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mmu_circItga6_1547
Basic information of circular RNA
PanCircBase ID:
mmu_circItga6_1547
mm39_Chr. Position ID:
chr2|71648824|71669065|+
Gene name:
Itga6
Transcript:
ENSMUST00000112101.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
4,5,6,7,8,9,10,11,12,13,14
Exon/intron offsets:
0,1518,3957,7028,7909,8242,9415,15215,15528,19787,20097
Genomic length:
20241
Exon/intron sizes in nt:
80,25,61,32,21,11,94,80,00,00,00,00,00,000
Flanking exon/introns:
chr2:71647098-71648824|chr2:71669065-71670905
Splice length:
1547
Other database IDs:
circAtlas: mmu-Itga6_0025
Human Ortholog IDs:
Mature spliced Sequence:
CTGATCCTATGTCAGAAAGCAAGGAAGACCAGTGGATGGGAGTCACTGTTCAGAGCCAAGGTCCAGGGGGCAAAGTGGTGACGTGTGCACATCGATATGAGAAACGGCAGCACGTCAACACGAAGCAGGAGTCGCGGGATATCTTTGGAAGATGTTATGTCCTAAGTCAGAATCTCAGAATTGAAGATGATATGGACGGAGGAGACTGGAGTTTCTGCGATGGCCGGTTGAGAGGCCATGAAAAGTTTGGCTCCTGTCAGCAAGGAGTAGCGGCTACTTTCACTAAGGACTTTCATTACATTGTTTTTGGAGCCCCAGGGACTTACAACTGGAAAGGGATCGTCCGTGTAGAACAAAAGAATAACACTTTTTTTGACATGAACATCTTTGAAGATGGGCCCTATGAAGTTGGTGGAGAGACTGATCATGATGAAAGTCTCGTGCCCGTTCCTGCTAACAGTTACCTAGGCTTTTCACTGGACTCAGGGAAGGGTATTGTTTCTAAAGATGACATCACTTTTGTGTCTGGTGCTCCAAGAGCCAATCACAGTGGGGCTGTAGTTTTGCTAAAAAGAGACATGAAGTCCGCGCATCTGCTCCCTGAGTATATATTTGACGGAGAAGGCCTGGCTTCCTCGTTTGGCTATGATGTGGCAGTGGTGGACCTCAATGCAGATGGGTGGCAAGACATTGTTATCGGAGCTCCACAGTATTTTGATAGGGATGGTGAAGTCGGGGGTGCAGTTTACGTCTACATTAACCAGCAAGGCAAATGGAGTAATGTGAAGCCGATTCGTCTAAATGGGACCAAAGACTCGATGTTTGGAATCTCTGTGAAAAATATAGGTGATATTAACCAAGATGGCTATCCAGATATTGCTGTTGGAGCTCCCTATGATGATCTGGGGAAGGTTTTTATCTATCATGGATCCCCGACTGGCATAATTACCAAGCCAACACAGGTTCTCGAGGGGACATCGCCTTACTTCGGCTATTCAATCGCTGGGAATATGGACCTGGATCGGAATTCCTACCCCGACCTTGCTGTGGGCTCCCTCTCAGACTCGGTCACTATTTTCAGATCCCGGCCAGTGATTAACATTCTAAAAACCATCACAGTGACTCCTAACAGAATTGACCTCCGCCAGAAGTCCATGTGTGGCTCACCTAGCGGGATATGCCTCAAGGTTAAAGCCTGTTTTGAATATACTGCGAAACCTTCCGGTTATAACCCTCCAATATCAATTTTGGGTATTCTCGAAGCTGAAAAAGAAAGAAGAAAGTCAGGGTTGTCATCGAGAGTTCAGTTTCGAAACCAAGGTTCCGAGCCAAAGTATACTCAGGAGCTGACCCTGAATCGGCAGAAGCAGCGGGCGTGCATGGAGGAGACCCTCTGGCTGCAGGAGAACATCAGAGACAAGCTGCGTCCCATCCCCATCACGGCTTCTGTGGAGATCCAGGAGCCCAGCTCTCGCCGGCGGGTGAACTCACTCCCCGAAGTTCTTCCCATCCTGAATTCAAATGAAGCCAAAACGGTCCAGACAGAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACTCCCCGAAGTTCTTCCC
60.04
GTGCACACGTCACCACTTTG
60.25
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTGAACTCACTCCCCGAAG
60.04
GTGCACACGTCACCACTTTG
60.25
157
PCR template sequence:
TGTGGAGATCCAGGAGCCCAGCTCTCGCCGGCGGGTGAACTCACTCCCCGAAGTTCTTCCCATCCTGAATTCAAATGAAGCCAAAACGGTCCAGACAGATCTGATCCTATGTCAGAAAGCAAGGAAGACCAGTGGATGGGAGTCACTGTTCAGAGCCAAGGTCCAGGGGGCAAAGTGGTGACGTGTGCACATCGATATGA
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
GGTCCAGACAGATCTGATCCTATGTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCITGA6_1547_ORF_1
0.9461
0.208738843
0.999875101
1620
ORF sequence:
ATGTCAGAAAGCAAGGAAGACCAGTGGATGGGAGTCACTGTTCAGAGCCAAGGTCCAGGGGGCAAAGTGGTGACGTGTGCACATCGATATGAGAAACGGCAGCACGTCAACACGAAGCAGGAGTCGCGGGATATCTTTGGAAGATGTTATGTCCTAAGTCAGAATCTCAGAATTGAAGATGATATGGACGGAGGAGACTGGAGTTTCTGCGATGGCCGGTTGAGAGGCCATGAAAAGTTTGGCTCCTGTCAGCAAGGAGTAGCGGCTACTTTCACTAAGGACTTTCATTACATTGTTTTTGGAGCCCCAGGGACTTACAACTGGAAAGGGATCGTCCGTGTAGAACAAAAGAATAACACTTTTTTTGACATGAACATCTTTGAAGATGGGCCCTATGAAGTTGGTGGAGAGACTGATCATGATGAAAGTCTCGTGCCCGTTCCTGCTAACAGTTACCTAGGCTTTTCACTGGACTCAGGGAAGGGTATTGTTTCTAAAGATGACATCACTTTTGTGTCTGGTGCTCCAAGAGCCAATCACAGTGGGGCTGTAGTTTTGCTAAAAAGAGACATGAAGTCCGCGCATCTGCTCCCTGAGTATATATTTGACGGAGAAGGCCTGGCTTCCTCGTTTGGCTATGATGTGGCAGTGGTGGACCTCAATGCAGATGGGTGGCAAGACATTGTTATCGGAGCTCCACAGTATTTTGATAGGGATGGTGAAGTCGGGGGTGCAGTTTACGTCTACATTAACCAGCAAGGCAAATGGAGTAATGTGAAGCCGATTCGTCTAAATGGGACCAAAGACTCGATGTTTGGAATCTCTGTGAAAAATATAGGTGATATTAACCAAGATGGCTATCCAGATATTGCTGTTGGAGCTCCCTATGATGATCTGGGGAAGGTTTTTATCTATCATGGATCCCCGACTGGCATAATTACCAAGCCAACACAGGTTCTCGAGGGGACATCGCCTTACTTCGGCTATTCAATCGCTGGGAATATGGACCTGGATCGGAATTCCTACCCCGACCTTGCTGTGGGCTCCCTCTCAGACTCGGTCACTATTTTCAGATCCCGGCCAGTGATTAACATTCTAAAAACCATCACAGTGACTCCTAACAGAATTGACCTCCGCCAGAAGTCCATGTGTGGCTCACCTAGCGGGATATGCCTCAAGGTTAAAGCCTGTTTTGAATATACTGCGAAACCTTCCGGTTATAACCCTCCAATATCAATTTTGGGTATTCTCGAAGCTGAAAAAGAAAGAAGAAAGTCAGGGTTGTCATCGAGAGTTCAGTTTCGAAACCAAGGTTCCGAGCCAAAGTATACTCAGGAGCTGACCCTGAATCGGCAGAAGCAGCGGGCGTGCATGGAGGAGACCCTCTGGCTGCAGGAGAACATCAGAGACAAGCTGCGTCCCATCCCCATCACGGCTTCTGTGGAGATCCAGGAGCCCAGCTCTCGCCGGCGGGTGAACTCACTCCCCGAAGTTCTTCCCATCCTGAATTCAAATGAAGCCAAAACGGTCCAGACAGATCTGATCCTATGTCAGAAAGCAAGGAAGACCAGTGGATGGGAGTCACTGTTCAGAGCCAAGGTCCAGGGGGCAAAGTGGTGA
Peptide sequence:
MSESKEDQWMGVTVQSQGPGGKVVTCAHRYEKRQHVNTKQESRDIFGRCYVLSQNLRIEDDMDGGDWSFCDGRLRGHEKFGSCQQGVAATFTKDFHYIVFGAPGTYNWKGIVRVEQKNNTFFDMNIFEDGPYEVGGETDHDESLVPVPANSYLGFSLDSGKGIVSKDDITFVSGAPRANHSGAVVLLKRDMKSAHLLPEYIFDGEGLASSFGYDVAVVDLNADGWQDIVIGAPQYFDRDGEVGGAVYVYINQQGKWSNVKPIRLNGTKDSMFGISVKNIGDINQDGYPDIAVGAPYDDLGKVFIYHGSPTGIITKPTQVLEGTSPYFGYSIAGNMDLDRNSYPDLAVGSLSDSVTIFRSRPVINILKTITVTPNRIDLRQKSMCGSPSGICLKVKACFEYTAKPSGYNPPISILGILEAEKERRKSGLSSRVQFRNQGSEPKYTQELTLNRQKQRACMEETLWLQENIRDKLRPIPITASVEIQEPSSRRRVNSLPEVLPILNSNEAKTVQTDLILCQKARKTSGWESLFRAKVQGAKW
IRESfinder result
IRESfinder score
0.500564434
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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