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mmu_circAbcb4_1311
Basic information of circular RNA
PanCircBase ID:
mmu_circAbcb4_1311
mm39_Chr. Position ID:
chr5|8968658|8986889|+
Gene name:
Abcb4
Transcript:
ENSMUST00000003717.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
10,11,12,13,14,15,16,17,18
Exon/intron offsets:
0,1361,1676,9112,9748,12083,15497,16517,18126
Genomic length:
18231
Exon/intron sizes in nt:
11,41,11,12,62,04,17,10,00,00,00,00,000
Flanking exon/introns:
chr5:8965127-8968658|chr5:8986889-8988578
Splice length:
1311
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTCTTCTTCTCAATCCTCATCGGGGCTTTCAGTGTGGGGCAGGCTGCCCCCTGTATTGATGCTTTCGCTAATGCAAGAGGAGCAGCCTATGTGATCTTTGACATTATTGATAATAATCCTAAAATTGACAGTTTTTCAGAGAGAGGACACAAACCAGACAACATCAAAGGAAATTTGGAGTTCAGTGATGTTCATTTTTCCTATCCATCTCGGGCTAATATCAAGATCTTGAAGGGCCTCAACCTGAAGGTGAAGAGTGGACAGACAGTGGCTCTGGTTGGCAACAGCGGCTGTGGAAAAAGCACAACTGTCCAGCTGCTGCAGAGGCTCTACGACCCCACAGAGGGTAAGATTAGCATCGATGGGCAGGATATCAGGAACTTTAACGTCAGGTGTCTAAGGGAAATCATTGGTGTGGTAAGTCAAGAGCCCGTGCTGTTCTCTACTACGATCGCTGAAAATATCCGCTATGGCCGTGGGAATGTAACGATGGATGAGATTGAGAAAGCCGTCAAAGAGGCCAATGCCTATGACTTCATCATGAAACTGCCCCAGAAATTTGACACCCTGGTTGGTGATAGAGGGGCGCAGCTGAGTGGGGGACAGAAACAGAGAATCGCCATTGCCCGGGCCCTGGTCCGCAACCCCAAGATCCTCCTGCTGGACGAGGCCACCTCAGCCCTGGACACTGAAAGTGAAGCTGAGGTGCAGGCCGCACTGGATAAGGCCAGAGAAGGCCGAACCACCATTGTGATAGCTCACCGATTGTCTACCATCCGGAACGCAGATGTCATCGCTGGGTTTGAGGATGGAGTCATTGTGGAACAAGGAAGTCACAGTGAGCTGATGAAGAAGGAAGGGATCTACTTCAGACTCGTTAACATGCAGACAGCAGGAAGCCAGATCCTGTCAGAAGAATTTGAAGTTGAGCTAAGTGACGAAAAGGCTGCTGGAGATGTGGCCCCAAATGGCTGGAAAGCACGCATATTTAGGAATTCTACAAAGAAAAGTCTTAAAAGTCCACATCAGAATAGGCTGGATGAAGAAACCAATGAACTTGATGCAAACGTGCCACCAGTGTCTTTTCTGAAGGTCTTAAAACTGAATAAAACAGAGTGGCCCTACTTTGTGGTGGGAACAGTCTGTGCCATTGCCAATGGAGCCCTCCAGCCGGCTTTCTCCATCATCCTGTCTGAGATGATAGCTATCTTTGGCCCTGGGGATGACGCAGTGAAGCAGCAAAAGTGTAACATGTTCTCCCTGGTCTTCTTGGGCCTAGGAGTCCTCTCCTTCTTTACTTTCTTCCTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGCAGTGAAGCAGCAAAAGT
59.97
CATAGGCTGCTCCTCTTGCA
59.82
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGCAGTGAAGCAGCAAAAG
59.97
CATAGGCTGCTCCTCTTGCA
59.82
177
PCR template sequence:
TGGCCCTGGGGATGACGCAGTGAAGCAGCAAAAGTGTAACATGTTCTCCCTGGTCTTCTTGGGCCTAGGAGTCCTCTCCTTCTTTACTTTCTTCCTTCAGGTCTTCTTCTCAATCCTCATCGGGGCTTTCAGTGTGGGGCAGGCTGCCCCCTGTATTGATGCTTTCGCTAATGCAAGAGGAGCAGCCTATGTGATCTTTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-320-3p(1), mmu-miR-433-3p(1), mmu-miR-433-5p(1), mmu-miR-182-5p(1), mmu-miR-218-5p(1), mmu-miR-183-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTCTTCCTTCAGGTCTTCTTCTCAA
siRNA sets
GAGAAGAAGACCTGAAGGA, TTGAGAAGAAGACCTGAAG, TGAGAAGAAGACCTGAAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCB4_1311_ORF_1
1.1494
0.356805183
0.99999886
2133
ORF sequence:
ATGGATGAGATTGAGAAAGCCGTCAAAGAGGCCAATGCCTATGACTTCATCATGAAACTGCCCCAGAAATTTGACACCCTGGTTGGTGATAGAGGGGCGCAGCTGAGTGGGGGACAGAAACAGAGAATCGCCATTGCCCGGGCCCTGGTCCGCAACCCCAAGATCCTCCTGCTGGACGAGGCCACCTCAGCCCTGGACACTGAAAGTGAAGCTGAGGTGCAGGCCGCACTGGATAAGGCCAGAGAAGGCCGAACCACCATTGTGATAGCTCACCGATTGTCTACCATCCGGAACGCAGATGTCATCGCTGGGTTTGAGGATGGAGTCATTGTGGAACAAGGAAGTCACAGTGAGCTGATGAAGAAGGAAGGGATCTACTTCAGACTCGTTAACATGCAGACAGCAGGAAGCCAGATCCTGTCAGAAGAATTTGAAGTTGAGCTAAGTGACGAAAAGGCTGCTGGAGATGTGGCCCCAAATGGCTGGAAAGCACGCATATTTAGGAATTCTACAAAGAAAAGTCTTAAAAGTCCACATCAGAATAGGCTGGATGAAGAAACCAATGAACTTGATGCAAACGTGCCACCAGTGTCTTTTCTGAAGGTCTTAAAACTGAATAAAACAGAGTGGCCCTACTTTGTGGTGGGAACAGTCTGTGCCATTGCCAATGGAGCCCTCCAGCCGGCTTTCTCCATCATCCTGTCTGAGATGATAGCTATCTTTGGCCCTGGGGATGACGCAGTGAAGCAGCAAAAGTGTAACATGTTCTCCCTGGTCTTCTTGGGCCTAGGAGTCCTCTCCTTCTTTACTTTCTTCCTTCAGGTCTTCTTCTCAATCCTCATCGGGGCTTTCAGTGTGGGGCAGGCTGCCCCCTGTATTGATGCTTTCGCTAATGCAAGAGGAGCAGCCTATGTGATCTTTGACATTATTGATAATAATCCTAAAATTGACAGTTTTTCAGAGAGAGGACACAAACCAGACAACATCAAAGGAAATTTGGAGTTCAGTGATGTTCATTTTTCCTATCCATCTCGGGCTAATATCAAGATCTTGAAGGGCCTCAACCTGAAGGTGAAGAGTGGACAGACAGTGGCTCTGGTTGGCAACAGCGGCTGTGGAAAAAGCACAACTGTCCAGCTGCTGCAGAGGCTCTACGACCCCACAGAGGGTAAGATTAGCATCGATGGGCAGGATATCAGGAACTTTAACGTCAGGTGTCTAAGGGAAATCATTGGTGTGGTAAGTCAAGAGCCCGTGCTGTTCTCTACTACGATCGCTGAAAATATCCGCTATGGCCGTGGGAATGTAACGATGGATGAGATTGAGAAAGCCGTCAAAGAGGCCAATGCCTATGACTTCATCATGAAACTGCCCCAGAAATTTGACACCCTGGTTGGTGATAGAGGGGCGCAGCTGAGTGGGGGACAGAAACAGAGAATCGCCATTGCCCGGGCCCTGGTCCGCAACCCCAAGATCCTCCTGCTGGACGAGGCCACCTCAGCCCTGGACACTGAAAGTGAAGCTGAGGTGCAGGCCGCACTGGATAAGGCCAGAGAAGGCCGAACCACCATTGTGATAGCTCACCGATTGTCTACCATCCGGAACGCAGATGTCATCGCTGGGTTTGAGGATGGAGTCATTGTGGAACAAGGAAGTCACAGTGAGCTGATGAAGAAGGAAGGGATCTACTTCAGACTCGTTAACATGCAGACAGCAGGAAGCCAGATCCTGTCAGAAGAATTTGAAGTTGAGCTAAGTGACGAAAAGGCTGCTGGAGATGTGGCCCCAAATGGCTGGAAAGCACGCATATTTAGGAATTCTACAAAGAAAAGTCTTAAAAGTCCACATCAGAATAGGCTGGATGAAGAAACCAATGAACTTGATGCAAACGTGCCACCAGTGTCTTTTCTGAAGGTCTTAAAACTGAATAAAACAGAGTGGCCCTACTTTGTGGTGGGAACAGTCTGTGCCATTGCCAATGGAGCCCTCCAGCCGGCTTTCTCCATCATCCTGTCTGAGATGATAGCTATCTTTGGCCCTGGGGATGACGCAGTGAAGCAGCAAAAGTGTAACATGTTCTCCCTGGTCTTCTTGGGCCTAGGAGTCCTCTCCTTCTTTACTTTCTTCCTTCAG
Peptide sequence:
MDEIEKAVKEANAYDFIMKLPQKFDTLVGDRGAQLSGGQKQRIAIARALVRNPKILLLDEATSALDTESEAEVQAALDKAREGRTTIVIAHRLSTIRNADVIAGFEDGVIVEQGSHSELMKKEGIYFRLVNMQTAGSQILSEEFEVELSDEKAAGDVAPNGWKARIFRNSTKKSLKSPHQNRLDEETNELDANVPPVSFLKVLKLNKTEWPYFVVGTVCAIANGALQPAFSIILSEMIAIFGPGDDAVKQQKCNMFSLVFLGLGVLSFFTFFLQVFFSILIGAFSVGQAAPCIDAFANARGAAYVIFDIIDNNPKIDSFSERGHKPDNIKGNLEFSDVHFSYPSRANIKILKGLNLKVKSGQTVALVGNSGCGKSTTVQLLQRLYDPTEGKISIDGQDIRNFNVRCLREIIGVVSQEPVLFSTTIAENIRYGRGNVTMDEIEKAVKEANAYDFIMKLPQKFDTLVGDRGAQLSGGQKQRIAIARALVRNPKILLLDEATSALDTESEAEVQAALDKAREGRTTIVIAHRLSTIRNADVIAGFEDGVIVEQGSHSELMKKEGIYFRLVNMQTAGSQILSEEFEVELSDEKAAGDVAPNGWKARIFRNSTKKSLKSPHQNRLDEETNELDANVPPVSFLKVLKLNKTEWPYFVVGTVCAIANGALQPAFSIILSEMIAIFGPGDDAVKQQKCNMFSLVFLGLGVLSFFTFFLQ
IRESfinder result
IRESfinder score
0.512783086
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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