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mmu_circItga6_1242
Basic information of circular RNA
PanCircBase ID:
mmu_circItga6_1242
mm39_Chr. Position ID:
chr2|71648824|71664414|+
Gene name:
Itga6
Transcript:
ENSMUST00000112101.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
4,5,6,7,8,9,10,11,12
Exon/intron offsets:
0,1518,3957,7028,7909,8242,9415,15215,15528
Genomic length:
15590
Exon/intron sizes in nt:
80,256,132,211,194,89,119,99,62
Flanking exon/introns:
chr2:71647098-71648824|chr2:71664414-71668611
Splice length:
1242
Other database IDs:
circAtlas: mmu-Itga6_0022
Human Ortholog IDs:
Mature spliced Sequence:
CTGATCCTATGTCAGAAAGCAAGGAAGACCAGTGGATGGGAGTCACTGTTCAGAGCCAAGGTCCAGGGGGCAAAGTGGTGACGTGTGCACATCGATATGAGAAACGGCAGCACGTCAACACGAAGCAGGAGTCGCGGGATATCTTTGGAAGATGTTATGTCCTAAGTCAGAATCTCAGAATTGAAGATGATATGGACGGAGGAGACTGGAGTTTCTGCGATGGCCGGTTGAGAGGCCATGAAAAGTTTGGCTCCTGTCAGCAAGGAGTAGCGGCTACTTTCACTAAGGACTTTCATTACATTGTTTTTGGAGCCCCAGGGACTTACAACTGGAAAGGGATCGTCCGTGTAGAACAAAAGAATAACACTTTTTTTGACATGAACATCTTTGAAGATGGGCCCTATGAAGTTGGTGGAGAGACTGATCATGATGAAAGTCTCGTGCCCGTTCCTGCTAACAGTTACCTAGGCTTTTCACTGGACTCAGGGAAGGGTATTGTTTCTAAAGATGACATCACTTTTGTGTCTGGTGCTCCAAGAGCCAATCACAGTGGGGCTGTAGTTTTGCTAAAAAGAGACATGAAGTCCGCGCATCTGCTCCCTGAGTATATATTTGACGGAGAAGGCCTGGCTTCCTCGTTTGGCTATGATGTGGCAGTGGTGGACCTCAATGCAGATGGGTGGCAAGACATTGTTATCGGAGCTCCACAGTATTTTGATAGGGATGGTGAAGTCGGGGGTGCAGTTTACGTCTACATTAACCAGCAAGGCAAATGGAGTAATGTGAAGCCGATTCGTCTAAATGGGACCAAAGACTCGATGTTTGGAATCTCTGTGAAAAATATAGGTGATATTAACCAAGATGGCTATCCAGATATTGCTGTTGGAGCTCCCTATGATGATCTGGGGAAGGTTTTTATCTATCATGGATCCCCGACTGGCATAATTACCAAGCCAACACAGGTTCTCGAGGGGACATCGCCTTACTTCGGCTATTCAATCGCTGGGAATATGGACCTGGATCGGAATTCCTACCCCGACCTTGCTGTGGGCTCCCTCTCAGACTCGGTCACTATTTTCAGATCCCGGCCAGTGATTAACATTCTAAAAACCATCACAGTGACTCCTAACAGAATTGACCTCCGCCAGAAGTCCATGTGTGGCTCACCTAGCGGGATATGCCTCAAGGTTAAAGCCTGTTTTGAATATACTGCGAAACCTTCCGGTTATAACCCTCCAATAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGAAGTCCATGTGTGGCT
59.96
GGCTCTGAACAGTGACTCCC
60.04
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGAAGTCCATGTGTGGCT
59.96
TGACTCCCATCCACTGGTCT
59.88
143
PCR template sequence:
CGCCAGAAGTCCATGTGTGGCTCACCTAGCGGGATATGCCTCAAGGTTAAAGCCTGTTTTGAATATACTGCGAAACCTTCCGGTTATAACCCTCCAATATCTGATCCTATGTCAGAAAGCAAGGAAGACCAGTGGATGGGAGTCACTGTTCAGAGCCAAGGTCCAGGGGGCAAAGTGGTGACGTGTGCACATCGATATGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-452-3p(2), mmu-miR-9-5p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-29b-3p(1), mmu-miR-33-5p(1), mmu-miR-136-5p(1), mmu-miR-433-3p(1), mmu-miR-431-5p(1), mmu-miR-125a-5p(1), mmu-miR-541-5p(1), mmu-miR-670-5p(1), mmu-miR-323-3p(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AACCCTCCAATATCTGATCCTATGTC
siRNA sets
TAGGATCAGATATTGGAGG, AGGATCAGATATTGGAGGG, ACATAGGATCAGATATTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCITGA6_1242_ORF_1
1.1771
0.197430104
0.999999824
2475
ORF sequence:
ATGTCAGAAAGCAAGGAAGACCAGTGGATGGGAGTCACTGTTCAGAGCCAAGGTCCAGGGGGCAAAGTGGTGACGTGTGCACATCGATATGAGAAACGGCAGCACGTCAACACGAAGCAGGAGTCGCGGGATATCTTTGGAAGATGTTATGTCCTAAGTCAGAATCTCAGAATTGAAGATGATATGGACGGAGGAGACTGGAGTTTCTGCGATGGCCGGTTGAGAGGCCATGAAAAGTTTGGCTCCTGTCAGCAAGGAGTAGCGGCTACTTTCACTAAGGACTTTCATTACATTGTTTTTGGAGCCCCAGGGACTTACAACTGGAAAGGGATCGTCCGTGTAGAACAAAAGAATAACACTTTTTTTGACATGAACATCTTTGAAGATGGGCCCTATGAAGTTGGTGGAGAGACTGATCATGATGAAAGTCTCGTGCCCGTTCCTGCTAACAGTTACCTAGGCTTTTCACTGGACTCAGGGAAGGGTATTGTTTCTAAAGATGACATCACTTTTGTGTCTGGTGCTCCAAGAGCCAATCACAGTGGGGCTGTAGTTTTGCTAAAAAGAGACATGAAGTCCGCGCATCTGCTCCCTGAGTATATATTTGACGGAGAAGGCCTGGCTTCCTCGTTTGGCTATGATGTGGCAGTGGTGGACCTCAATGCAGATGGGTGGCAAGACATTGTTATCGGAGCTCCACAGTATTTTGATAGGGATGGTGAAGTCGGGGGTGCAGTTTACGTCTACATTAACCAGCAAGGCAAATGGAGTAATGTGAAGCCGATTCGTCTAAATGGGACCAAAGACTCGATGTTTGGAATCTCTGTGAAAAATATAGGTGATATTAACCAAGATGGCTATCCAGATATTGCTGTTGGAGCTCCCTATGATGATCTGGGGAAGGTTTTTATCTATCATGGATCCCCGACTGGCATAATTACCAAGCCAACACAGGTTCTCGAGGGGACATCGCCTTACTTCGGCTATTCAATCGCTGGGAATATGGACCTGGATCGGAATTCCTACCCCGACCTTGCTGTGGGCTCCCTCTCAGACTCGGTCACTATTTTCAGATCCCGGCCAGTGATTAACATTCTAAAAACCATCACAGTGACTCCTAACAGAATTGACCTCCGCCAGAAGTCCATGTGTGGCTCACCTAGCGGGATATGCCTCAAGGTTAAAGCCTGTTTTGAATATACTGCGAAACCTTCCGGTTATAACCCTCCAATATCTGATCCTATGTCAGAAAGCAAGGAAGACCAGTGGATGGGAGTCACTGTTCAGAGCCAAGGTCCAGGGGGCAAAGTGGTGACGTGTGCACATCGATATGAGAAACGGCAGCACGTCAACACGAAGCAGGAGTCGCGGGATATCTTTGGAAGATGTTATGTCCTAAGTCAGAATCTCAGAATTGAAGATGATATGGACGGAGGAGACTGGAGTTTCTGCGATGGCCGGTTGAGAGGCCATGAAAAGTTTGGCTCCTGTCAGCAAGGAGTAGCGGCTACTTTCACTAAGGACTTTCATTACATTGTTTTTGGAGCCCCAGGGACTTACAACTGGAAAGGGATCGTCCGTGTAGAACAAAAGAATAACACTTTTTTTGACATGAACATCTTTGAAGATGGGCCCTATGAAGTTGGTGGAGAGACTGATCATGATGAAAGTCTCGTGCCCGTTCCTGCTAACAGTTACCTAGGCTTTTCACTGGACTCAGGGAAGGGTATTGTTTCTAAAGATGACATCACTTTTGTGTCTGGTGCTCCAAGAGCCAATCACAGTGGGGCTGTAGTTTTGCTAAAAAGAGACATGAAGTCCGCGCATCTGCTCCCTGAGTATATATTTGACGGAGAAGGCCTGGCTTCCTCGTTTGGCTATGATGTGGCAGTGGTGGACCTCAATGCAGATGGGTGGCAAGACATTGTTATCGGAGCTCCACAGTATTTTGATAGGGATGGTGAAGTCGGGGGTGCAGTTTACGTCTACATTAACCAGCAAGGCAAATGGAGTAATGTGAAGCCGATTCGTCTAAATGGGACCAAAGACTCGATGTTTGGAATCTCTGTGAAAAATATAGGTGATATTAACCAAGATGGCTATCCAGATATTGCTGTTGGAGCTCCCTATGATGATCTGGGGAAGGTTTTTATCTATCATGGATCCCCGACTGGCATAATTACCAAGCCAACACAGGTTCTCGAGGGGACATCGCCTTACTTCGGCTATTCAATCGCTGGGAATATGGACCTGGATCGGAATTCCTACCCCGACCTTGCTGTGGGCTCCCTCTCAGACTCGGTCACTATTTTCAGATCCCGGCCAGTGATTAACATTCTAAAAACCATCACAGTGACTCCTAACAGAATTGACCTCCGCCAGAAGTCCATGTGTGGCTCACCTAGCGGGATATGCCTCAAGGTTAAAGCCTGTTTTGAATATACTGCGAAACCTTCCGGTTATAACCCTCCAATA
Peptide sequence:
MSESKEDQWMGVTVQSQGPGGKVVTCAHRYEKRQHVNTKQESRDIFGRCYVLSQNLRIEDDMDGGDWSFCDGRLRGHEKFGSCQQGVAATFTKDFHYIVFGAPGTYNWKGIVRVEQKNNTFFDMNIFEDGPYEVGGETDHDESLVPVPANSYLGFSLDSGKGIVSKDDITFVSGAPRANHSGAVVLLKRDMKSAHLLPEYIFDGEGLASSFGYDVAVVDLNADGWQDIVIGAPQYFDRDGEVGGAVYVYINQQGKWSNVKPIRLNGTKDSMFGISVKNIGDINQDGYPDIAVGAPYDDLGKVFIYHGSPTGIITKPTQVLEGTSPYFGYSIAGNMDLDRNSYPDLAVGSLSDSVTIFRSRPVINILKTITVTPNRIDLRQKSMCGSPSGICLKVKACFEYTAKPSGYNPPISDPMSESKEDQWMGVTVQSQGPGGKVVTCAHRYEKRQHVNTKQESRDIFGRCYVLSQNLRIEDDMDGGDWSFCDGRLRGHEKFGSCQQGVAATFTKDFHYIVFGAPGTYNWKGIVRVEQKNNTFFDMNIFEDGPYEVGGETDHDESLVPVPANSYLGFSLDSGKGIVSKDDITFVSGAPRANHSGAVVLLKRDMKSAHLLPEYIFDGEGLASSFGYDVAVVDLNADGWQDIVIGAPQYFDRDGEVGGAVYVYINQQGKWSNVKPIRLNGTKDSMFGISVKNIGDINQDGYPDIAVGAPYDDLGKVFIYHGSPTGIITKPTQVLEGTSPYFGYSIAGNMDLDRNSYPDLAVGSLSDSVTIFRSRPVINILKTITVTPNRIDLRQKSMCGSPSGICLKVKACFEYTAKPSGYNPPI
IRESfinder result
IRESfinder score
0.515981388
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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