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mmu_circXrcc5_916
Basic information of circular RNA
PanCircBase ID:
mmu_circXrcc5_916
mm39_Chr. Position ID:
chr1|72349593|72365513|+
Gene name:
Xrcc5
Transcript:
ENSMUST00000027379.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
2,3,4,5,6,7,8
Exon/intron offsets:
0,1973,3719,5024,8564,14639,15781
Genomic length:
15920
Exon/intron sizes in nt:
1,14,18,44,91,23,19,21,00,000
Flanking exon/introns:
chr1:72346726-72349593|chr1:72365513-72369084
Splice length:
916
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_342985
Human Ortholog IDs:
Mature spliced Sequence:
GCAGCTGTTGTGCTGTGTGTGGATGTGGGGGTTGCCATGGGTAACTCCTTTCCTGGTGAAGAATCTCCAATTGAACAAGCAAAGAAAGTGATGACTATGTTTGTCCAACGACAGGTATTTTCGGAGAGCAAAGATGAGATTGCGTTAGTCCTCTATGGCACAGATGGCACTGATAATGCCCTTGCTGGCAAGGACCAGTATCAGAACATCACAGTGTGCAGACACCTGATGCTACCAGATTTTGATTTGCTGGAAGACATCGGAAACAAAATCCAGCCAAGTTCCCAGCAAGCCGACTTCCTGGACGCCCTGATTGTGTGCATGGATTTGATTCAGCGTGAAACCATAGGGAAGAAGTTTGGGAAGAAGCATATTGAAGTGTTCACTGACCTCAGCAGCCCGTTCAGCCAGGACCAACTGGACGTTATAATTTGTAACTTGAAGAAGTCTGGCATCTCTCTGCAGTTCTTTTTGCCTTTTCCAATCGACAAGAATGGCGAGCCTGGCGAGAGAGGGGACCTGGACTCTGGCTTGGACCACCTCAAACCCTCCTTCCCTCAAAAAGGACTTACTGAGCAGCAAAAGGAAGGCATCCGCATGGTGACAAGGGTGATGCTGTCCTTAGAAGGCGAAGACGGGCTGGATGAAATTTATTCCTTCAGTGAGAGTCTACGACAACTGTGCGTCTTTAAGAAGATTGAGAGGCGTTCCATGCCCTGGCCCTGCCAACTGACCATTGGCCCCAACTTGTCTATAAAGATTGTAGCCTATAAATCGATTGTACAGGAGAAATTTAAGAAGAGTTGGGTAGTTGTGGACGCAAGAACGCTAAAGAAGGAAGATATACAAAAAGAGACTGTTTATTGCCTAAATGACGATGATGAAACTGAAGTTTCCAAAGAGGACACTATTCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGCAAGAACGCTAAAGAAGG
59.2
AGGAGTTACCCATGGCAACC
59.67
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGCAAGAACGCTAAAGAAGGA
58.93
AGGAGTTACCCATGGCAACC
59.67
147
PCR template sequence:
GACGCAAGAACGCTAAAGAAGGAAGATATACAAAAAGAGACTGTTTATTGCCTAAATGACGATGATGAAACTGAAGTTTCCAAAGAGGACACTATTCAAGGCAGCTGTTGTGCTGTGTGTGGATGTGGGGGTTGCCATGGGTAACTCCTTTCCTGGTGAAGAATCTCCAATTGAACAAGCAAAGAAAGTGATGACTATGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-495-3p(1), mmu-miR-212-3p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACACTATTCAAGGCAGCTGTTGTGC
siRNA sets
AACAGCTGCCTTGAATAGT, ACAGCTGCCTTGAATAGTG, CAACAGCTGCCTTGAATAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCXRCC5_916_ORF_1
1.2295
0.280780892
0.993795053
960
ORF sequence:
ATGACGATGATGAAACTGAAGTTTCCAAAGAGGACACTATTCAAGGCAGCTGTTGTGCTGTGTGTGGATGTGGGGGTTGCCATGGGTAACTCCTTTCCTGGTGAAGAATCTCCAATTGAACAAGCAAAGAAAGTGATGACTATGTTTGTCCAACGACAGGTATTTTCGGAGAGCAAAGATGAGATTGCGTTAGTCCTCTATGGCACAGATGGCACTGATAATGCCCTTGCTGGCAAGGACCAGTATCAGAACATCACAGTGTGCAGACACCTGATGCTACCAGATTTTGATTTGCTGGAAGACATCGGAAACAAAATCCAGCCAAGTTCCCAGCAAGCCGACTTCCTGGACGCCCTGATTGTGTGCATGGATTTGATTCAGCGTGAAACCATAGGGAAGAAGTTTGGGAAGAAGCATATTGAAGTGTTCACTGACCTCAGCAGCCCGTTCAGCCAGGACCAACTGGACGTTATAATTTGTAACTTGAAGAAGTCTGGCATCTCTCTGCAGTTCTTTTTGCCTTTTCCAATCGACAAGAATGGCGAGCCTGGCGAGAGAGGGGACCTGGACTCTGGCTTGGACCACCTCAAACCCTCCTTCCCTCAAAAAGGACTTACTGAGCAGCAAAAGGAAGGCATCCGCATGGTGACAAGGGTGATGCTGTCCTTAGAAGGCGAAGACGGGCTGGATGAAATTTATTCCTTCAGTGAGAGTCTACGACAACTGTGCGTCTTTAAGAAGATTGAGAGGCGTTCCATGCCCTGGCCCTGCCAACTGACCATTGGCCCCAACTTGTCTATAAAGATTGTAGCCTATAAATCGATTGTACAGGAGAAATTTAAGAAGAGTTGGGTAGTTGTGGACGCAAGAACGCTAAAGAAGGAAGATATACAAAAAGAGACTGTTTATTGCCTAAATGACGATGATGAAACTGAAGTTTCCAAAGAGGACACTATTCAA
Peptide sequence:
MTMMKLKFPKRTLFKAAVVLCVDVGVAMGNSFPGEESPIEQAKKVMTMFVQRQVFSESKDEIALVLYGTDGTDNALAGKDQYQNITVCRHLMLPDFDLLEDIGNKIQPSSQQADFLDALIVCMDLIQRETIGKKFGKKHIEVFTDLSSPFSQDQLDVIICNLKKSGISLQFFLPFPIDKNGEPGERGDLDSGLDHLKPSFPQKGLTEQQKEGIRMVTRVMLSLEGEDGLDEIYSFSESLRQLCVFKKIERRSMPWPCQLTIGPNLSIKIVAYKSIVQEKFKKSWVVVDARTLKKEDIQKETVYCLNDDDETEVSKEDTIQ
IRESfinder result
IRESfinder score
0.499209862
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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