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mmu_circOfd1_2212
Basic information of circular RNA
PanCircBase ID:
mmu_circOfd1_2212
mm39_Chr. Position ID:
chrX|165186537|165214866|-
Gene name:
Ofd1
Transcript:
ENSMUST00000049501.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
15
Exon/intron indexes:
18,17,16,15,14,13,12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,1884,2455,5047,5946,7064,8274,9759,11434,21434,23278,23626,24986,28147,28260
Genomic length:
28329
Exon/intron sizes in nt:
98,157,612,112,131,190,92,74,120,107,174,137,108,31,69
Flanking exon/introns:
chrX:165184029-165186537|chrX:165214866-165218330
Splice length:
2212
Other database IDs:
CIRCpedia: MMU_CIRCpedia_11587, circAtlas: mmu-Ofd1_0004
CIRCpedia: HSA_CIRCpedia_351605
Human Ortholog IDs:
Mature spliced Sequence:
ATATTTACTATGCAGGATCTACTACAACTCATTCGGATTAACCCCTCATCCAGTCTCTATAAATCATTGATTTCAGGATTTGATAAAGAAAATAAAAAAGGTTTTCTTATGAGTTTCTTAAAGGAGTTGGCAGAATATTATCAAGCTAAAGAGAGCTGTGATGCGGAAACTCAGACAAGCACCACATTTCCCAGCCAAGTGTCCCTAGCCGAGAAGTTTCAGCTTATTGACGCTCAATTTGCAGATGGTTTTCCTCACCGTTCCAAGCTAGAATCTTTAGAGACAAAGTTAAACGAGTATAAGAAAGAAGTACAACACCAGCTTCAGGTAGAAATGTGTCATAAGCTGAAGTATTTTAGAGAAGCTGAAATAACAAAAGTTAAGATGGAAGAGAGAAGAAAGTATGAAAAGGAATTGGCTGAGTTCCAGAATGAATTTGAAAGAACTTGTCAAGCAAAAAATGAAGCCCTCATTTCTCAGGAGAAGAATTCTCTGGAAAGAATTAAAAAACACCGAGAGATGGAATCAAAAGAAATTTATGCTCAAAGACAGCTTCTACTAAATGATATAGCTTTGCTTAGAGGTAGAGAAGCAGAGCTGAAGGAGCGAATCGAAACTTTTGAATTGACCCAGAAGCTCCAAGAAGAAAAAATTAAAAGTGAGGCTGAGGCACTTGAGAGACGGGAACAGAATCTGAAGAATATTGAAGACACCTATGATCAGAAACTCAAAACTGAACTGCTAAAGTACCAACTGGAGCTAAAGGATGACTACATCACTAGGACAAATAAACTCCTGGAAGAGGAAAGGAAGAATAAAGAAAAAACTATTCATTTGCAAGAGGAGCTCACAGTTATTAATTCAAAAAAGGAAGAACTCAGTAAATCTGTTAAGCATATGAAAGAAGTTGAGCTGGAACTGGAGTCTGTGAAAGCTCAGTTTTTAGCAATATCAAAACAAAACCACTTGCTGAATGAAAAGGTGAGAGAGATGAGTGATTACTCACAACTGAAAGAAGAGAAAGTGGAGCTTCAGGCACAAAATAAACTACTTAAACTGCAACTGGAAGAGACTAGGAATGAAAACTTACGACTCCTAGACCGCATAACTCAGCCACCTCCTGAGCTTGTGATTTTTCAGAAGGAATTACAGAAAACAGAAAAGGCTATGGAACTGGAGCACAAGGACTTTGAAACTCATAGGCAGGCTCTTGAGAAACAGCTGCAGAGTGAAATTGAAAATTCTGCACAGCTAAGGACCCAGATAGCAGAATATGATGCTTCTGTCAAAAGGTTAACTGTTCAGGTGGCTGAGTTAAAGTCACAACTAAAACAAACTCAGATAGCCCTAGAGAATGAAGTGTACCGAAATCCAAAACACTCTCTGATTCATTCCCTGAGTGGCCTCCTATTGAGCGGCAAGATGGCACCCCACAGTGAAGATAAAAGTGGGGATTTCTTGAATGTACCCCTTGAACAGAACAAGGTTATAGCAGGTGCAGTTATGTCAAGGGTCCCACCTTATGTAAATACAGCAACAGAAGCTAGTTCCCCAGAGTCTGACTTTGAGTTTATAGCCAGTAGTACTAAAGCCAAAGTAAGAGAGCTAGAGCAAGAGGCTGAACGCTTGGAAAAGGCATTCAGAACTTACTATCAAAGAGCTACTCAGAATCCTTCTACGAGCCCTCAGCCGGCAAAGAGTCCTCCATCTGTAAACTCGGTGGCAGCTCTCAGAAGCATAGCTTCCAGTTCCATGGACAGACCTGTTTCTGCAGAGGACAGAGTTGTCTCGGAACAGCCTCTTGGGGACATGCTGAAGGAAGAAATGAGTGATATGTCCAAAGCATTCATGGGCAGTGTGGTTTCACGGCCACGCAGGACCTCTTCCTCCACACGCCTCTCCTCTACACCCCATCCAAAATCGAGAAGAAGTCTTGATAATGAAATGTATCTGGAAGGTCTCGGGAGATTACACATGACTTCCTCCAGCCCTCTTCTTGACAGAGTTTCTGCATCACCTGCTGCTTCCCCTAGTCCTTGTCCTGAGAGAACAGCCCAGGCGTCACCTGTTCCATCTAGGCACAGCTTCTCTGGTCTTCCAGAGCAAAATGCCTGTTTATATCAGAGACAAACTGAAACGCAAGATAAAAGTGAGCTTTCAAATGTGGACAAGCAATCTTTGAAAGATGAGAAATTTGAACCACCTTTCAGAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGAGACAAACTGAAACGCA
58.1
ACTGGATGAGGGGTTAATCCG
59.23
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGAGACAAACTGAAACGCA
58.1
CTGGATGAGGGGTTAATCCGA
58.95
145
PCR template sequence:
TGTTTATATCAGAGACAAACTGAAACGCAAGATAAAAGTGAGCTTTCAAATGTGGACAAGCAATCTTTGAAAGATGAGAAATTTGAACCACCTTTCAGATATATTTACTATGCAGGATCTACTACAACTCATTCGGATTAACCCCTCATCCAGTCTCTATAAATCATTGATTTCAGGATTTGATAAAGAAAATAAAAAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
21
Interacting miRNAs (#binding sites)
mmu-miR-335-3p(2), mmu-miR-137-3p(1), mmu-miR-140-5p(1), mmu-miR-15a-5p(1), mmu-miR-7b-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-7a-5p(1), mmu-miR-196a-5p(1), mmu-miR-138-5p(1), mmu-miR-127-5p(1), mmu-miR-541-5p(1), mmu-miR-425-5p(1), mmu-miR-324-3p(1), mmu-miR-342-5p(1), mmu-miR-207(1), mmu-miR-673-5p(1), mmu-miR-5101(1), mmu-miR-3470b(1), mmu-miR-1904(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCACCTTTCAGATATATTTACTATGC
siRNA sets
AAATATATCTGAAAGGTGG, TAAATATATCTGAAAGGTG, AGTAAATATATCTGAAAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCOFD1_2212_ORF_1
1.0834
0.09360387
0.99999823
2244
ORF sequence:
ATGCAGGATCTACTACAACTCATTCGGATTAACCCCTCATCCAGTCTCTATAAATCATTGATTTCAGGATTTGATAAAGAAAATAAAAAAGGTTTTCTTATGAGTTTCTTAAAGGAGTTGGCAGAATATTATCAAGCTAAAGAGAGCTGTGATGCGGAAACTCAGACAAGCACCACATTTCCCAGCCAAGTGTCCCTAGCCGAGAAGTTTCAGCTTATTGACGCTCAATTTGCAGATGGTTTTCCTCACCGTTCCAAGCTAGAATCTTTAGAGACAAAGTTAAACGAGTATAAGAAAGAAGTACAACACCAGCTTCAGGTAGAAATGTGTCATAAGCTGAAGTATTTTAGAGAAGCTGAAATAACAAAAGTTAAGATGGAAGAGAGAAGAAAGTATGAAAAGGAATTGGCTGAGTTCCAGAATGAATTTGAAAGAACTTGTCAAGCAAAAAATGAAGCCCTCATTTCTCAGGAGAAGAATTCTCTGGAAAGAATTAAAAAACACCGAGAGATGGAATCAAAAGAAATTTATGCTCAAAGACAGCTTCTACTAAATGATATAGCTTTGCTTAGAGGTAGAGAAGCAGAGCTGAAGGAGCGAATCGAAACTTTTGAATTGACCCAGAAGCTCCAAGAAGAAAAAATTAAAAGTGAGGCTGAGGCACTTGAGAGACGGGAACAGAATCTGAAGAATATTGAAGACACCTATGATCAGAAACTCAAAACTGAACTGCTAAAGTACCAACTGGAGCTAAAGGATGACTACATCACTAGGACAAATAAACTCCTGGAAGAGGAAAGGAAGAATAAAGAAAAAACTATTCATTTGCAAGAGGAGCTCACAGTTATTAATTCAAAAAAGGAAGAACTCAGTAAATCTGTTAAGCATATGAAAGAAGTTGAGCTGGAACTGGAGTCTGTGAAAGCTCAGTTTTTAGCAATATCAAAACAAAACCACTTGCTGAATGAAAAGGTGAGAGAGATGAGTGATTACTCACAACTGAAAGAAGAGAAAGTGGAGCTTCAGGCACAAAATAAACTACTTAAACTGCAACTGGAAGAGACTAGGAATGAAAACTTACGACTCCTAGACCGCATAACTCAGCCACCTCCTGAGCTTGTGATTTTTCAGAAGGAATTACAGAAAACAGAAAAGGCTATGGAACTGGAGCACAAGGACTTTGAAACTCATAGGCAGGCTCTTGAGAAACAGCTGCAGAGTGAAATTGAAAATTCTGCACAGCTAAGGACCCAGATAGCAGAATATGATGCTTCTGTCAAAAGGTTAACTGTTCAGGTGGCTGAGTTAAAGTCACAACTAAAACAAACTCAGATAGCCCTAGAGAATGAAGTGTACCGAAATCCAAAACACTCTCTGATTCATTCCCTGAGTGGCCTCCTATTGAGCGGCAAGATGGCACCCCACAGTGAAGATAAAAGTGGGGATTTCTTGAATGTACCCCTTGAACAGAACAAGGTTATAGCAGGTGCAGTTATGTCAAGGGTCCCACCTTATGTAAATACAGCAACAGAAGCTAGTTCCCCAGAGTCTGACTTTGAGTTTATAGCCAGTAGTACTAAAGCCAAAGTAAGAGAGCTAGAGCAAGAGGCTGAACGCTTGGAAAAGGCATTCAGAACTTACTATCAAAGAGCTACTCAGAATCCTTCTACGAGCCCTCAGCCGGCAAAGAGTCCTCCATCTGTAAACTCGGTGGCAGCTCTCAGAAGCATAGCTTCCAGTTCCATGGACAGACCTGTTTCTGCAGAGGACAGAGTTGTCTCGGAACAGCCTCTTGGGGACATGCTGAAGGAAGAAATGAGTGATATGTCCAAAGCATTCATGGGCAGTGTGGTTTCACGGCCACGCAGGACCTCTTCCTCCACACGCCTCTCCTCTACACCCCATCCAAAATCGAGAAGAAGTCTTGATAATGAAATGTATCTGGAAGGTCTCGGGAGATTACACATGACTTCCTCCAGCCCTCTTCTTGACAGAGTTTCTGCATCACCTGCTGCTTCCCCTAGTCCTTGTCCTGAGAGAACAGCCCAGGCGTCACCTGTTCCATCTAGGCACAGCTTCTCTGGTCTTCCAGAGCAAAATGCCTGTTTATATCAGAGACAAACTGAAACGCAAGATAAAAGTGAGCTTTCAAATGTGGACAAGCAATCTTTGAAAGATGAGAAATTTGAACCACCTTTCAGATATATTTACTATGCAGGATCTACTACAACTCATTCGGATTAA
Peptide sequence:
MQDLLQLIRINPSSSLYKSLISGFDKENKKGFLMSFLKELAEYYQAKESCDAETQTSTTFPSQVSLAEKFQLIDAQFADGFPHRSKLESLETKLNEYKKEVQHQLQVEMCHKLKYFREAEITKVKMEERRKYEKELAEFQNEFERTCQAKNEALISQEKNSLERIKKHREMESKEIYAQRQLLLNDIALLRGREAELKERIETFELTQKLQEEKIKSEAEALERREQNLKNIEDTYDQKLKTELLKYQLELKDDYITRTNKLLEEERKNKEKTIHLQEELTVINSKKEELSKSVKHMKEVELELESVKAQFLAISKQNHLLNEKVREMSDYSQLKEEKVELQAQNKLLKLQLEETRNENLRLLDRITQPPPELVIFQKELQKTEKAMELEHKDFETHRQALEKQLQSEIENSAQLRTQIAEYDASVKRLTVQVAELKSQLKQTQIALENEVYRNPKHSLIHSLSGLLLSGKMAPHSEDKSGDFLNVPLEQNKVIAGAVMSRVPPYVNTATEASSPESDFEFIASSTKAKVRELEQEAERLEKAFRTYYQRATQNPSTSPQPAKSPPSVNSVAALRSIASSSMDRPVSAEDRVVSEQPLGDMLKEEMSDMSKAFMGSVVSRPRRTSSSTRLSSTPHPKSRRSLDNEMYLEGLGRLHMTSSSPLLDRVSASPAASPSPCPERTAQASPVPSRHSFSGLPEQNACLYQRQTETQDKSELSNVDKQSLKDEKFEPPFRYIYYAGSTTTHSD
IRESfinder result
IRESfinder score
0.656595139
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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