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mmu_circFaf1_1446
Basic information of circular RNA
PanCircBase ID:
mmu_circFaf1_1446
mm39_Chr. Position ID:
chr4|109567986|109748187|+
Gene name:
Faf1
Transcript:
ENSMUST00000102724.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
14
Exon/intron indexes:
2,3,4,5,6,7,8,9,10,11,12,13,14,15
Exon/intron offsets:
0,9966,16600,25801,32076,46790,83978,119016,129526,130519,131498,151019,172846,180112
Genomic length:
180201
Exon/intron sizes in nt:
69,47,203,92,92,106,87,96,127,64,82,155,137,89
Flanking exon/introns:
chr4:109534269-109567986|chr4:109748187-109782494
Splice length:
1446
Other database IDs:
circAtlas: mmu-Faf1_0054
Human Ortholog IDs:
Mature spliced Sequence:
GCATGTACTGGTATTGAAAACATCGATGAAGCTATTACACTGCTTGAGCAAAATAACTGGGACTTGGTGGCAGCTATTAATGGTGTAATACCACAGGAAAATGGCATTCTACAAAGTGACTTTGGAGGTGAGACCATGCCAGGACCCACATTTGATCCAGCAAGTCACCCTGCTCCAGCTTCAACTCCCTCTTCTTCAGCGTTTCGACCTGTAATGCCATCCAGGCAGATTGTAGAAAGGCAGCCTCGAATGCTAGACTTCAGAGTTGAATACAGAGACAGAAATGTTGATGTGGTACTTGAAGACAGCTGTACTGTTGGAGAGATCAAACAGATTCTAGAAAATGAGCTTCAGATACCTGTGCCTAAAATGCTGTTAAAAGGCTGGAAGACTGGAGACGTGGAAGACAGTACGGTCTTAAAATCACTACACTTGCCAAAAAACAACAGTCTTTATGTCCTTACACCAGACTTGCCACCGCCTTCATCATCCAGCCATGCTGGTGCCCTGCAGGAATCATTAAATCAAAACTTCATGCTGATCATCACCCACCGAGAGGTCCAGCGGGAGTACAACCTGAACTTCTCAGGAAGCAGTACCGTTCAAGAGGTAAAGAGAAATGTGTATGACCTTACAAGCATACCTGTTCGACATCAGTTATGGGAGGGCTGGCCAGCTTCTGCCACCGATGACTCAATGTGTCTTGCTGAATCAGGCCTCTCTTATCCCTGCCATCGATTAACTGTGGGAAGAAGAACTTCACCTGTACAGACCCGTGAGCAATCAGAAGAGCAAAGCACGGATGTTCATATGGTTAGTGATAGTGATGGCGATGACTTTGAAGATGCTTCAGAATTTGGAGTGGATGACGGAGAAGTATTTGGCATGGCATCATCTACCCTGAGAAAATCTCCAATGATGCCAGAAAACGCAGAAAATGAAGGAGATGCCTTATTACAATTTACAGCAGAGTTTTCTTCAAGATATGGTGACTGCCATCCTGTATTTTTTATTGGCTCATTAGAAGCTGCTTTCCAAGAGGCCTTCTATGTGAAAGCCCGAGACAGAAAACTTCTTGCTATCTACCTCCACCATGATGAAAGTGTACTAACCAACGTGTTCTGCTCACAAATGCTTTGTGCTGAATCCATTGTTTCCTATCTGAGTCAAAATTTTATAACCTGGGCTTGGGATCTGACAAAGGACACCAACAGAGCAAGATTTCTGACAATGTGCAATAGACACTTTGGCAGCGTTATTGCACAAACTATTCGGACTCAAAAGACAGATCAGTTTCCACTTTTCCTGATTATCATGGGAAAGCGATCATCTAATGAAGTGTTAAATGTGATACAAGGTAATACAACAGTGGATGAGTTAATGATGAGACTCATGGCTGCAATGGAGATTTTCTCAGCTCAACAACAGGAAGACATTAAGGATGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGATGAGACTCATGGCTGCA
59.09
AATAGCTGCCACCAAGTCCC
60.03
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGATGAGACTCATGGCTGCAA
59.72
AATAGCTGCCACCAAGTCCC
60.03
143
PCR template sequence:
TGTGATACAAGGTAATACAACAGTGGATGAGTTAATGATGAGACTCATGGCTGCAATGGAGATTTTCTCAGCTCAACAACAGGAAGACATTAAGGATGAGGCATGTACTGGTATTGAAAACATCGATGAAGCTATTACACTGCTTGAGCAAAATAACTGGGACTTGGTGGCAGCTATTAATGGTGTAATACCACAGGAAA
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-23b-3p(1), mmu-miR-32-5p(1), mmu-miR-34c-5p(1), mmu-miR-92a-3p(1), mmu-miR-23a-3p(1), mmu-miR-25-3p(1), mmu-miR-363-3p(1), mmu-miR-127-5p(1), mmu-miR-182-5p(1), mmu-miR-301b-3p(1), mmu-miR-34b-5p(1), mmu-miR-301a-3p(1), mmu-miR-680(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CATTAAGGATGAGGCATGTACTGGTA
siRNA sets
ACCAGTACATGCCTCATCC, TACCAGTACATGCCTCATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFAF1_1446_ORF_1
0.8533
0.097244862
0.999999936
2757
ORF sequence:
ATGCCAGGACCCACATTTGATCCAGCAAGTCACCCTGCTCCAGCTTCAACTCCCTCTTCTTCAGCGTTTCGACCTGTAATGCCATCCAGGCAGATTGTAGAAAGGCAGCCTCGAATGCTAGACTTCAGAGTTGAATACAGAGACAGAAATGTTGATGTGGTACTTGAAGACAGCTGTACTGTTGGAGAGATCAAACAGATTCTAGAAAATGAGCTTCAGATACCTGTGCCTAAAATGCTGTTAAAAGGCTGGAAGACTGGAGACGTGGAAGACAGTACGGTCTTAAAATCACTACACTTGCCAAAAAACAACAGTCTTTATGTCCTTACACCAGACTTGCCACCGCCTTCATCATCCAGCCATGCTGGTGCCCTGCAGGAATCATTAAATCAAAACTTCATGCTGATCATCACCCACCGAGAGGTCCAGCGGGAGTACAACCTGAACTTCTCAGGAAGCAGTACCGTTCAAGAGGTAAAGAGAAATGTGTATGACCTTACAAGCATACCTGTTCGACATCAGTTATGGGAGGGCTGGCCAGCTTCTGCCACCGATGACTCAATGTGTCTTGCTGAATCAGGCCTCTCTTATCCCTGCCATCGATTAACTGTGGGAAGAAGAACTTCACCTGTACAGACCCGTGAGCAATCAGAAGAGCAAAGCACGGATGTTCATATGGTTAGTGATAGTGATGGCGATGACTTTGAAGATGCTTCAGAATTTGGAGTGGATGACGGAGAAGTATTTGGCATGGCATCATCTACCCTGAGAAAATCTCCAATGATGCCAGAAAACGCAGAAAATGAAGGAGATGCCTTATTACAATTTACAGCAGAGTTTTCTTCAAGATATGGTGACTGCCATCCTGTATTTTTTATTGGCTCATTAGAAGCTGCTTTCCAAGAGGCCTTCTATGTGAAAGCCCGAGACAGAAAACTTCTTGCTATCTACCTCCACCATGATGAAAGTGTACTAACCAACGTGTTCTGCTCACAAATGCTTTGTGCTGAATCCATTGTTTCCTATCTGAGTCAAAATTTTATAACCTGGGCTTGGGATCTGACAAAGGACACCAACAGAGCAAGATTTCTGACAATGTGCAATAGACACTTTGGCAGCGTTATTGCACAAACTATTCGGACTCAAAAGACAGATCAGTTTCCACTTTTCCTGATTATCATGGGAAAGCGATCATCTAATGAAGTGTTAAATGTGATACAAGGTAATACAACAGTGGATGAGTTAATGATGAGACTCATGGCTGCAATGGAGATTTTCTCAGCTCAACAACAGGAAGACATTAAGGATGAGGCATGTACTGGTATTGAAAACATCGATGAAGCTATTACACTGCTTGAGCAAAATAACTGGGACTTGGTGGCAGCTATTAATGGTGTAATACCACAGGAAAATGGCATTCTACAAAGTGACTTTGGAGGTGAGACCATGCCAGGACCCACATTTGATCCAGCAAGTCACCCTGCTCCAGCTTCAACTCCCTCTTCTTCAGCGTTTCGACCTGTAATGCCATCCAGGCAGATTGTAGAAAGGCAGCCTCGAATGCTAGACTTCAGAGTTGAATACAGAGACAGAAATGTTGATGTGGTACTTGAAGACAGCTGTACTGTTGGAGAGATCAAACAGATTCTAGAAAATGAGCTTCAGATACCTGTGCCTAAAATGCTGTTAAAAGGCTGGAAGACTGGAGACGTGGAAGACAGTACGGTCTTAAAATCACTACACTTGCCAAAAAACAACAGTCTTTATGTCCTTACACCAGACTTGCCACCGCCTTCATCATCCAGCCATGCTGGTGCCCTGCAGGAATCATTAAATCAAAACTTCATGCTGATCATCACCCACCGAGAGGTCCAGCGGGAGTACAACCTGAACTTCTCAGGAAGCAGTACCGTTCAAGAGGTAAAGAGAAATGTGTATGACCTTACAAGCATACCTGTTCGACATCAGTTATGGGAGGGCTGGCCAGCTTCTGCCACCGATGACTCAATGTGTCTTGCTGAATCAGGCCTCTCTTATCCCTGCCATCGATTAACTGTGGGAAGAAGAACTTCACCTGTACAGACCCGTGAGCAATCAGAAGAGCAAAGCACGGATGTTCATATGGTTAGTGATAGTGATGGCGATGACTTTGAAGATGCTTCAGAATTTGGAGTGGATGACGGAGAAGTATTTGGCATGGCATCATCTACCCTGAGAAAATCTCCAATGATGCCAGAAAACGCAGAAAATGAAGGAGATGCCTTATTACAATTTACAGCAGAGTTTTCTTCAAGATATGGTGACTGCCATCCTGTATTTTTTATTGGCTCATTAGAAGCTGCTTTCCAAGAGGCCTTCTATGTGAAAGCCCGAGACAGAAAACTTCTTGCTATCTACCTCCACCATGATGAAAGTGTACTAACCAACGTGTTCTGCTCACAAATGCTTTGTGCTGAATCCATTGTTTCCTATCTGAGTCAAAATTTTATAACCTGGGCTTGGGATCTGACAAAGGACACCAACAGAGCAAGATTTCTGACAATGTGCAATAGACACTTTGGCAGCGTTATTGCACAAACTATTCGGACTCAAAAGACAGATCAGTTTCCACTTTTCCTGATTATCATGGGAAAGCGATCATCTAATGAAGTGTTAAATGTGATACAAGGTAATACAACAGTGGATGAGTTAATGATGAGACTCATGGCTGCAATGGAGATTTTCTCAGCTCAACAACAGGAAGACATTAAGGATGAG
Peptide sequence:
MPGPTFDPASHPAPASTPSSSAFRPVMPSRQIVERQPRMLDFRVEYRDRNVDVVLEDSCTVGEIKQILENELQIPVPKMLLKGWKTGDVEDSTVLKSLHLPKNNSLYVLTPDLPPPSSSSHAGALQESLNQNFMLIITHREVQREYNLNFSGSSTVQEVKRNVYDLTSIPVRHQLWEGWPASATDDSMCLAESGLSYPCHRLTVGRRTSPVQTREQSEEQSTDVHMVSDSDGDDFEDASEFGVDDGEVFGMASSTLRKSPMMPENAENEGDALLQFTAEFSSRYGDCHPVFFIGSLEAAFQEAFYVKARDRKLLAIYLHHDESVLTNVFCSQMLCAESIVSYLSQNFITWAWDLTKDTNRARFLTMCNRHFGSVIAQTIRTQKTDQFPLFLIIMGKRSSNEVLNVIQGNTTVDELMMRLMAAMEIFSAQQQEDIKDEACTGIENIDEAITLLEQNNWDLVAAINGVIPQENGILQSDFGGETMPGPTFDPASHPAPASTPSSSAFRPVMPSRQIVERQPRMLDFRVEYRDRNVDVVLEDSCTVGEIKQILENELQIPVPKMLLKGWKTGDVEDSTVLKSLHLPKNNSLYVLTPDLPPPSSSSHAGALQESLNQNFMLIITHREVQREYNLNFSGSSTVQEVKRNVYDLTSIPVRHQLWEGWPASATDDSMCLAESGLSYPCHRLTVGRRTSPVQTREQSEEQSTDVHMVSDSDGDDFEDASEFGVDDGEVFGMASSTLRKSPMMPENAENEGDALLQFTAEFSSRYGDCHPVFFIGSLEAAFQEAFYVKARDRKLLAIYLHHDESVLTNVFCSQMLCAESIVSYLSQNFITWAWDLTKDTNRARFLTMCNRHFGSVIAQTIRTQKTDQFPLFLIIMGKRSSNEVLNVIQGNTTVDELMMRLMAAMEIFSAQQQEDIKDE
IRESfinder result
IRESfinder score
0.507533744
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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