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mmu_circAbcb4_2108
Basic information of circular RNA
PanCircBase ID:
mmu_circAbcb4_2108
mm39_Chr. Position ID:
chr5|8955974|8988656|+
Gene name:
Abcb4
Transcript:
ENSMUST00000003717.13
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:
0,1233,3127,4644,8981,12684,14045,14360,21796,22432,24767,28181,29201,30810,32604
Genomic length:
32682
Exon/intron sizes in nt:
58,192,172,125,172,114,111,126,204,171,162,171,147,105,78
Flanking exon/introns:
chr5:8949718-8955974|chr5:8988656-8989833
Splice length:
2108
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TGAATTTTTCATTGTCAATGCTAAATCCAGGAAGAATTTTGGAAGAAGAAATGACTAGATATGCATACTACTATTCGGGACTAGGTGGTGGAGTTCTTGTGGCTGCCTATATCCAAGTCTCATTCTGGACTTTGGCAGCTGGCCGACAAATAAAGAAAATCAGGCAAAAATTTTTTCATGCCATCCTCCGACAAGAAATGGGCTGGTTTGACATCAAGGGCACCACTGAACTCAACACACGTCTAACAGATGACGTCTCCAAAATCAGTGAAGGAATTGGTGACAAGGTTGGAATGTTCTTTCAAGCAATAGCCACGTTTTTTGCAGGATTCATAGTGGGGTTCATCAGAGGATGGAAGCTCACCCTCGTGATCATGGCCATCAGCCCCATCCTGGGGCTCTCTACAGCTGTTTGGGCAAAGATACTCTCAACATTTAGTGACAAAGAGCTAGCTGCATATGCAAAAGCAGGTGCCGTGGCTGAAGAGGCTCTGGGAGCCATCAGGACCGTGATAGCTTTCGGGGGCCAGAACAAAGAGCTAGAAAGGTATCAGAAACATTTAGAAAATGCCAAAAAGATTGGAATTAAAAAGGCTATCTCAGCCAACATCTCCATGGGTATTGCTTTCTTGTTAATATATGCATCCTATGCACTGGCCTTCTGGTATGGATCCACTCTGGTTATATCAAAAGAATATACAATTGGAAATGCAATGACAGTCTTCTTCTCAATCCTCATCGGGGCTTTCAGTGTGGGGCAGGCTGCCCCCTGTATTGATGCTTTCGCTAATGCAAGAGGAGCAGCCTATGTGATCTTTGACATTATTGATAATAATCCTAAAATTGACAGTTTTTCAGAGAGAGGACACAAACCAGACAACATCAAAGGAAATTTGGAGTTCAGTGATGTTCATTTTTCCTATCCATCTCGGGCTAATATCAAGATCTTGAAGGGCCTCAACCTGAAGGTGAAGAGTGGACAGACAGTGGCTCTGGTTGGCAACAGCGGCTGTGGAAAAAGCACAACTGTCCAGCTGCTGCAGAGGCTCTACGACCCCACAGAGGGTAAGATTAGCATCGATGGGCAGGATATCAGGAACTTTAACGTCAGGTGTCTAAGGGAAATCATTGGTGTGGTAAGTCAAGAGCCCGTGCTGTTCTCTACTACGATCGCTGAAAATATCCGCTATGGCCGTGGGAATGTAACGATGGATGAGATTGAGAAAGCCGTCAAAGAGGCCAATGCCTATGACTTCATCATGAAACTGCCCCAGAAATTTGACACCCTGGTTGGTGATAGAGGGGCGCAGCTGAGTGGGGGACAGAAACAGAGAATCGCCATTGCCCGGGCCCTGGTCCGCAACCCCAAGATCCTCCTGCTGGACGAGGCCACCTCAGCCCTGGACACTGAAAGTGAAGCTGAGGTGCAGGCCGCACTGGATAAGGCCAGAGAAGGCCGAACCACCATTGTGATAGCTCACCGATTGTCTACCATCCGGAACGCAGATGTCATCGCTGGGTTTGAGGATGGAGTCATTGTGGAACAAGGAAGTCACAGTGAGCTGATGAAGAAGGAAGGGATCTACTTCAGACTCGTTAACATGCAGACAGCAGGAAGCCAGATCCTGTCAGAAGAATTTGAAGTTGAGCTAAGTGACGAAAAGGCTGCTGGAGATGTGGCCCCAAATGGCTGGAAAGCACGCATATTTAGGAATTCTACAAAGAAAAGTCTTAAAAGTCCACATCAGAATAGGCTGGATGAAGAAACCAATGAACTTGATGCAAACGTGCCACCAGTGTCTTTTCTGAAGGTCTTAAAACTGAATAAAACAGAGTGGCCCTACTTTGTGGTGGGAACAGTCTGTGCCATTGCCAATGGAGCCCTCCAGCCGGCTTTCTCCATCATCCTGTCTGAGATGATAGCTATCTTTGGCCCTGGGGATGACGCAGTGAAGCAGCAAAAGTGTAACATGTTCTCCCTGGTCTTCTTGGGCCTAGGAGTCCTCTCCTTCTTTACTTTCTTCCTTCAGGGCTTCACGTTTGGGAAAGCTGGAGAGATCCTCACCACAAGGCTCCGGTCCATGGCCTTTAAAGCGATGCTAAGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTCCTTCAGGGCTTCACGT
59.96
TCCACCACCTAGTCCCGAAT
59.96
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGGCTTCACGTTTGGGAAA
60.11
TCCACCACCTAGTCCCGAAT
59.96
172
PCR template sequence:
CTTCTTTACTTTCTTCCTTCAGGGCTTCACGTTTGGGAAAGCTGGAGAGATCCTCACCACAAGGCTCCGGTCCATGGCCTTTAAAGCGATGCTAAGGCAGTGAATTTTTCATTGTCAATGCTAAATCCAGGAAGAATTTTGGAAGAAGAAATGACTAGATATGCATACTACTATTCGGGACTAGGTGGTGGAGTTCTTGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-182-5p(2), mmu-miR-137-3p(1), mmu-miR-7b-5p(1), mmu-miR-7a-5p(1), mmu-miR-320-3p(1), mmu-miR-433-3p(1), mmu-miR-433-5p(1), mmu-miR-22-3p(1), mmu-miR-199b-3p(1), mmu-miR-218-5p(1), mmu-miR-199a-3p(1), mmu-miR-183-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-410-3p(1), mmu-miR-344d-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GATGCTAAGGCAGTGAATTTTTCATT
siRNA sets
AAAATTCACTGCCTTAGCA, AATGAAAAATTCACTGCCT, AAAAATTCACTGCCTTAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCB4_2108_ORF_1
1.175
0.263146703
0.999997807
2094
ORF sequence:
ATGCTAAATCCAGGAAGAATTTTGGAAGAAGAAATGACTAGATATGCATACTACTATTCGGGACTAGGTGGTGGAGTTCTTGTGGCTGCCTATATCCAAGTCTCATTCTGGACTTTGGCAGCTGGCCGACAAATAAAGAAAATCAGGCAAAAATTTTTTCATGCCATCCTCCGACAAGAAATGGGCTGGTTTGACATCAAGGGCACCACTGAACTCAACACACGTCTAACAGATGACGTCTCCAAAATCAGTGAAGGAATTGGTGACAAGGTTGGAATGTTCTTTCAAGCAATAGCCACGTTTTTTGCAGGATTCATAGTGGGGTTCATCAGAGGATGGAAGCTCACCCTCGTGATCATGGCCATCAGCCCCATCCTGGGGCTCTCTACAGCTGTTTGGGCAAAGATACTCTCAACATTTAGTGACAAAGAGCTAGCTGCATATGCAAAAGCAGGTGCCGTGGCTGAAGAGGCTCTGGGAGCCATCAGGACCGTGATAGCTTTCGGGGGCCAGAACAAAGAGCTAGAAAGGTATCAGAAACATTTAGAAAATGCCAAAAAGATTGGAATTAAAAAGGCTATCTCAGCCAACATCTCCATGGGTATTGCTTTCTTGTTAATATATGCATCCTATGCACTGGCCTTCTGGTATGGATCCACTCTGGTTATATCAAAAGAATATACAATTGGAAATGCAATGACAGTCTTCTTCTCAATCCTCATCGGGGCTTTCAGTGTGGGGCAGGCTGCCCCCTGTATTGATGCTTTCGCTAATGCAAGAGGAGCAGCCTATGTGATCTTTGACATTATTGATAATAATCCTAAAATTGACAGTTTTTCAGAGAGAGGACACAAACCAGACAACATCAAAGGAAATTTGGAGTTCAGTGATGTTCATTTTTCCTATCCATCTCGGGCTAATATCAAGATCTTGAAGGGCCTCAACCTGAAGGTGAAGAGTGGACAGACAGTGGCTCTGGTTGGCAACAGCGGCTGTGGAAAAAGCACAACTGTCCAGCTGCTGCAGAGGCTCTACGACCCCACAGAGGGTAAGATTAGCATCGATGGGCAGGATATCAGGAACTTTAACGTCAGGTGTCTAAGGGAAATCATTGGTGTGGTAAGTCAAGAGCCCGTGCTGTTCTCTACTACGATCGCTGAAAATATCCGCTATGGCCGTGGGAATGTAACGATGGATGAGATTGAGAAAGCCGTCAAAGAGGCCAATGCCTATGACTTCATCATGAAACTGCCCCAGAAATTTGACACCCTGGTTGGTGATAGAGGGGCGCAGCTGAGTGGGGGACAGAAACAGAGAATCGCCATTGCCCGGGCCCTGGTCCGCAACCCCAAGATCCTCCTGCTGGACGAGGCCACCTCAGCCCTGGACACTGAAAGTGAAGCTGAGGTGCAGGCCGCACTGGATAAGGCCAGAGAAGGCCGAACCACCATTGTGATAGCTCACCGATTGTCTACCATCCGGAACGCAGATGTCATCGCTGGGTTTGAGGATGGAGTCATTGTGGAACAAGGAAGTCACAGTGAGCTGATGAAGAAGGAAGGGATCTACTTCAGACTCGTTAACATGCAGACAGCAGGAAGCCAGATCCTGTCAGAAGAATTTGAAGTTGAGCTAAGTGACGAAAAGGCTGCTGGAGATGTGGCCCCAAATGGCTGGAAAGCACGCATATTTAGGAATTCTACAAAGAAAAGTCTTAAAAGTCCACATCAGAATAGGCTGGATGAAGAAACCAATGAACTTGATGCAAACGTGCCACCAGTGTCTTTTCTGAAGGTCTTAAAACTGAATAAAACAGAGTGGCCCTACTTTGTGGTGGGAACAGTCTGTGCCATTGCCAATGGAGCCCTCCAGCCGGCTTTCTCCATCATCCTGTCTGAGATGATAGCTATCTTTGGCCCTGGGGATGACGCAGTGAAGCAGCAAAAGTGTAACATGTTCTCCCTGGTCTTCTTGGGCCTAGGAGTCCTCTCCTTCTTTACTTTCTTCCTTCAGGGCTTCACGTTTGGGAAAGCTGGAGAGATCCTCACCACAAGGCTCCGGTCCATGGCCTTTAAAGCGATGCTAAGGCAGTGA
Peptide sequence:
MLNPGRILEEEMTRYAYYYSGLGGGVLVAAYIQVSFWTLAAGRQIKKIRQKFFHAILRQEMGWFDIKGTTELNTRLTDDVSKISEGIGDKVGMFFQAIATFFAGFIVGFIRGWKLTLVIMAISPILGLSTAVWAKILSTFSDKELAAYAKAGAVAEEALGAIRTVIAFGGQNKELERYQKHLENAKKIGIKKAISANISMGIAFLLIYASYALAFWYGSTLVISKEYTIGNAMTVFFSILIGAFSVGQAAPCIDAFANARGAAYVIFDIIDNNPKIDSFSERGHKPDNIKGNLEFSDVHFSYPSRANIKILKGLNLKVKSGQTVALVGNSGCGKSTTVQLLQRLYDPTEGKISIDGQDIRNFNVRCLREIIGVVSQEPVLFSTTIAENIRYGRGNVTMDEIEKAVKEANAYDFIMKLPQKFDTLVGDRGAQLSGGQKQRIAIARALVRNPKILLLDEATSALDTESEAEVQAALDKAREGRTTIVIAHRLSTIRNADVIAGFEDGVIVEQGSHSELMKKEGIYFRLVNMQTAGSQILSEEFEVELSDEKAAGDVAPNGWKARIFRNSTKKSLKSPHQNRLDEETNELDANVPPVSFLKVLKLNKTEWPYFVVGTVCAIANGALQPAFSIILSEMIAIFGPGDDAVKQQKCNMFSLVFLGLGVLSFFTFFLQGFTFGKAGEILTTRLRSMAFKAMLRQ
IRESfinder result
IRESfinder score
0.496662753
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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