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mmu_circCarmil1_1392
Basic information of circular RNA
PanCircBase ID:
mmu_circCarmil1_1392
mm39_Chr. Position ID:
chr13|24228156|24278553|-
Gene name:
Carmil1
Transcript:
ENSMUST00000125901.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
18,17,16,15,14,13,12,11,10,9,8,7
Exon/intron offsets:
0,842,5469,20403,22958,25457,29766,31438,37755,44804,48332,50224
Genomic length:
50397
Exon/intron sizes in nt:
197,67,18,150,88,176,132,129,99,94,69,173
Flanking exon/introns:
chr13:24225768-24228156|chr13:24278553-24282788
Splice length:
1392
Other database IDs:
circAtlas: mmu-Lrrc16a_0011
circBase: hsa_circ_0131590, circAtlas: hsa-LRRC16A_0030, CIRCpedia: HSA_CIRCpedia_54685
Human Ortholog IDs:
Mature spliced Sequence:
CCTCTGCAGTCGTTGTCCCTGGCTGACTCAAAACTCAAGGCTGAGGTCACCATCATCATCAATGCCCTGGGCAGCAACACCTCCCTGACCAAAGTGGACATCAGTGGGAATGGCATGGGGGACATGGGAGCGAAGATGCTGGCCAAGGCTCTCCAGATCAACACCAAACTCAGGACAGTCATCTGGGACAAAAACAACATCACTGCACAAGGCTTTCAAGACATAGCTGTTGCTATGGAAAAGAACTACACACTGCGATTTATGCCAATTCCGATGTATGATGCCGCTCAAGCTCTCAAAACCAACCCCGAGAAAACAGAAGAGGCTCTGCAGAAGATAGAAAATTATCTGCTCCGGAATCACGAGACCAGGAAATACCTTCAGGAGCAGGCCTATCGCCTCCAGCAGGGCATCGTCACCAGCACCACCCAGCAGATGATTGACCGGATATGTGTGAAGGTTCAGGATCACCTCAACTCCTTACGAGCCTGTGGGGGTGATGCTATTCAGGAGGATTTAAAGGCAGCGGAGCGGCTCATGCGAGATGCTAAGAACTCTAAAACATTGTTGCCCAATTTATATCATGTGGGCGGTGCATCCTGGGCAGGAGCCAGTGGGCTGTCATCCAGTCCCATTCAGGAGACCCTGGAGTCGATGGCTGGAGAAGTCACAAGAGTGGTGGATGAACAACTGAAGGATTTGCTAGAATCCATGGTGGACGCAGCCGAGACCCTCTGCCCCAACGTCATGAGAAAAGCCCACATCCGACAGGACCTGATCCATGCCAGCACCGAAAAGATTTCCATCCCACGTACCTTTGTTAAAAATGTCCTGTTGGAACAGTCCGGGATTGACATTCTTAACAAAATCAGTGAGGTGAAGCTGACAGTGGCCTCGTTCTTGTCTGACCGGATCGTCGATGAGATCCTGGATTCTCTCTCCAGCAGCCATCGGAAGCTGGCCAACCATTTCAGCAGGCTAAACAAGAGCCTTCCCCAGCGAGAGGACCTAGAGGTGGAGCTGGTGGAGGAGAAGCCGGTGAAACGGGCCATCCTCACGGTAGAGGATCTCACAGAGGTGGAGAGGCTGGAAGACCTAGACACTTGTATGACTCTCTGCTGTACAAGTATGACTCCTAAGTCCAAGAGGAAGAGCATCCACAGCCGAATGCTGCGGCCTGTCTCCAGGGCCTTCGAAATGGAGTTTGATCTTGATAAAGCCCTGGAAGAGGTGCCGATTCACATCGAAGACCCACCTTTCCCATCAGTCCGGCAAGAGAAGCGAAGCTCGGGGTTAATCTCTGAGCTGCCCTCGGAGGAAGGCAGGAGACTGGAACACTTCACCAAGTTAAGGCCCAAGCGGAACAAGAAGCAGCAACCTACGCAAGCAGCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGTTAAGGCCCAAGCGGAA
59.89
GTCCACTTTGGTCAGGGAGG
59.96
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTAAGGCCCAAGCGGAACAA
60.18
GTCCACTTTGGTCAGGGAGG
59.96
144
PCR template sequence:
GTTAATCTCTGAGCTGCCCTCGGAGGAAGGCAGGAGACTGGAACACTTCACCAAGTTAAGGCCCAAGCGGAACAAGAAGCAGCAACCTACGCAAGCAGCGCCTCTGCAGTCGTTGTCCCTGGCTGACTCAAAACTCAAGGCTGAGGTCACCATCATCATCAATGCCCTGGGCAGCAACACCTCCCTGACCAAAGTGGACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-370-3p(2), mmu-miR-207(2), mmu-miR-9-5p(1), mmu-miR-322-5p(1), mmu-miR-203-3p(1), mmu-miR-185-5p(1), mmu-miR-381-3p(1), mmu-miR-149-5p(1), mmu-miR-758-3p(1), mmu-miR-5101(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TACGCAAGCAGCGCCTCTGCAGTCGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCARMIL1_1392_ORF_1
1.2592
0.4243431
0.999999985
2670
ORF sequence:
ATGGGGGACATGGGAGCGAAGATGCTGGCCAAGGCTCTCCAGATCAACACCAAACTCAGGACAGTCATCTGGGACAAAAACAACATCACTGCACAAGGCTTTCAAGACATAGCTGTTGCTATGGAAAAGAACTACACACTGCGATTTATGCCAATTCCGATGTATGATGCCGCTCAAGCTCTCAAAACCAACCCCGAGAAAACAGAAGAGGCTCTGCAGAAGATAGAAAATTATCTGCTCCGGAATCACGAGACCAGGAAATACCTTCAGGAGCAGGCCTATCGCCTCCAGCAGGGCATCGTCACCAGCACCACCCAGCAGATGATTGACCGGATATGTGTGAAGGTTCAGGATCACCTCAACTCCTTACGAGCCTGTGGGGGTGATGCTATTCAGGAGGATTTAAAGGCAGCGGAGCGGCTCATGCGAGATGCTAAGAACTCTAAAACATTGTTGCCCAATTTATATCATGTGGGCGGTGCATCCTGGGCAGGAGCCAGTGGGCTGTCATCCAGTCCCATTCAGGAGACCCTGGAGTCGATGGCTGGAGAAGTCACAAGAGTGGTGGATGAACAACTGAAGGATTTGCTAGAATCCATGGTGGACGCAGCCGAGACCCTCTGCCCCAACGTCATGAGAAAAGCCCACATCCGACAGGACCTGATCCATGCCAGCACCGAAAAGATTTCCATCCCACGTACCTTTGTTAAAAATGTCCTGTTGGAACAGTCCGGGATTGACATTCTTAACAAAATCAGTGAGGTGAAGCTGACAGTGGCCTCGTTCTTGTCTGACCGGATCGTCGATGAGATCCTGGATTCTCTCTCCAGCAGCCATCGGAAGCTGGCCAACCATTTCAGCAGGCTAAACAAGAGCCTTCCCCAGCGAGAGGACCTAGAGGTGGAGCTGGTGGAGGAGAAGCCGGTGAAACGGGCCATCCTCACGGTAGAGGATCTCACAGAGGTGGAGAGGCTGGAAGACCTAGACACTTGTATGACTCTCTGCTGTACAAGTATGACTCCTAAGTCCAAGAGGAAGAGCATCCACAGCCGAATGCTGCGGCCTGTCTCCAGGGCCTTCGAAATGGAGTTTGATCTTGATAAAGCCCTGGAAGAGGTGCCGATTCACATCGAAGACCCACCTTTCCCATCAGTCCGGCAAGAGAAGCGAAGCTCGGGGTTAATCTCTGAGCTGCCCTCGGAGGAAGGCAGGAGACTGGAACACTTCACCAAGTTAAGGCCCAAGCGGAACAAGAAGCAGCAACCTACGCAAGCAGCGCCTCTGCAGTCGTTGTCCCTGGCTGACTCAAAACTCAAGGCTGAGGTCACCATCATCATCAATGCCCTGGGCAGCAACACCTCCCTGACCAAAGTGGACATCAGTGGGAATGGCATGGGGGACATGGGAGCGAAGATGCTGGCCAAGGCTCTCCAGATCAACACCAAACTCAGGACAGTCATCTGGGACAAAAACAACATCACTGCACAAGGCTTTCAAGACATAGCTGTTGCTATGGAAAAGAACTACACACTGCGATTTATGCCAATTCCGATGTATGATGCCGCTCAAGCTCTCAAAACCAACCCCGAGAAAACAGAAGAGGCTCTGCAGAAGATAGAAAATTATCTGCTCCGGAATCACGAGACCAGGAAATACCTTCAGGAGCAGGCCTATCGCCTCCAGCAGGGCATCGTCACCAGCACCACCCAGCAGATGATTGACCGGATATGTGTGAAGGTTCAGGATCACCTCAACTCCTTACGAGCCTGTGGGGGTGATGCTATTCAGGAGGATTTAAAGGCAGCGGAGCGGCTCATGCGAGATGCTAAGAACTCTAAAACATTGTTGCCCAATTTATATCATGTGGGCGGTGCATCCTGGGCAGGAGCCAGTGGGCTGTCATCCAGTCCCATTCAGGAGACCCTGGAGTCGATGGCTGGAGAAGTCACAAGAGTGGTGGATGAACAACTGAAGGATTTGCTAGAATCCATGGTGGACGCAGCCGAGACCCTCTGCCCCAACGTCATGAGAAAAGCCCACATCCGACAGGACCTGATCCATGCCAGCACCGAAAAGATTTCCATCCCACGTACCTTTGTTAAAAATGTCCTGTTGGAACAGTCCGGGATTGACATTCTTAACAAAATCAGTGAGGTGAAGCTGACAGTGGCCTCGTTCTTGTCTGACCGGATCGTCGATGAGATCCTGGATTCTCTCTCCAGCAGCCATCGGAAGCTGGCCAACCATTTCAGCAGGCTAAACAAGAGCCTTCCCCAGCGAGAGGACCTAGAGGTGGAGCTGGTGGAGGAGAAGCCGGTGAAACGGGCCATCCTCACGGTAGAGGATCTCACAGAGGTGGAGAGGCTGGAAGACCTAGACACTTGTATGACTCTCTGCTGTACAAGTATGACTCCTAAGTCCAAGAGGAAGAGCATCCACAGCCGAATGCTGCGGCCTGTCTCCAGGGCCTTCGAAATGGAGTTTGATCTTGATAAAGCCCTGGAAGAGGTGCCGATTCACATCGAAGACCCACCTTTCCCATCAGTCCGGCAAGAGAAGCGAAGCTCGGGGTTAATCTCTGAGCTGCCCTCGGAGGAAGGCAGGAGACTGGAACACTTCACCAAGTTAAGGCCCAAGCGGAACAAGAAGCAGCAACCTACGCAAGCAGCG
Peptide sequence:
MGDMGAKMLAKALQINTKLRTVIWDKNNITAQGFQDIAVAMEKNYTLRFMPIPMYDAAQALKTNPEKTEEALQKIENYLLRNHETRKYLQEQAYRLQQGIVTSTTQQMIDRICVKVQDHLNSLRACGGDAIQEDLKAAERLMRDAKNSKTLLPNLYHVGGASWAGASGLSSSPIQETLESMAGEVTRVVDEQLKDLLESMVDAAETLCPNVMRKAHIRQDLIHASTEKISIPRTFVKNVLLEQSGIDILNKISEVKLTVASFLSDRIVDEILDSLSSSHRKLANHFSRLNKSLPQREDLEVELVEEKPVKRAILTVEDLTEVERLEDLDTCMTLCCTSMTPKSKRKSIHSRMLRPVSRAFEMEFDLDKALEEVPIHIEDPPFPSVRQEKRSSGLISELPSEEGRRLEHFTKLRPKRNKKQQPTQAAPLQSLSLADSKLKAEVTIIINALGSNTSLTKVDISGNGMGDMGAKMLAKALQINTKLRTVIWDKNNITAQGFQDIAVAMEKNYTLRFMPIPMYDAAQALKTNPEKTEEALQKIENYLLRNHETRKYLQEQAYRLQQGIVTSTTQQMIDRICVKVQDHLNSLRACGGDAIQEDLKAAERLMRDAKNSKTLLPNLYHVGGASWAGASGLSSSPIQETLESMAGEVTRVVDEQLKDLLESMVDAAETLCPNVMRKAHIRQDLIHASTEKISIPRTFVKNVLLEQSGIDILNKISEVKLTVASFLSDRIVDEILDSLSSSHRKLANHFSRLNKSLPQREDLEVELVEEKPVKRAILTVEDLTEVERLEDLDTCMTLCCTSMTPKSKRKSIHSRMLRPVSRAFEMEFDLDKALEEVPIHIEDPPFPSVRQEKRSSGLISELPSEEGRRLEHFTKLRPKRNKKQQPTQAA
IRESfinder result
IRESfinder score
0.35569949
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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