQKQKLRLLSSVKPKTGEKNRDDALEAIKGNLDGFSRDAKMHPTPASHPKKQGPSLEEKLLVSCDVSASGQEHIKLNTPDAGHKAIVPGSSKNCPGLMAHNRGAVDGCVSGPASAEAEKTSDQTLSKEESGVGVFPSQDPAQSRMPPWIYNESLVPDAYKKILETTMTPTGIDTAKLYPILMSSGLPRETLGQIWALANRTTPGRLTKEELYTVLAMVAVTQRGVPAMSPDALSQFPAAPIPTLSGFPMTLPTPVSQPTAMPSGPTGSMPLTLGQPIMGINLVGPVGGAAAPTSSGFMPAYPSNQVGKTEEDDFQDFQDASKSGSIDDSFTDFQEMPASSKTSNSQHGNSAPSLLIPFPGTKASTDKYAVFKGISTDKPSENPASFGESGDKYSAFRELEQTTDSKPL
IRESfinder result
IRESfinder score
0.458468543
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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