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mmu_circSec23b_1848
Basic information of circular RNA
PanCircBase ID:
mmu_circSec23b_1848
mm39_Chr. Position ID:
chr2|144408682|144429487|+
Gene name:
Sec23b
Transcript:
ENSMUST00000028916.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
15
Exon/intron indexes:
5,6,7,8,9,10,11,12,13,14,15,16,17,18,19
Exon/intron offsets:
0,338,1120,1853,2337,5716,7904,11569,12534,15181,16928,18835,19611,20103,20739
Genomic length:
20805
Exon/intron sizes in nt:
237,86,145,159,116,124,81,90,107,154,78,162,87,156,66
Flanking exon/introns:
chr2:144406572-144408682|chr2:144429487-144432205
Splice length:
1848
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGAGGTGCTCGGTCTCCTCTGATCTTTCTCTATGTGGTTGACACGTGTTTGGAGGAAGATGACCTTCAAGCACTCAAAGAGTCCCTGCAGATGTCTCTGAGTCTCCTTCCTCCAGATGCCCTGGTTGGTCTCATCACTTTTGGGAGGATGGTGCAGGTTCATGAGCTAAGCTGTGAAGGAATCTCCAAGAGCTATGTCTTCCGAGGGACCAAGGATTTAACTGCAAAGCAAATACAGGAGATGCTGGGCCTGACCAAGTCAGCCATGCCTGTGCAGCAAGCCAGACCTGCTCAACCTCAGGAGCAGCCTTTTGTTTCCAGCAGATTTCTACAGCCCATTCACAAGATTGACATGAACCTCACAGATCTTCTCGGGGAGCTGCAGAGGGACCCATGGCCAGTAACTCAGGGGAAGAGACCACTGCGGTCCACTGGTGTTGCTTTGTCCATTGCTGTTGGCTTGTTGGAGGGGACTTTCCCAAATACTGGAGCCAGGATCATGCTGTTCACTGGCGGGCCCCCGACCCAAGGACCTGGCATGGTGGTTGGAGATGAGTTGAAGACTCCTATTCGTTCCTGGCACGACATTGAGAAAGATAACGCACGATTCATGAAGAAGGCAACCAAGCATTATGAGATGCTTGCTAATCGAACTGCTACAAATGGCCACTGCATTGATATTTATGCTTGTGCCCTTGACCAAACTGGACTTCTGGAGATGAAGTGCTGTCCAAATCTTACAGGAGGCCACATGGTGATGGGAGATTCTTTCAACACTTCTCTTTTCAAGCAGACATTCCAAAGAATTTTTAGTAAAGACTTCAACGGAGATTTCAGAATGGCGTTTGGTGCTACGTTGGATGTAAAGACCTCTCGGGAACTGAAGATTGCAGGAGCCATTGGTCCATGCGTGTCTCTGAATGTGAAAGGGCCATGCGTGTCAGAAAATGAGCTTGGTGTTGGTGGCACAAGTCAGTGGAAGATCTGTGGCCTGGATCCCTCATCTACTCTTGGCATCTACTTTGAAGTTGTCAATCAGCACAATGCTCCAGTTCCCCAGGGAGGCAGAGGTGCCATCCAGTTTGTCACACAGTATCAGCATTCCAGCACTCAGAAGCGCATCCGAGTGACCACCATTGCCCGCAATTGGGCAGATGCACAGAGTCAGCTGAGGCACATAGAAGCAGCATTTGACCAGGAGGCCGCAGCAGTCCTGATGGCACGGCTTGGAGTGTTCCGCGCAGAGTCAGAGGAGGGGCCTGACGTGCTTCGGTGGCTGGATCGGCAACTCATCAGACTGTGTCAGAAGTTTGGGCAGTATAACAAAGAAGACCCTACGTCTTTCAGATTGTCAGACTCCTTTTCTCTGTATCCTCAGTTCATGTTCCATCTGAGAAGATCTCCATTTCTTCAAGTATTTAACAACAGTCCTGATGAGTCCTCCTATTATAGACACCATTTTGCCCGGCAGGATCTGACTCAGTCCCTCATTATGATCCAGCCCATTCTCTATTCTTACTCCTTCCACGGACCACCAGAGCCTGTACTCCTGGACAGCAGTAGCATTCTAGCTGACAGAATTCTGCTGATGGATACTTTCTTCCAAATTGTCATTTACCTTGGTGAGACCATAGCCCAGTGGCGGAAGGCTGGATACCAGGACATGCCCGAGTATGAAAACTTCAAGCACCTTCTTCAGGCGCCCCTGGATGATGCCCAAGAAATTCTGCAAGCACGCTTCCCAATGCCACGTTATATCAACACAGAGCATGGCGGCAGTCAGGCTCGGTTCCTGTTGTCTAAAGTTAACCCATCTCAGACACACAATAACCTGTATGCCTGGGGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTCGGTTCCTGTTGTCTA
59.39
AGAGACATCTGCAGGGACTCT
59.99
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCAACACAGAGCATGGCGG
61.03
CCTCCAAACACGTGTCAACC
59.34
148
PCR template sequence:
ACGTTATATCAACACAGAGCATGGCGGCAGTCAGGCTCGGTTCCTGTTGTCTAAAGTTAACCCATCTCAGACACACAATAACCTGTATGCCTGGGGGCAGAGAGGTGCTCGGTCTCCTCTGATCTTTCTCTATGTGGTTGACACGTGTTTGGAGGAAGATGACCTTCAAGCACTCAAAGAGTCCCTGCAGATGTCTCTGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-7b-5p(1), mmu-miR-31-5p(1), mmu-miR-18a-5p(1), mmu-miR-7a-5p(1), mmu-miR-23a-3p(1), mmu-miR-181b-5p(1), mmu-miR-149-5p(1), mmu-miR-351-5p(1), mmu-miR-362-5p(1), mmu-miR-383-5p(1), mmu-miR-680(1), mmu-miR-29b-2-5p(1), mmu-miR-673-5p(1), mmu-miR-335-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCCTGGGGGCAGAGAGGTGCTCGGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC23B_1848_ORF_1
1.077
0.219235964
1
3606
ORF sequence:
ATGTCTCTGAGTCTCCTTCCTCCAGATGCCCTGGTTGGTCTCATCACTTTTGGGAGGATGGTGCAGGTTCATGAGCTAAGCTGTGAAGGAATCTCCAAGAGCTATGTCTTCCGAGGGACCAAGGATTTAACTGCAAAGCAAATACAGGAGATGCTGGGCCTGACCAAGTCAGCCATGCCTGTGCAGCAAGCCAGACCTGCTCAACCTCAGGAGCAGCCTTTTGTTTCCAGCAGATTTCTACAGCCCATTCACAAGATTGACATGAACCTCACAGATCTTCTCGGGGAGCTGCAGAGGGACCCATGGCCAGTAACTCAGGGGAAGAGACCACTGCGGTCCACTGGTGTTGCTTTGTCCATTGCTGTTGGCTTGTTGGAGGGGACTTTCCCAAATACTGGAGCCAGGATCATGCTGTTCACTGGCGGGCCCCCGACCCAAGGACCTGGCATGGTGGTTGGAGATGAGTTGAAGACTCCTATTCGTTCCTGGCACGACATTGAGAAAGATAACGCACGATTCATGAAGAAGGCAACCAAGCATTATGAGATGCTTGCTAATCGAACTGCTACAAATGGCCACTGCATTGATATTTATGCTTGTGCCCTTGACCAAACTGGACTTCTGGAGATGAAGTGCTGTCCAAATCTTACAGGAGGCCACATGGTGATGGGAGATTCTTTCAACACTTCTCTTTTCAAGCAGACATTCCAAAGAATTTTTAGTAAAGACTTCAACGGAGATTTCAGAATGGCGTTTGGTGCTACGTTGGATGTAAAGACCTCTCGGGAACTGAAGATTGCAGGAGCCATTGGTCCATGCGTGTCTCTGAATGTGAAAGGGCCATGCGTGTCAGAAAATGAGCTTGGTGTTGGTGGCACAAGTCAGTGGAAGATCTGTGGCCTGGATCCCTCATCTACTCTTGGCATCTACTTTGAAGTTGTCAATCAGCACAATGCTCCAGTTCCCCAGGGAGGCAGAGGTGCCATCCAGTTTGTCACACAGTATCAGCATTCCAGCACTCAGAAGCGCATCCGAGTGACCACCATTGCCCGCAATTGGGCAGATGCACAGAGTCAGCTGAGGCACATAGAAGCAGCATTTGACCAGGAGGCCGCAGCAGTCCTGATGGCACGGCTTGGAGTGTTCCGCGCAGAGTCAGAGGAGGGGCCTGACGTGCTTCGGTGGCTGGATCGGCAACTCATCAGACTGTGTCAGAAGTTTGGGCAGTATAACAAAGAAGACCCTACGTCTTTCAGATTGTCAGACTCCTTTTCTCTGTATCCTCAGTTCATGTTCCATCTGAGAAGATCTCCATTTCTTCAAGTATTTAACAACAGTCCTGATGAGTCCTCCTATTATAGACACCATTTTGCCCGGCAGGATCTGACTCAGTCCCTCATTATGATCCAGCCCATTCTCTATTCTTACTCCTTCCACGGACCACCAGAGCCTGTACTCCTGGACAGCAGTAGCATTCTAGCTGACAGAATTCTGCTGATGGATACTTTCTTCCAAATTGTCATTTACCTTGGTGAGACCATAGCCCAGTGGCGGAAGGCTGGATACCAGGACATGCCCGAGTATGAAAACTTCAAGCACCTTCTTCAGGCGCCCCTGGATGATGCCCAAGAAATTCTGCAAGCACGCTTCCCAATGCCACGTTATATCAACACAGAGCATGGCGGCAGTCAGGCTCGGTTCCTGTTGTCTAAAGTTAACCCATCTCAGACACACAATAACCTGTATGCCTGGGGGCAGAGAGGTGCTCGGTCTCCTCTGATCTTTCTCTATGTGGTTGACACGTGTTTGGAGGAAGATGACCTTCAAGCACTCAAAGAGTCCCTGCAGATGTCTCTGAGTCTCCTTCCTCCAGATGCCCTGGTTGGTCTCATCACTTTTGGGAGGATGGTGCAGGTTCATGAGCTAAGCTGTGAAGGAATCTCCAAGAGCTATGTCTTCCGAGGGACCAAGGATTTAACTGCAAAGCAAATACAGGAGATGCTGGGCCTGACCAAGTCAGCCATGCCTGTGCAGCAAGCCAGACCTGCTCAACCTCAGGAGCAGCCTTTTGTTTCCAGCAGATTTCTACAGCCCATTCACAAGATTGACATGAACCTCACAGATCTTCTCGGGGAGCTGCAGAGGGACCCATGGCCAGTAACTCAGGGGAAGAGACCACTGCGGTCCACTGGTGTTGCTTTGTCCATTGCTGTTGGCTTGTTGGAGGGGACTTTCCCAAATACTGGAGCCAGGATCATGCTGTTCACTGGCGGGCCCCCGACCCAAGGACCTGGCATGGTGGTTGGAGATGAGTTGAAGACTCCTATTCGTTCCTGGCACGACATTGAGAAAGATAACGCACGATTCATGAAGAAGGCAACCAAGCATTATGAGATGCTTGCTAATCGAACTGCTACAAATGGCCACTGCATTGATATTTATGCTTGTGCCCTTGACCAAACTGGACTTCTGGAGATGAAGTGCTGTCCAAATCTTACAGGAGGCCACATGGTGATGGGAGATTCTTTCAACACTTCTCTTTTCAAGCAGACATTCCAAAGAATTTTTAGTAAAGACTTCAACGGAGATTTCAGAATGGCGTTTGGTGCTACGTTGGATGTAAAGACCTCTCGGGAACTGAAGATTGCAGGAGCCATTGGTCCATGCGTGTCTCTGAATGTGAAAGGGCCATGCGTGTCAGAAAATGAGCTTGGTGTTGGTGGCACAAGTCAGTGGAAGATCTGTGGCCTGGATCCCTCATCTACTCTTGGCATCTACTTTGAAGTTGTCAATCAGCACAATGCTCCAGTTCCCCAGGGAGGCAGAGGTGCCATCCAGTTTGTCACACAGTATCAGCATTCCAGCACTCAGAAGCGCATCCGAGTGACCACCATTGCCCGCAATTGGGCAGATGCACAGAGTCAGCTGAGGCACATAGAAGCAGCATTTGACCAGGAGGCCGCAGCAGTCCTGATGGCACGGCTTGGAGTGTTCCGCGCAGAGTCAGAGGAGGGGCCTGACGTGCTTCGGTGGCTGGATCGGCAACTCATCAGACTGTGTCAGAAGTTTGGGCAGTATAACAAAGAAGACCCTACGTCTTTCAGATTGTCAGACTCCTTTTCTCTGTATCCTCAGTTCATGTTCCATCTGAGAAGATCTCCATTTCTTCAAGTATTTAACAACAGTCCTGATGAGTCCTCCTATTATAGACACCATTTTGCCCGGCAGGATCTGACTCAGTCCCTCATTATGATCCAGCCCATTCTCTATTCTTACTCCTTCCACGGACCACCAGAGCCTGTACTCCTGGACAGCAGTAGCATTCTAGCTGACAGAATTCTGCTGATGGATACTTTCTTCCAAATTGTCATTTACCTTGGTGAGACCATAGCCCAGTGGCGGAAGGCTGGATACCAGGACATGCCCGAGTATGAAAACTTCAAGCACCTTCTTCAGGCGCCCCTGGATGATGCCCAAGAAATTCTGCAAGCACGCTTCCCAATGCCACGTTATATCAACACAGAGCATGGCGGCAGTCAGGCTCGGTTCCTGTTGTCTAAAGTTAACCCATCTCAGACACACAATAACCTGTATGCCTGGGGGCAG
Peptide sequence:
MSLSLLPPDALVGLITFGRMVQVHELSCEGISKSYVFRGTKDLTAKQIQEMLGLTKSAMPVQQARPAQPQEQPFVSSRFLQPIHKIDMNLTDLLGELQRDPWPVTQGKRPLRSTGVALSIAVGLLEGTFPNTGARIMLFTGGPPTQGPGMVVGDELKTPIRSWHDIEKDNARFMKKATKHYEMLANRTATNGHCIDIYACALDQTGLLEMKCCPNLTGGHMVMGDSFNTSLFKQTFQRIFSKDFNGDFRMAFGATLDVKTSRELKIAGAIGPCVSLNVKGPCVSENELGVGGTSQWKICGLDPSSTLGIYFEVVNQHNAPVPQGGRGAIQFVTQYQHSSTQKRIRVTTIARNWADAQSQLRHIEAAFDQEAAAVLMARLGVFRAESEEGPDVLRWLDRQLIRLCQKFGQYNKEDPTSFRLSDSFSLYPQFMFHLRRSPFLQVFNNSPDESSYYRHHFARQDLTQSLIMIQPILYSYSFHGPPEPVLLDSSSILADRILLMDTFFQIVIYLGETIAQWRKAGYQDMPEYENFKHLLQAPLDDAQEILQARFPMPRYINTEHGGSQARFLLSKVNPSQTHNNLYAWGQRGARSPLIFLYVVDTCLEEDDLQALKESLQMSLSLLPPDALVGLITFGRMVQVHELSCEGISKSYVFRGTKDLTAKQIQEMLGLTKSAMPVQQARPAQPQEQPFVSSRFLQPIHKIDMNLTDLLGELQRDPWPVTQGKRPLRSTGVALSIAVGLLEGTFPNTGARIMLFTGGPPTQGPGMVVGDELKTPIRSWHDIEKDNARFMKKATKHYEMLANRTATNGHCIDIYACALDQTGLLEMKCCPNLTGGHMVMGDSFNTSLFKQTFQRIFSKDFNGDFRMAFGATLDVKTSRELKIAGAIGPCVSLNVKGPCVSENELGVGGTSQWKICGLDPSSTLGIYFEVVNQHNAPVPQGGRGAIQFVTQYQHSSTQKRIRVTTIARNWADAQSQLRHIEAAFDQEAAAVLMARLGVFRAESEEGPDVLRWLDRQLIRLCQKFGQYNKEDPTSFRLSDSFSLYPQFMFHLRRSPFLQVFNNSPDESSYYRHHFARQDLTQSLIMIQPILYSYSFHGPPEPVLLDSSSILADRILLMDTFFQIVIYLGETIAQWRKAGYQDMPEYENFKHLLQAPLDDAQEILQARFPMPRYINTEHGGSQARFLLSKVNPSQTHNNLYAWGQ
IRESfinder result
IRESfinder score
0.541685524
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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