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mmu_circCog4_807
Basic information of circular RNA
PanCircBase ID:
mmu_circCog4_807
mm39_Chr. Position ID:
chr8|111577967|111586576|+
Gene name:
Cog4
Transcript:
ENSMUST00000165867.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
3,4,5,6,7,8
Exon/intron offsets:
0,950,2334,6601,7201,8550
Genomic length:
8609
Exon/intron sizes in nt:
115,175,194,106,158,59
Flanking exon/introns:
chr8:111576582-111577967|chr8:111586576-111589882
Splice length:
807
Other database IDs:
CIRCpedia: MMU_CIRCpedia_40236, circAtlas: mmu-Cog4_0004
circAtlas: hsa-COG4_0009, CIRCpedia: HSA_CIRCpedia_18518
Human Ortholog IDs:
Mature spliced Sequence:
TCCCAGCCTGCAGTTGATTGAGGGAGACGCAAAGCAACTGGCTGGAATGATCACCTTTACCTGCAGCCTAGCTGAAAACGTGTCGAGCAAAGTCCGTCAGCTTGACCTGGCCAAGAACCGCCTCTATCAGGCCATTCAGAGAGCCGATGACATCTTGGACCTGAAGTTCTGCATGGATGGAGTTCAGACTGCTTTGAGGAATGAGGATTATGAGCAGGCTGCAGCCCACATTCATCGTTACTTGTGCCTGGACAAGTCAGTCATTGAGCTCAGCCGACAAGGCAAAGAAGGAAGCATGATTGATGCCAACCTGAAATTACTGCAGGAAGCTGAGCAACGTCTTAAGGCCATAGTCGCAGAGAAGTTTGCTATCGCTACCAAAGAAGGTGATTTGCCCCAGGTGGAGCGATTCTTCAAGATCTTCCCACTGCTGGGTTTACATGAGGATGGCCTGAGCAAGTTCTCGGAATACCTGTGCAAACAGGTCGCCAGTAAGGCTGAGGAGAATCTGTTGTTGGTGCTGGGCTCAGACATGAGTGATCGGAGAGCTGCGGTCATCTTTGCGGATACTCTCACACTCCTGTTTGAAGGGATCGCCCGAATTGTGGAAACTCACCAACCCATCGTGGAGACTTACTATGGACCAGGGCGACTCTTTACCCTGATCAAATATCTTCAAGTAGAATGTGACACACAGGTGGAGAAGGTCGTAAACAAGTTCATCAAGCAAAGGGACTACCACCAGCAGTTTCGGCTCGTCCAGAGTAATTTGATGAGAAATTCTGCAACAGAAAAAATTGAACCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTACCACCAGCAGTTTCGG
59.97
GCTAGGCTGCAGGTAAAGGT
59.75
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTACCACCAGCAGTTTCGG
59.97
TTGCTCGACACGTTTTCAGC
59.7
163
PCR template sequence:
TCGTAAACAAGTTCATCAAGCAAAGGGACTACCACCAGCAGTTTCGGCTCGTCCAGAGTAATTTGATGAGAAATTCTGCAACAGAAAAAATTGAACCAAGTCCCAGCCTGCAGTTGATTGAGGGAGACGCAAAGCAACTGGCTGGAATGATCACCTTTACCTGCAGCCTAGCTGAAAACGTGTCGAGCAAAGTCCGTCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-122-5p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAATTGAACCAAGTCCCAGCCTGCAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCOG4_807_ORF_1
1.2274
0.403985813
0.999952474
1566
ORF sequence:
ATGATCACCTTTACCTGCAGCCTAGCTGAAAACGTGTCGAGCAAAGTCCGTCAGCTTGACCTGGCCAAGAACCGCCTCTATCAGGCCATTCAGAGAGCCGATGACATCTTGGACCTGAAGTTCTGCATGGATGGAGTTCAGACTGCTTTGAGGAATGAGGATTATGAGCAGGCTGCAGCCCACATTCATCGTTACTTGTGCCTGGACAAGTCAGTCATTGAGCTCAGCCGACAAGGCAAAGAAGGAAGCATGATTGATGCCAACCTGAAATTACTGCAGGAAGCTGAGCAACGTCTTAAGGCCATAGTCGCAGAGAAGTTTGCTATCGCTACCAAAGAAGGTGATTTGCCCCAGGTGGAGCGATTCTTCAAGATCTTCCCACTGCTGGGTTTACATGAGGATGGCCTGAGCAAGTTCTCGGAATACCTGTGCAAACAGGTCGCCAGTAAGGCTGAGGAGAATCTGTTGTTGGTGCTGGGCTCAGACATGAGTGATCGGAGAGCTGCGGTCATCTTTGCGGATACTCTCACACTCCTGTTTGAAGGGATCGCCCGAATTGTGGAAACTCACCAACCCATCGTGGAGACTTACTATGGACCAGGGCGACTCTTTACCCTGATCAAATATCTTCAAGTAGAATGTGACACACAGGTGGAGAAGGTCGTAAACAAGTTCATCAAGCAAAGGGACTACCACCAGCAGTTTCGGCTCGTCCAGAGTAATTTGATGAGAAATTCTGCAACAGAAAAAATTGAACCAAGTCCCAGCCTGCAGTTGATTGAGGGAGACGCAAAGCAACTGGCTGGAATGATCACCTTTACCTGCAGCCTAGCTGAAAACGTGTCGAGCAAAGTCCGTCAGCTTGACCTGGCCAAGAACCGCCTCTATCAGGCCATTCAGAGAGCCGATGACATCTTGGACCTGAAGTTCTGCATGGATGGAGTTCAGACTGCTTTGAGGAATGAGGATTATGAGCAGGCTGCAGCCCACATTCATCGTTACTTGTGCCTGGACAAGTCAGTCATTGAGCTCAGCCGACAAGGCAAAGAAGGAAGCATGATTGATGCCAACCTGAAATTACTGCAGGAAGCTGAGCAACGTCTTAAGGCCATAGTCGCAGAGAAGTTTGCTATCGCTACCAAAGAAGGTGATTTGCCCCAGGTGGAGCGATTCTTCAAGATCTTCCCACTGCTGGGTTTACATGAGGATGGCCTGAGCAAGTTCTCGGAATACCTGTGCAAACAGGTCGCCAGTAAGGCTGAGGAGAATCTGTTGTTGGTGCTGGGCTCAGACATGAGTGATCGGAGAGCTGCGGTCATCTTTGCGGATACTCTCACACTCCTGTTTGAAGGGATCGCCCGAATTGTGGAAACTCACCAACCCATCGTGGAGACTTACTATGGACCAGGGCGACTCTTTACCCTGATCAAATATCTTCAAGTAGAATGTGACACACAGGTGGAGAAGGTCGTAAACAAGTTCATCAAGCAAAGGGACTACCACCAGCAGTTTCGGCTCGTCCAGAGTAATTTGATGAGAAATTCTGCAACAGAAAAAATTGAACCA
Peptide sequence:
MITFTCSLAENVSSKVRQLDLAKNRLYQAIQRADDILDLKFCMDGVQTALRNEDYEQAAAHIHRYLCLDKSVIELSRQGKEGSMIDANLKLLQEAEQRLKAIVAEKFAIATKEGDLPQVERFFKIFPLLGLHEDGLSKFSEYLCKQVASKAEENLLLVLGSDMSDRRAAVIFADTLTLLFEGIARIVETHQPIVETYYGPGRLFTLIKYLQVECDTQVEKVVNKFIKQRDYHQQFRLVQSNLMRNSATEKIEPSPSLQLIEGDAKQLAGMITFTCSLAENVSSKVRQLDLAKNRLYQAIQRADDILDLKFCMDGVQTALRNEDYEQAAAHIHRYLCLDKSVIELSRQGKEGSMIDANLKLLQEAEQRLKAIVAEKFAIATKEGDLPQVERFFKIFPLLGLHEDGLSKFSEYLCKQVASKAEENLLLVLGSDMSDRRAAVIFADTLTLLFEGIARIVETHQPIVETYYGPGRLFTLIKYLQVECDTQVEKVVNKFIKQRDYHQQFRLVQSNLMRNSATEKIEP
IRESfinder result
IRESfinder score
0.454961073
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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