top of page
mmu_circAff4_1605
Basic information of circular RNA
PanCircBase ID:
mmu_circAff4_1605
mm39_Chr. Position ID:
chr11|53287365|53297502|+
Gene name:
Aff4
Transcript:
ENSMUST00000060945.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
8,9,10,11,12,13,14
Exon/intron offsets:
0,1293,1698,3050,5939,7817,10042
Genomic length:
10137
Exon/intron sizes in nt:
55,38,163,918,89,247,95
Flanking exon/introns:
chr11:53283643-53287365|chr11:53297502-53298706
Splice length:
1605
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
TATGTTAAAAGATGACTTAAAACTAAGCAGCAGTGAAGACAGTGATGGGGAACAGGATTGTGATAAGACAATGCCAAGGAGTACACCAGGAAGTAACTCTGAACCTTCACACCATAACAGTGAGGGAGCAGACAACTCCAGGGATGACTCGAGCAGCCACAGTGGATCTGAGAGCAGCTCTGGGTCTGACTCGGAGAGTGAGAGCAGCTCCAGTGACAGTGAGGCTAATGAGCCGTCGCAGAGCGCATCTCCTGAGCCTGAACCACCACCAACAAACAAGTGGCAACTTGATAATTGGTTGAATAAAGTGAACCCACATAAAGTATCCCCAGCTTCCTCTGTAGACAGCAACATCCCATCTTCTCAAGCCTACAAGAAAGAAGGCCGGGAGCAGGGCACTGCCAGTAACTACACAGATCCAGGGGGGACAAAAGAAACGAGCTCTGCCACCCCAGGACGAGACTCTAAAACCATCCAAAAGGGATCAGAAAGTGGCCGTGGGAGGCAGAAGTCTCCTGCACAGAGCGACAGTACCACTCAGAGGAGAACTGTCGGCAAAAAACAACCCAAAAAACCTGAGAAGTCAGCTGCTGAAGAGCCTCGTGGAGGCCTGAAGATAGAAAGTGAGACCCCTGTGGACATGGCTGCCAGCATGCCCTCCAGCAGGCACAAAGCAGCCACCAAGGGCTCGAGGAAACCCAACATCAAAAAGGAATCAAAATCTTCTCCTCGACCTACGGCAGAGAAGAAGAAGTACAAGTCAGCCAGTAAACCGTCCCAGAAGTCTCGGGAGATCATAGAGACTGACACCTCGTCCTCAGACTCGGACGGCAGCGAGAGCCTGCCTCCCTCCTCACAGACTCCTAAGTACCCTGAAAGCAACAGGACTCCTGTCAAACCCTCCTCAGTGGAGGAAGAAGATAGCTTTTTTCGGCAACGAATGTTCTCTCCTATGGAAGAGAAGGAGCTCCTTTCCCCACTCAGTGAGCCTGATGACAGGTATCCACTCATTGTGAAGATTGACCTCAATCTTCTGACTCGAATACCCGGGAAGCCTTACAAAGAAACAGAGCCACCCAAGGGGGAAAAGAAAAATGTTCCAGAGAAACACTCGAGAGAGGTGCAGAAGCAAGCCTCAGAAAAGGCTTCCAACAAAGGCAAGAGGAAACACAAGAATGATGATGATACCCGAGCCAGTGAGAGCAAAAAACCCAAAACAGAGGACAAGAACTCATCAGGCCACAAGCCATCCAGCAGCAGAGAGTCATCTAAGCAGAGTAGTACAAAAGAAAAGGACTTGCTACCTTCACCTGCTGGGCCCATTCTTTCAAAAGATTCAAAAACAGAGCATGGTTCTCGGAAGAGGACTGTCAGTCAGTCGTCGTCCTTAAAGTCCAGTGGGACCAGCAGCAAAGAGAACAGTGGCAGCAGCAGCAAGAGCAGCTCCTCCTCCACAGCGAAGCAGAAGAAGACTGAAGGCAAGGGTCCCAGCAGCTCCAAGGAGGCCAAGGAGAAGGCTCCAAATAGCTCCTCTAATTGTCCTCCGTCTACACCAACTTCTGAGTCTTCGAAGCCTCGGAGAACAAAGCTTGCCTTTGATGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCCTCCGTCTACACCAAC
59.04
TCCTGGTGTACTCCTTGGCA
60.47
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCCTCCGTCTACACCAAC
59.04
CCTGGTGTACTCCTTGGCAT
59.38
158
PCR template sequence:
CCAAGGAGAAGGCTCCAAATAGCTCCTCTAATTGTCCTCCGTCTACACCAACTTCTGAGTCTTCGAAGCCTCGGAGAACAAAGCTTGCCTTTGATGACAGTATGTTAAAAGATGACTTAAAACTAAGCAGCAGTGAAGACAGTGATGGGGAACAGGATTGTGATAAGACAATGCCAAGGAGTACACCAGGAAGTAACTCT
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-129-5p(2), mmu-miR-34a-5p(1), mmu-miR-211-5p(1), mmu-miR-185-5p(1), mmu-miR-149-5p(1), mmu-miR-676-3p(1), mmu-miR-370-3p(1), mmu-miR-98-5p(1), mmu-miR-207(1), mmu-miR-5101(1), mmu-miR-484(1), mmu-miR-452-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CCTTTGATGACAGTATGTTAAAAGAT
siRNA sets
AACATACTGTCATCAAAGG, TAACATACTGTCATCAAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFF4_1605_ORF_1
0.9488
0.283713671
0.999999999
3207
ORF sequence:
ATGTTAAAAGATGACTTAAAACTAAGCAGCAGTGAAGACAGTGATGGGGAACAGGATTGTGATAAGACAATGCCAAGGAGTACACCAGGAAGTAACTCTGAACCTTCACACCATAACAGTGAGGGAGCAGACAACTCCAGGGATGACTCGAGCAGCCACAGTGGATCTGAGAGCAGCTCTGGGTCTGACTCGGAGAGTGAGAGCAGCTCCAGTGACAGTGAGGCTAATGAGCCGTCGCAGAGCGCATCTCCTGAGCCTGAACCACCACCAACAAACAAGTGGCAACTTGATAATTGGTTGAATAAAGTGAACCCACATAAAGTATCCCCAGCTTCCTCTGTAGACAGCAACATCCCATCTTCTCAAGCCTACAAGAAAGAAGGCCGGGAGCAGGGCACTGCCAGTAACTACACAGATCCAGGGGGGACAAAAGAAACGAGCTCTGCCACCCCAGGACGAGACTCTAAAACCATCCAAAAGGGATCAGAAAGTGGCCGTGGGAGGCAGAAGTCTCCTGCACAGAGCGACAGTACCACTCAGAGGAGAACTGTCGGCAAAAAACAACCCAAAAAACCTGAGAAGTCAGCTGCTGAAGAGCCTCGTGGAGGCCTGAAGATAGAAAGTGAGACCCCTGTGGACATGGCTGCCAGCATGCCCTCCAGCAGGCACAAAGCAGCCACCAAGGGCTCGAGGAAACCCAACATCAAAAAGGAATCAAAATCTTCTCCTCGACCTACGGCAGAGAAGAAGAAGTACAAGTCAGCCAGTAAACCGTCCCAGAAGTCTCGGGAGATCATAGAGACTGACACCTCGTCCTCAGACTCGGACGGCAGCGAGAGCCTGCCTCCCTCCTCACAGACTCCTAAGTACCCTGAAAGCAACAGGACTCCTGTCAAACCCTCCTCAGTGGAGGAAGAAGATAGCTTTTTTCGGCAACGAATGTTCTCTCCTATGGAAGAGAAGGAGCTCCTTTCCCCACTCAGTGAGCCTGATGACAGGTATCCACTCATTGTGAAGATTGACCTCAATCTTCTGACTCGAATACCCGGGAAGCCTTACAAAGAAACAGAGCCACCCAAGGGGGAAAAGAAAAATGTTCCAGAGAAACACTCGAGAGAGGTGCAGAAGCAAGCCTCAGAAAAGGCTTCCAACAAAGGCAAGAGGAAACACAAGAATGATGATGATACCCGAGCCAGTGAGAGCAAAAAACCCAAAACAGAGGACAAGAACTCATCAGGCCACAAGCCATCCAGCAGCAGAGAGTCATCTAAGCAGAGTAGTACAAAAGAAAAGGACTTGCTACCTTCACCTGCTGGGCCCATTCTTTCAAAAGATTCAAAAACAGAGCATGGTTCTCGGAAGAGGACTGTCAGTCAGTCGTCGTCCTTAAAGTCCAGTGGGACCAGCAGCAAAGAGAACAGTGGCAGCAGCAGCAAGAGCAGCTCCTCCTCCACAGCGAAGCAGAAGAAGACTGAAGGCAAGGGTCCCAGCAGCTCCAAGGAGGCCAAGGAGAAGGCTCCAAATAGCTCCTCTAATTGTCCTCCGTCTACACCAACTTCTGAGTCTTCGAAGCCTCGGAGAACAAAGCTTGCCTTTGATGACAGTATGTTAAAAGATGACTTAAAACTAAGCAGCAGTGAAGACAGTGATGGGGAACAGGATTGTGATAAGACAATGCCAAGGAGTACACCAGGAAGTAACTCTGAACCTTCACACCATAACAGTGAGGGAGCAGACAACTCCAGGGATGACTCGAGCAGCCACAGTGGATCTGAGAGCAGCTCTGGGTCTGACTCGGAGAGTGAGAGCAGCTCCAGTGACAGTGAGGCTAATGAGCCGTCGCAGAGCGCATCTCCTGAGCCTGAACCACCACCAACAAACAAGTGGCAACTTGATAATTGGTTGAATAAAGTGAACCCACATAAAGTATCCCCAGCTTCCTCTGTAGACAGCAACATCCCATCTTCTCAAGCCTACAAGAAAGAAGGCCGGGAGCAGGGCACTGCCAGTAACTACACAGATCCAGGGGGGACAAAAGAAACGAGCTCTGCCACCCCAGGACGAGACTCTAAAACCATCCAAAAGGGATCAGAAAGTGGCCGTGGGAGGCAGAAGTCTCCTGCACAGAGCGACAGTACCACTCAGAGGAGAACTGTCGGCAAAAAACAACCCAAAAAACCTGAGAAGTCAGCTGCTGAAGAGCCTCGTGGAGGCCTGAAGATAGAAAGTGAGACCCCTGTGGACATGGCTGCCAGCATGCCCTCCAGCAGGCACAAAGCAGCCACCAAGGGCTCGAGGAAACCCAACATCAAAAAGGAATCAAAATCTTCTCCTCGACCTACGGCAGAGAAGAAGAAGTACAAGTCAGCCAGTAAACCGTCCCAGAAGTCTCGGGAGATCATAGAGACTGACACCTCGTCCTCAGACTCGGACGGCAGCGAGAGCCTGCCTCCCTCCTCACAGACTCCTAAGTACCCTGAAAGCAACAGGACTCCTGTCAAACCCTCCTCAGTGGAGGAAGAAGATAGCTTTTTTCGGCAACGAATGTTCTCTCCTATGGAAGAGAAGGAGCTCCTTTCCCCACTCAGTGAGCCTGATGACAGGTATCCACTCATTGTGAAGATTGACCTCAATCTTCTGACTCGAATACCCGGGAAGCCTTACAAAGAAACAGAGCCACCCAAGGGGGAAAAGAAAAATGTTCCAGAGAAACACTCGAGAGAGGTGCAGAAGCAAGCCTCAGAAAAGGCTTCCAACAAAGGCAAGAGGAAACACAAGAATGATGATGATACCCGAGCCAGTGAGAGCAAAAAACCCAAAACAGAGGACAAGAACTCATCAGGCCACAAGCCATCCAGCAGCAGAGAGTCATCTAAGCAGAGTAGTACAAAAGAAAAGGACTTGCTACCTTCACCTGCTGGGCCCATTCTTTCAAAAGATTCAAAAACAGAGCATGGTTCTCGGAAGAGGACTGTCAGTCAGTCGTCGTCCTTAAAGTCCAGTGGGACCAGCAGCAAAGAGAACAGTGGCAGCAGCAGCAAGAGCAGCTCCTCCTCCACAGCGAAGCAGAAGAAGACTGAAGGCAAGGGTCCCAGCAGCTCCAAGGAGGCCAAGGAGAAGGCTCCAAATAGCTCCTCTAATTGTCCTCCGTCTACACCAACTTCTGAGTCTTCGAAGCCTCGGAGAACAAAGCTTGCCTTTGATGAC
Peptide sequence:
MLKDDLKLSSSEDSDGEQDCDKTMPRSTPGSNSEPSHHNSEGADNSRDDSSSHSGSESSSGSDSESESSSSDSEANEPSQSASPEPEPPPTNKWQLDNWLNKVNPHKVSPASSVDSNIPSSQAYKKEGREQGTASNYTDPGGTKETSSATPGRDSKTIQKGSESGRGRQKSPAQSDSTTQRRTVGKKQPKKPEKSAAEEPRGGLKIESETPVDMAASMPSSRHKAATKGSRKPNIKKESKSSPRPTAEKKKYKSASKPSQKSREIIETDTSSSDSDGSESLPPSSQTPKYPESNRTPVKPSSVEEEDSFFRQRMFSPMEEKELLSPLSEPDDRYPLIVKIDLNLLTRIPGKPYKETEPPKGEKKNVPEKHSREVQKQASEKASNKGKRKHKNDDDTRASESKKPKTEDKNSSGHKPSSSRESSKQSSTKEKDLLPSPAGPILSKDSKTEHGSRKRTVSQSSSLKSSGTSSKENSGSSSKSSSSSTAKQKKTEGKGPSSSKEAKEKAPNSSSNCPPSTPTSESSKPRRTKLAFDDSMLKDDLKLSSSEDSDGEQDCDKTMPRSTPGSNSEPSHHNSEGADNSRDDSSSHSGSESSSGSDSESESSSSDSEANEPSQSASPEPEPPPTNKWQLDNWLNKVNPHKVSPASSVDSNIPSSQAYKKEGREQGTASNYTDPGGTKETSSATPGRDSKTIQKGSESGRGRQKSPAQSDSTTQRRTVGKKQPKKPEKSAAEEPRGGLKIESETPVDMAASMPSSRHKAATKGSRKPNIKKESKSSPRPTAEKKKYKSASKPSQKSREIIETDTSSSDSDGSESLPPSSQTPKYPESNRTPVKPSSVEEEDSFFRQRMFSPMEEKELLSPLSEPDDRYPLIVKIDLNLLTRIPGKPYKETEPPKGEKKNVPEKHSREVQKQASEKASNKGKRKHKNDDDTRASESKKPKTEDKNSSGHKPSSSRESSKQSSTKEKDLLPSPAGPILSKDSKTEHGSRKRTVSQSSSLKSSGTSSKENSGSSSKSSSSSTAKQKKTEGKGPSSSKEAKEKAPNSSSNCPPSTPTSESSKPRRTKLAFDD
IRESfinder result
IRESfinder score
0.449949035
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page