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mmu_circChaf1a_981
Basic information of circular RNA
PanCircBase ID:
mmu_circChaf1a_981
mm39_Chr. Position ID:
chr17|56363420|56370420|+
Gene name:
Chaf1a
Transcript:
ENSMUST00000002914.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
4,5,6,7,8,9,10,11
Exon/intron offsets:
0,1297,2563,2837,5664,6130,6390,6907
Genomic length:
7000
Exon/intron sizes in nt:
57,203,82,69,227,169,81,93
Flanking exon/introns:
chr17:56354634-56363420|chr17:56370420-56371000
Splice length:
981
Other database IDs:
circAtlas: mmu-Chaf1a_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTTGCCAAGAACTTTGTCAAAGGCTCCACAGAGAAGGGCAGGAGCAAACTGCACAGAGATAGAGAACAGCAGAGGGAAGAGAAGGAAAAGCTGAGGGAAGAGATACGACGAGCCAAGGAGGAGGCACGGAAGAAGAAGGAGGAGGAGAAGGAGCTGAAGGAAAAGGAGCGGAGGGAAAAGCGGGAGAAAGATGAGAAGGAGAAGGCGGAGAAGCAGCGGCTAAAGGAGGAAAAACGCAAGGAGCGGCAGGAAGCTCTGGAGGCTAAACTGGAGGAGAAGAGGAAGAAGGAGGAAGAGAAGCGGTTACGGGAGGAAGAGAAGCGGTTACGGGAAGAAGAGAAGCGCATTAAGGCAGAAAAGGCAGAGATCACTCGATTCTTCCAGAAACCGAAGACTCCGCAGGCTCCCAAGACCCTGGCCGGTTCCTGTGGTAAGTTTGCCCCCTTTGAAATCAAAGAACACATGGTGCTGGCTCCACGGTGCCGAGCTGCCTTGGATCAAGACCTGTGCGATCAGCTGGACCAGCTCCTGCAGCAGCAGAGTGTGGCAAGCACCTTCCTCAGTGACCTAAAAAGCCGGCTGCCCTTGAGATCGGGGCCCACCCGGGTCTGTGGCCATGACACAGACATCATGAACAGGGATGTGGTCATTGTGGAGAGCAGCAAGGTGGACGGTGTGTCTGAAAGGAAGAAGTTTGGCCGCATGAAGCTTCTGCAGTTCTCAGAGAACCACCGGCCAGCATACTGGGGGACGTGGAACAAGAAGACAGCCATCATCCGCCCCCGGAACCCCTGGGCCCAGGACAAAGACCTTCTTGACTATGAGGTAGACAGTGACGATGAGTGGGAAGAGGAGGAACCTGGGGAGTCTTTGTCCCACAGTGAGGGGGATGAGGATGACGATGTGGGGGAAGATGAGGATGAGGACGATGGCTTCTTTGTGCCCCATGGGTACTTATCTGAAGATGAAGGCGTGACTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGGGGATGAGGATGACGAT
59.81
TTTGCTCCTGCCCTTCTCTG
59.96
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGGGGATGAGGATGACGAT
59.81
GTTTGCTCCTGCCCTTCTCT
59.96
147
PCR template sequence:
TGAGGGGGATGAGGATGACGATGTGGGGGAAGATGAGGATGAGGACGATGGCTTCTTTGTGCCCCATGGGTACTTATCTGAAGATGAAGGCGTGACTGAGGTTGCCAAGAACTTTGTCAAAGGCTCCACAGAGAAGGGCAGGAGCAAACTGCACAGAGATAGAGAACAGCAGAGGGAAGAGAAGGAAAAGCTGAGGGAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-207(3), mmu-miR-296-5p(1), mmu-miR-205-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-146a-5p(1), mmu-miR-25-3p(1), mmu-miR-1198-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGGCGTGACTGAGGTTGCCAAGAACT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHAF1A_981_ORF_1
1.1173
0.579834695
0.999953869
1500
ORF sequence:
ATGGTGCTGGCTCCACGGTGCCGAGCTGCCTTGGATCAAGACCTGTGCGATCAGCTGGACCAGCTCCTGCAGCAGCAGAGTGTGGCAAGCACCTTCCTCAGTGACCTAAAAAGCCGGCTGCCCTTGAGATCGGGGCCCACCCGGGTCTGTGGCCATGACACAGACATCATGAACAGGGATGTGGTCATTGTGGAGAGCAGCAAGGTGGACGGTGTGTCTGAAAGGAAGAAGTTTGGCCGCATGAAGCTTCTGCAGTTCTCAGAGAACCACCGGCCAGCATACTGGGGGACGTGGAACAAGAAGACAGCCATCATCCGCCCCCGGAACCCCTGGGCCCAGGACAAAGACCTTCTTGACTATGAGGTAGACAGTGACGATGAGTGGGAAGAGGAGGAACCTGGGGAGTCTTTGTCCCACAGTGAGGGGGATGAGGATGACGATGTGGGGGAAGATGAGGATGAGGACGATGGCTTCTTTGTGCCCCATGGGTACTTATCTGAAGATGAAGGCGTGACTGAGGTTGCCAAGAACTTTGTCAAAGGCTCCACAGAGAAGGGCAGGAGCAAACTGCACAGAGATAGAGAACAGCAGAGGGAAGAGAAGGAAAAGCTGAGGGAAGAGATACGACGAGCCAAGGAGGAGGCACGGAAGAAGAAGGAGGAGGAGAAGGAGCTGAAGGAAAAGGAGCGGAGGGAAAAGCGGGAGAAAGATGAGAAGGAGAAGGCGGAGAAGCAGCGGCTAAAGGAGGAAAAACGCAAGGAGCGGCAGGAAGCTCTGGAGGCTAAACTGGAGGAGAAGAGGAAGAAGGAGGAAGAGAAGCGGTTACGGGAGGAAGAGAAGCGGTTACGGGAAGAAGAGAAGCGCATTAAGGCAGAAAAGGCAGAGATCACTCGATTCTTCCAGAAACCGAAGACTCCGCAGGCTCCCAAGACCCTGGCCGGTTCCTGTGGTAAGTTTGCCCCCTTTGAAATCAAAGAACACATGGTGCTGGCTCCACGGTGCCGAGCTGCCTTGGATCAAGACCTGTGCGATCAGCTGGACCAGCTCCTGCAGCAGCAGAGTGTGGCAAGCACCTTCCTCAGTGACCTAAAAAGCCGGCTGCCCTTGAGATCGGGGCCCACCCGGGTCTGTGGCCATGACACAGACATCATGAACAGGGATGTGGTCATTGTGGAGAGCAGCAAGGTGGACGGTGTGTCTGAAAGGAAGAAGTTTGGCCGCATGAAGCTTCTGCAGTTCTCAGAGAACCACCGGCCAGCATACTGGGGGACGTGGAACAAGAAGACAGCCATCATCCGCCCCCGGAACCCCTGGGCCCAGGACAAAGACCTTCTTGACTATGAGGTAGACAGTGACGATGAGTGGGAAGAGGAGGAACCTGGGGAGTCTTTGTCCCACAGTGAGGGGGATGAGGATGACGATGTGGGGGAAGATGAGGATGAGGACGATGGCTTCTTTGTGCCCCATGGGTACTTATCTGAAGATGAAGGCGTGACTGAG
Peptide sequence:
MVLAPRCRAALDQDLCDQLDQLLQQQSVASTFLSDLKSRLPLRSGPTRVCGHDTDIMNRDVVIVESSKVDGVSERKKFGRMKLLQFSENHRPAYWGTWNKKTAIIRPRNPWAQDKDLLDYEVDSDDEWEEEEPGESLSHSEGDEDDDVGEDEDEDDGFFVPHGYLSEDEGVTEVAKNFVKGSTEKGRSKLHRDREQQREEKEKLREEIRRAKEEARKKKEEEKELKEKERREKREKDEKEKAEKQRLKEEKRKERQEALEAKLEEKRKKEEEKRLREEEKRLREEEKRIKAEKAEITRFFQKPKTPQAPKTLAGSCGKFAPFEIKEHMVLAPRCRAALDQDLCDQLDQLLQQQSVASTFLSDLKSRLPLRSGPTRVCGHDTDIMNRDVVIVESSKVDGVSERKKFGRMKLLQFSENHRPAYWGTWNKKTAIIRPRNPWAQDKDLLDYEVDSDDEWEEEEPGESLSHSEGDEDDDVGEDEDEDDGFFVPHGYLSEDEGVTE
IRESfinder result
IRESfinder score
0.217993223
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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