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mmu_circCarmil1_1347
Basic information of circular RNA
PanCircBase ID:
mmu_circCarmil1_1347
mm39_Chr. Position ID:
chr13|24248559|24283646|-
Gene name:
Carmil1
Transcript:
ENSMUST00000125901.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
15,14,13,12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,2555,5054,9363,11035,17352,24401,27929,29821,34229,34384,35005
Genomic length:
35087
Exon/intron sizes in nt:
150,88,176,132,129,99,94,69,173,55,100,82
Flanking exon/introns:
chr13:24233643-24248559|chr13:24283646-24286054
Splice length:
1347
Other database IDs:
CIRCpedia: MMU_CIRCpedia_221709, circAtlas: mmu-Lrrc16a_0028
circBase: hsa_circ_0131587, circAtlas: hsa-LRRC16A_0017, CIRCpedia: HSA_CIRCpedia_122977
Human Ortholog IDs:
Mature spliced Sequence:
CTGAGGTCAGGAGGAGCTCAAGTGTTAGAAGGCTGCATCGCTGAAATCCACAACATCACCAGCTTAGATATCTCTGACAATGGTTTAGAATCCGACCTATCTACCCTAATTGTGTGGCTCAGTAAAAACAGATCAATACAGCACCTGGCATTGGGCAAAAATTTTAATAATATGAAATCCAAAAATCTGACGCCTGTGTTGGACAACTTAGTGCAGATGATCCAAGATGAAGACTCTCCTCTGCAGTCGTTGTCCCTGGCTGACTCAAAACTCAAGGCTGAGGTCACCATCATCATCAATGCCCTGGGCAGCAACACCTCCCTGACCAAAGTGGACATCAGTGGGAATGGCATGGGGGACATGGGAGCGAAGATGCTGGCCAAGGCTCTCCAGATCAACACCAAACTCAGGACAGTCATCTGGGACAAAAACAACATCACTGCACAAGGCTTTCAAGACATAGCTGTTGCTATGGAAAAGAACTACACACTGCGATTTATGCCAATTCCGATGTATGATGCCGCTCAAGCTCTCAAAACCAACCCCGAGAAAACAGAAGAGGCTCTGCAGAAGATAGAAAATTATCTGCTCCGGAATCACGAGACCAGGAAATACCTTCAGGAGCAGGCCTATCGCCTCCAGCAGGGCATCGTCACCAGCACCACCCAGCAGATGATTGACCGGATATGTGTGAAGGTTCAGGATCACCTCAACTCCTTACGAGCCTGTGGGGGTGATGCTATTCAGGAGGATTTAAAGGCAGCGGAGCGGCTCATGCGAGATGCTAAGAACTCTAAAACATTGTTGCCCAATTTATATCATGTGGGCGGTGCATCCTGGGCAGGAGCCAGTGGGCTGTCATCCAGTCCCATTCAGGAGACCCTGGAGTCGATGGCTGGAGAAGTCACAAGAGTGGTGGATGAACAACTGAAGGATTTGCTAGAATCCATGGTGGACGCAGCCGAGACCCTCTGCCCCAACGTCATGAGAAAAGCCCACATCCGACAGGACCTGATCCATGCCAGCACCGAAAAGATTTCCATCCCACGTACCTTTGTTAAAAATGTCCTGTTGGAACAGTCCGGGATTGACATTCTTAACAAAATCAGTGAGGTGAAGCTGACAGTGGCCTCGTTCTTGTCTGACCGGATCGTCGATGAGATCCTGGATTCTCTCTCCAGCAGCCATCGGAAGCTGGCCAACCATTTCAGCAGGCTAAACAAGAGCCTTCCCCAGCGAGAGGACCTAGAGGTGGAGCTGGTGGAGGAGAAGCCGGTGAAACGGGCCATCCTCACGGTAGAGGATCTCACAGAGGTGGAGAGGCTGGAAGACCTAGACACTTGTATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGCTGGTGGAGGAGAAG
60.91
GTGGATTTCAGCGATGCAGC
60.25
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGCTGGTGGAGGAGAAG
60.91
TTTCAGCGATGCAGCCTTCT
60.32
141
PCR template sequence:
AGAGGTGGAGCTGGTGGAGGAGAAGCCGGTGAAACGGGCCATCCTCACGGTAGAGGATCTCACAGAGGTGGAGAGGCTGGAAGACCTAGACACTTGTATGCTGAGGTCAGGAGGAGCTCAAGTGTTAGAAGGCTGCATCGCTGAAATCCACAACATCACCAGCTTAGATATCTCTGACAATGGTTTAGAATCCGACCTAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
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-298-5p(1), mmu-miR-203-3p(1), mmu-miR-138-5p(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
AGACACTTGTATGCTGAGGTCAGGAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCARMIL1_1347_ORF_1
1.2538
0.421141262
0.999999957
2523
ORF sequence:
ATGAAATCCAAAAATCTGACGCCTGTGTTGGACAACTTAGTGCAGATGATCCAAGATGAAGACTCTCCTCTGCAGTCGTTGTCCCTGGCTGACTCAAAACTCAAGGCTGAGGTCACCATCATCATCAATGCCCTGGGCAGCAACACCTCCCTGACCAAAGTGGACATCAGTGGGAATGGCATGGGGGACATGGGAGCGAAGATGCTGGCCAAGGCTCTCCAGATCAACACCAAACTCAGGACAGTCATCTGGGACAAAAACAACATCACTGCACAAGGCTTTCAAGACATAGCTGTTGCTATGGAAAAGAACTACACACTGCGATTTATGCCAATTCCGATGTATGATGCCGCTCAAGCTCTCAAAACCAACCCCGAGAAAACAGAAGAGGCTCTGCAGAAGATAGAAAATTATCTGCTCCGGAATCACGAGACCAGGAAATACCTTCAGGAGCAGGCCTATCGCCTCCAGCAGGGCATCGTCACCAGCACCACCCAGCAGATGATTGACCGGATATGTGTGAAGGTTCAGGATCACCTCAACTCCTTACGAGCCTGTGGGGGTGATGCTATTCAGGAGGATTTAAAGGCAGCGGAGCGGCTCATGCGAGATGCTAAGAACTCTAAAACATTGTTGCCCAATTTATATCATGTGGGCGGTGCATCCTGGGCAGGAGCCAGTGGGCTGTCATCCAGTCCCATTCAGGAGACCCTGGAGTCGATGGCTGGAGAAGTCACAAGAGTGGTGGATGAACAACTGAAGGATTTGCTAGAATCCATGGTGGACGCAGCCGAGACCCTCTGCCCCAACGTCATGAGAAAAGCCCACATCCGACAGGACCTGATCCATGCCAGCACCGAAAAGATTTCCATCCCACGTACCTTTGTTAAAAATGTCCTGTTGGAACAGTCCGGGATTGACATTCTTAACAAAATCAGTGAGGTGAAGCTGACAGTGGCCTCGTTCTTGTCTGACCGGATCGTCGATGAGATCCTGGATTCTCTCTCCAGCAGCCATCGGAAGCTGGCCAACCATTTCAGCAGGCTAAACAAGAGCCTTCCCCAGCGAGAGGACCTAGAGGTGGAGCTGGTGGAGGAGAAGCCGGTGAAACGGGCCATCCTCACGGTAGAGGATCTCACAGAGGTGGAGAGGCTGGAAGACCTAGACACTTGTATGCTGAGGTCAGGAGGAGCTCAAGTGTTAGAAGGCTGCATCGCTGAAATCCACAACATCACCAGCTTAGATATCTCTGACAATGGTTTAGAATCCGACCTATCTACCCTAATTGTGTGGCTCAGTAAAAACAGATCAATACAGCACCTGGCATTGGGCAAAAATTTTAATAATATGAAATCCAAAAATCTGACGCCTGTGTTGGACAACTTAGTGCAGATGATCCAAGATGAAGACTCTCCTCTGCAGTCGTTGTCCCTGGCTGACTCAAAACTCAAGGCTGAGGTCACCATCATCATCAATGCCCTGGGCAGCAACACCTCCCTGACCAAAGTGGACATCAGTGGGAATGGCATGGGGGACATGGGAGCGAAGATGCTGGCCAAGGCTCTCCAGATCAACACCAAACTCAGGACAGTCATCTGGGACAAAAACAACATCACTGCACAAGGCTTTCAAGACATAGCTGTTGCTATGGAAAAGAACTACACACTGCGATTTATGCCAATTCCGATGTATGATGCCGCTCAAGCTCTCAAAACCAACCCCGAGAAAACAGAAGAGGCTCTGCAGAAGATAGAAAATTATCTGCTCCGGAATCACGAGACCAGGAAATACCTTCAGGAGCAGGCCTATCGCCTCCAGCAGGGCATCGTCACCAGCACCACCCAGCAGATGATTGACCGGATATGTGTGAAGGTTCAGGATCACCTCAACTCCTTACGAGCCTGTGGGGGTGATGCTATTCAGGAGGATTTAAAGGCAGCGGAGCGGCTCATGCGAGATGCTAAGAACTCTAAAACATTGTTGCCCAATTTATATCATGTGGGCGGTGCATCCTGGGCAGGAGCCAGTGGGCTGTCATCCAGTCCCATTCAGGAGACCCTGGAGTCGATGGCTGGAGAAGTCACAAGAGTGGTGGATGAACAACTGAAGGATTTGCTAGAATCCATGGTGGACGCAGCCGAGACCCTCTGCCCCAACGTCATGAGAAAAGCCCACATCCGACAGGACCTGATCCATGCCAGCACCGAAAAGATTTCCATCCCACGTACCTTTGTTAAAAATGTCCTGTTGGAACAGTCCGGGATTGACATTCTTAACAAAATCAGTGAGGTGAAGCTGACAGTGGCCTCGTTCTTGTCTGACCGGATCGTCGATGAGATCCTGGATTCTCTCTCCAGCAGCCATCGGAAGCTGGCCAACCATTTCAGCAGGCTAAACAAGAGCCTTCCCCAGCGAGAGGACCTAGAGGTGGAGCTGGTGGAGGAGAAGCCGGTGAAACGGGCCATCCTCACGGTAGAGGATCTCACAGAGGTGGAGAGGCTGGAAGACCTAGACACTTGTATG
Peptide sequence:
MKSKNLTPVLDNLVQMIQDEDSPLQSLSLADSKLKAEVTIIINALGSNTSLTKVDISGNGMGDMGAKMLAKALQINTKLRTVIWDKNNITAQGFQDIAVAMEKNYTLRFMPIPMYDAAQALKTNPEKTEEALQKIENYLLRNHETRKYLQEQAYRLQQGIVTSTTQQMIDRICVKVQDHLNSLRACGGDAIQEDLKAAERLMRDAKNSKTLLPNLYHVGGASWAGASGLSSSPIQETLESMAGEVTRVVDEQLKDLLESMVDAAETLCPNVMRKAHIRQDLIHASTEKISIPRTFVKNVLLEQSGIDILNKISEVKLTVASFLSDRIVDEILDSLSSSHRKLANHFSRLNKSLPQREDLEVELVEEKPVKRAILTVEDLTEVERLEDLDTCMLRSGGAQVLEGCIAEIHNITSLDISDNGLESDLSTLIVWLSKNRSIQHLALGKNFNNMKSKNLTPVLDNLVQMIQDEDSPLQSLSLADSKLKAEVTIIINALGSNTSLTKVDISGNGMGDMGAKMLAKALQINTKLRTVIWDKNNITAQGFQDIAVAMEKNYTLRFMPIPMYDAAQALKTNPEKTEEALQKIENYLLRNHETRKYLQEQAYRLQQGIVTSTTQQMIDRICVKVQDHLNSLRACGGDAIQEDLKAAERLMRDAKNSKTLLPNLYHVGGASWAGASGLSSSPIQETLESMAGEVTRVVDEQLKDLLESMVDAAETLCPNVMRKAHIRQDLIHASTEKISIPRTFVKNVLLEQSGIDILNKISEVKLTVASFLSDRIVDEILDSLSSSHRKLANHFSRLNKSLPQREDLEVELVEEKPVKRAILTVEDLTEVERLEDLDTCM
IRESfinder result
IRESfinder score
0.411486901
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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