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mmu_circDepdc5_1130
Basic information of circular RNA
PanCircBase ID:
mmu_circDepdc5_1130
mm39_Chr. Position ID:
chr5|33091293|33113302|+
Gene name:
Depdc5
Transcript:
ENSMUST00000049780.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
25,26,27,28,29,30,31,32
Exon/intron offsets:
0,3598,4195,9282,10021,10973,12684,21903
Genomic length:
22009
Exon/intron sizes in nt:
66,15,71,61,11,81,68,20,00,00,000
Flanking exon/introns:
chr5:33085283-33091293|chr5:33113302-33113472
Splice length:
1130
Other database IDs:
circAtlas: mmu-Depdc5_0014
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_36473
Human Ortholog IDs:
Mature spliced Sequence:
GTGTGAATCCTAGGACCCAGAACAAGGACTCCCTAGAGGACAGTGTTTCTACCTCTCCAGACCCAATGCCAGGCTTCTGTTGCACAGTTGGAGTGGATTGGAAGTCTCTTACTACTCCTGCATGCCTTCCCCTCACCACTGACTACTTCCCGGACCGTCAGGGCCTGCAGAATGACTACACAGAGGGCTGCTATGATCTCCTCCCAGAAGCAGACATGGACAGGAGGGATGAGGAGGGTGTTCAAATGACAGCCCAGCAAGTGTTTGAAGAGTTCATCTGCCAGCGTCTCATGCAGGGTTACCAAATCATAGTACAGCCAAAGACCCAGAAACCCAACACCACAGTCCCACCCCCATTGAGCAGTAGCCCACTCTATAGCAGAGGCCTTGTGTCCCGAAATCGCCCTGAGGAGGAAGGCCAGTATTGGTTAAGTATGGGCAGAACTTTCCATAAGGTGACACTCAAGGACAAGATGATCACAGTAACTCGTTACCTTCCCAAGTACCCTTATGAATCTGCCCAGATCCATTACACCTACAGCCTCTGCCCTTCCCACTCTGACTCGGAGTTTGTCTCCTGTTGGGTGGATTTCTGCCACGAACGGCTCGAGGAATACAAGTGGAATTACTTAGATCAGTATATTTGTTCTGCTGGCTCTGAAGACTTCAGCTTAATCGAGTCTCTGAAGTTCTGGAGAACCCGATTTTTACTACTGCCAGCCTGTGTTACTGCCACCAAGCGCATCACAGAAGGGGAGGTGCACTGTGACATCTATGGGGACAAACCCCGTGCAGATGAAGATGAGTGGCAGCTTCTAGATGGCTTTATTCGCTTTGTAGAGGGCTTAAATCGCATCCGCAGGCGCCACCGCTCAGACCGCATGATTCGGAAGGGGACTGCCATGAAAGGCTTGCAGATGACCGGGCCCATCTCTGCACACTCTCTCGAGGCAGCAGGCCCTCCAGTCGGCAAGAAAGGAACCTCAGCTCTGTCTGCCCTGCTGGAGATGGAAGCTAGTCAGAAGAGCCTAGGAGAACAGCAGACGACTGTGCACGGAAAAAGCTCCACTCAGCCAGCTGAGAACAGCAGTGTTGCCATGACTCCCACCTATGTGGACAGCCCACGCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGTGCACGGAAAAAGCTCC
60.04
CTGGCATTGGGTCTGGAGAG
60.11
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGTGCACGGAAAAAGCTCC
60.04
CAACAGAAGCCTGGCATTGG
59.75
165
PCR template sequence:
AGGAGAACAGCAGACGACTGTGCACGGAAAAAGCTCCACTCAGCCAGCTGAGAACAGCAGTGTTGCCATGACTCCCACCTATGTGGACAGCCCACGCAAGGTGTGAATCCTAGGACCCAGAACAAGGACTCCCTAGAGGACAGTGTTTCTACCTCTCCAGACCCAATGCCAGGCTTCTGTTGCACAGTTGGAGTGGATTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-let-7b-5p(2), mmu-let-7a-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-429-3p(1), mmu-let-7e-5p(1), mmu-let-7c-5p(1), mmu-miR-298-5p(1), mmu-miR-214-3p(1), mmu-miR-128-3p(1), mmu-miR-98-5p(1), mmu-miR-802-5p(1), mmu-miR-207(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGCCCACGCAAGGTGTGAATCCTAG
siRNA sets
CTAGGATTCACACCTTGCG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDEPDC5_1130_ORF_1
0.7973
0.292104787
0.99399845
1071
ORF sequence:
ATGCCAGGCTTCTGTTGCACAGTTGGAGTGGATTGGAAGTCTCTTACTACTCCTGCATGCCTTCCCCTCACCACTGACTACTTCCCGGACCGTCAGGGCCTGCAGAATGACTACACAGAGGGCTGCTATGATCTCCTCCCAGAAGCAGACATGGACAGGAGGGATGAGGAGGGTGTTCAAATGACAGCCCAGCAAGTGTTTGAAGAGTTCATCTGCCAGCGTCTCATGCAGGGTTACCAAATCATAGTACAGCCAAAGACCCAGAAACCCAACACCACAGTCCCACCCCCATTGAGCAGTAGCCCACTCTATAGCAGAGGCCTTGTGTCCCGAAATCGCCCTGAGGAGGAAGGCCAGTATTGGTTAAGTATGGGCAGAACTTTCCATAAGGTGACACTCAAGGACAAGATGATCACAGTAACTCGTTACCTTCCCAAGTACCCTTATGAATCTGCCCAGATCCATTACACCTACAGCCTCTGCCCTTCCCACTCTGACTCGGAGTTTGTCTCCTGTTGGGTGGATTTCTGCCACGAACGGCTCGAGGAATACAAGTGGAATTACTTAGATCAGTATATTTGTTCTGCTGGCTCTGAAGACTTCAGCTTAATCGAGTCTCTGAAGTTCTGGAGAACCCGATTTTTACTACTGCCAGCCTGTGTTACTGCCACCAAGCGCATCACAGAAGGGGAGGTGCACTGTGACATCTATGGGGACAAACCCCGTGCAGATGAAGATGAGTGGCAGCTTCTAGATGGCTTTATTCGCTTTGTAGAGGGCTTAAATCGCATCCGCAGGCGCCACCGCTCAGACCGCATGATTCGGAAGGGGACTGCCATGAAAGGCTTGCAGATGACCGGGCCCATCTCTGCACACTCTCTCGAGGCAGCAGGCCCTCCAGTCGGCAAGAAAGGAACCTCAGCTCTGTCTGCCCTGCTGGAGATGGAAGCTAGTCAGAAGAGCCTAGGAGAACAGCAGACGACTGTGCACGGAAAAAGCTCCACTCAGCCAGCTGAGAACAGCAGTGTTGCCATGACTCCCACCTATGTGGACAGCCCACGCAAGGTGTGA
Peptide sequence:
MPGFCCTVGVDWKSLTTPACLPLTTDYFPDRQGLQNDYTEGCYDLLPEADMDRRDEEGVQMTAQQVFEEFICQRLMQGYQIIVQPKTQKPNTTVPPPLSSSPLYSRGLVSRNRPEEEGQYWLSMGRTFHKVTLKDKMITVTRYLPKYPYESAQIHYTYSLCPSHSDSEFVSCWVDFCHERLEEYKWNYLDQYICSAGSEDFSLIESLKFWRTRFLLLPACVTATKRITEGEVHCDIYGDKPRADEDEWQLLDGFIRFVEGLNRIRRRHRSDRMIRKGTAMKGLQMTGPISAHSLEAAGPPVGKKGTSALSALLEMEASQKSLGEQQTTVHGKSSTQPAENSSVAMTPTYVDSPRKV
IRESfinder result
IRESfinder score
0.462810502
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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