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mmu_circChfr_1168
Basic information of circular RNA
PanCircBase ID:
mmu_circChfr_1168
mm39_Chr. Position ID:
chr5|110299392|110317080|+
Gene name:
Chfr
Transcript:
ENSMUST00000112519.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
8,9,10,11,12,13,14,15,16,17
Exon/intron offsets:
0,809,1591,3310,7272,8631,11184,12479,16597,17615
Genomic length:
17688
Exon/intron sizes in nt:
160,155,163,146,120,84,71,88,108,73
Flanking exon/introns:
chr5:110294500-110299392|chr5:110317080-110318727
Splice length:
1168
Other database IDs:
CIRCpedia: MMU_CIRCpedia_2793, circAtlas: mmu-Chfr_0037
Human Ortholog IDs:
Mature spliced Sequence:
ATGGGGAACTTGACACGAACCTCCAGTTATTAGTTTCAGGCCAGCGTGGAAATGCCCAAACCTCAAGTGAAGATGTCAAAGATGCCTCTGTGAAGCCAGACAAGATGGAGGAGACACTAACCTGTATCATCTGCCAGGACCTTCTGCACGATTGTGTGAGTTTGCAGCCTTGTATGCACACATTTTGTGCGGCTTGCTACTCTGGTTGGATGGAGCGTTCATCTCTGTGCCCTACCTGCCGATGTCCAGTGGAGCGGATTTGCAAAAACCACATCCTGAACAACCTAGTGGAAGCATACCTTATCCAGCACCCAGATAAAAGTCGCAGTGAAGAAGATGTGAGAAGTATGGATGCAAGGAATAAAATCACTCAAGATATGCTGCAACCCAAAGTCAGGAGGTCTTTCTCTGATGAAGAGGGGAGTTCAGAGGACCTGCTAGAGCTGTCTGATGTCGACAGTGAATCCTCAGATATCAGTCAGCCATACATTGTCTGCAGACAGTGTCCTGAATACAGAAGGCAAGCGGTGCAGTCTCTTCCTTGCCCAGTCCCAGAGAGTGAGCTGGGAGCTACACTGGCCCTTGGTGGGGAGGCACCTTCAACATCTGCCAGCTTGCCAACAGCAGCCCCGGATTACATGTGCCCTCTTCAAGGAAGCCATGCCATATGCACCTGCTGCTTCCAGCCTATGCCTGACCGGAGAGCTGAACGGGAGCAGGATCCCCGCGTCGCCCCTCAGCAGTGTGCGGTGTGCCTGCAGCCCTTCTGCCACCTGTACTGGGGCTGCACGAGGACTGGCTGCTTTGGCTGCTTGGCCCCATTCTGTGAGCTCAACCTGGGGGACAAGTGCTTGGATGGAGTGCTGAACAATAACAATTATGAATCGGACATCCTGAAGAATTACCTGGCAACCAGGGGTCTGACATGGAAAAGTGTGTTGACAGAGAGTCTCCTGGCTCTGCAGCGAGGTGTATTTATGCTGTCTGATTACAGAATCACTGGAAATACTGTGCTGTGTTACTGCTGTGGTCTGCGTAGCTTCCGAGAGCTGACCTACCAGTATCGTCAGAACATTCCTGCTTCTGAGTTGCCAGTGACTGTAACATCCCGTCCTGACTGCTACTGGGGCCGTAACTGTCGCACTCAGGTGAAGGCTCACCATGCAAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGCTTCTGAGTTGCCAG
59.96
GAGGTTTGGGCATTTCCACG
59.76
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGCTTCTGAGTTGCCAGT
60.25
GAGGTTTGGGCATTTCCACG
59.76
156
PCR template sequence:
AGAACATTCCTGCTTCTGAGTTGCCAGTGACTGTAACATCCCGTCCTGACTGCTACTGGGGCCGTAACTGTCGCACTCAGGTGAAGGCTCACCATGCAATATGGGGAACTTGACACGAACCTCCAGTTATTAGTTTCAGGCCAGCGTGGAAATGCCCAAACCTCAAGTGAAGATGTCAAAGATGCCTCTGTGAAGCCAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-200a-3p(1), mmu-miR-7b-5p(1), mmu-miR-322-5p(1), mmu-miR-7a-5p(1), mmu-miR-143-3p(1), mmu-miR-381-3p(1), mmu-miR-214-3p(1), mmu-miR-182-5p(1), mmu-miR-680(1), mmu-miR-29b-2-5p(1), mmu-miR-802-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-300-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCACCATGCAATATGGGGAACTTGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHFR_1168_ORF_1
0.7123
0.194476661
0.994967419
1173
ORF sequence:
ATGCAATATGGGGAACTTGACACGAACCTCCAGTTATTAGTTTCAGGCCAGCGTGGAAATGCCCAAACCTCAAGTGAAGATGTCAAAGATGCCTCTGTGAAGCCAGACAAGATGGAGGAGACACTAACCTGTATCATCTGCCAGGACCTTCTGCACGATTGTGTGAGTTTGCAGCCTTGTATGCACACATTTTGTGCGGCTTGCTACTCTGGTTGGATGGAGCGTTCATCTCTGTGCCCTACCTGCCGATGTCCAGTGGAGCGGATTTGCAAAAACCACATCCTGAACAACCTAGTGGAAGCATACCTTATCCAGCACCCAGATAAAAGTCGCAGTGAAGAAGATGTGAGAAGTATGGATGCAAGGAATAAAATCACTCAAGATATGCTGCAACCCAAAGTCAGGAGGTCTTTCTCTGATGAAGAGGGGAGTTCAGAGGACCTGCTAGAGCTGTCTGATGTCGACAGTGAATCCTCAGATATCAGTCAGCCATACATTGTCTGCAGACAGTGTCCTGAATACAGAAGGCAAGCGGTGCAGTCTCTTCCTTGCCCAGTCCCAGAGAGTGAGCTGGGAGCTACACTGGCCCTTGGTGGGGAGGCACCTTCAACATCTGCCAGCTTGCCAACAGCAGCCCCGGATTACATGTGCCCTCTTCAAGGAAGCCATGCCATATGCACCTGCTGCTTCCAGCCTATGCCTGACCGGAGAGCTGAACGGGAGCAGGATCCCCGCGTCGCCCCTCAGCAGTGTGCGGTGTGCCTGCAGCCCTTCTGCCACCTGTACTGGGGCTGCACGAGGACTGGCTGCTTTGGCTGCTTGGCCCCATTCTGTGAGCTCAACCTGGGGGACAAGTGCTTGGATGGAGTGCTGAACAATAACAATTATGAATCGGACATCCTGAAGAATTACCTGGCAACCAGGGGTCTGACATGGAAAAGTGTGTTGACAGAGAGTCTCCTGGCTCTGCAGCGAGGTGTATTTATGCTGTCTGATTACAGAATCACTGGAAATACTGTGCTGTGTTACTGCTGTGGTCTGCGTAGCTTCCGAGAGCTGACCTACCAGTATCGTCAGAACATTCCTGCTTCTGAGTTGCCAGTGACTGTAACATCCCGTCCTGACTGCTACTGGGGCCGTAACTGTCGCACTCAGGTGAAGGCTCACCATGCA
Peptide sequence:
MQYGELDTNLQLLVSGQRGNAQTSSEDVKDASVKPDKMEETLTCIICQDLLHDCVSLQPCMHTFCAACYSGWMERSSLCPTCRCPVERICKNHILNNLVEAYLIQHPDKSRSEEDVRSMDARNKITQDMLQPKVRRSFSDEEGSSEDLLELSDVDSESSDISQPYIVCRQCPEYRRQAVQSLPCPVPESELGATLALGGEAPSTSASLPTAAPDYMCPLQGSHAICTCCFQPMPDRRAEREQDPRVAPQQCAVCLQPFCHLYWGCTRTGCFGCLAPFCELNLGDKCLDGVLNNNNYESDILKNYLATRGLTWKSVLTESLLALQRGVFMLSDYRITGNTVLCYCCGLRSFRELTYQYRQNIPASELPVTVTSRPDCYWGRNCRTQVKAHHA
IRESfinder result
IRESfinder score
0.485709073
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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