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mmu_circPgap1_594
Basic information of circular RNA
PanCircBase ID:
mmu_circPgap1_594
mm39_Chr. Position ID:
chr1|54549186|54564573|-
Gene name:
Pgap1
Transcript:
ENSMUST00000097739.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
19,18,17,16,15,14,13,12,11
Exon/intron offsets:
0,1366,1873,2569,2744,4809,11264,14288,15340
Genomic length:
15387
Exon/intron sizes in nt:
39,109,67,52,74,76,78,52,47
Flanking exon/introns:
chr1:54536786-54549186|chr1:54564573-54567670
Splice length:
594
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GATACAAATAGTTGGATTTTTGGCTGCATAAACAGCACTTCCATGTGCCGGCAAGGGGTTGATTTGTCATGGAAAGCTGAGCTGTTACCAACAATTAAGTCTCTGACGCTAAGACTTCAAGACTATCCATCCTTGTCGCATATTGTTGTCTATGTGCCATCTGTCCACGGAAGTAAGTTTGTTGTCGACTGTGAATTCTTTAAGAAAGAAGCGAGATCCATGCAGCTCCCTGTGACTCACCTTTTTTCCTTTGGACTGTCTTCCAGGAAGGTGACGTTAAATACAAACGGCCTATACTACAACATAGAGCTGCTGAACTTTGGACAGATATACCAAGCTTTTAAAGTCAACGTGGTCAGCAAGTGCACTGGAAGCAAAGAAGAAATAACCAGTATCTATAAACTTCATATCCCCTGGTCCTATGAAGATTCACTAACCATCGCACAGGTTCCATCTTCCACAGACATTTCTCTGAAGCTTCATGTTGCTCAGCCAGAAAATGACAGCCATGTGGCACTGTTAAAAATGTACACGTCGTCAGACTGTCAGTATGAGGTGACAATTAAGACTTCCTTCCCACAAATACTTGGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACGTCGTCAGACTGTCAGT
59.69
ACAGCTCAGCTTTCCATGACA
59.93
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACACGTCGTCAGACTGTCAG
59.69
ACAGCTCAGCTTTCCATGACA
59.93
150
PCR template sequence:
AGAAAATGACAGCCATGTGGCACTGTTAAAAATGTACACGTCGTCAGACTGTCAGTATGAGGTGACAATTAAGACTTCCTTCCCACAAATACTTGGACAGGATACAAATAGTTGGATTTTTGGCTGCATAAACAGCACTTCCATGTGCCGGCAAGGGGTTGATTTGTCATGGAAAGCTGAGCTGTTACCAACAATTAAGT
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-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-93-5p(1), mmu-miR-148a-3p(1), mmu-miR-127-5p(1), mmu-miR-194-5p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AATACTTGGACAGGATACAAATAGTT
siRNA sets
ATTTGTATCCTGTCCAAGT, AACTATTTGTATCCTGTCC, ACTATTTGTATCCTGTCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPGAP1_594_ORF_1
0.6861
0.079511056
0.990048157
1146
ORF sequence:
ATGTGCCGGCAAGGGGTTGATTTGTCATGGAAAGCTGAGCTGTTACCAACAATTAAGTCTCTGACGCTAAGACTTCAAGACTATCCATCCTTGTCGCATATTGTTGTCTATGTGCCATCTGTCCACGGAAGTAAGTTTGTTGTCGACTGTGAATTCTTTAAGAAAGAAGCGAGATCCATGCAGCTCCCTGTGACTCACCTTTTTTCCTTTGGACTGTCTTCCAGGAAGGTGACGTTAAATACAAACGGCCTATACTACAACATAGAGCTGCTGAACTTTGGACAGATATACCAAGCTTTTAAAGTCAACGTGGTCAGCAAGTGCACTGGAAGCAAAGAAGAAATAACCAGTATCTATAAACTTCATATCCCCTGGTCCTATGAAGATTCACTAACCATCGCACAGGTTCCATCTTCCACAGACATTTCTCTGAAGCTTCATGTTGCTCAGCCAGAAAATGACAGCCATGTGGCACTGTTAAAAATGTACACGTCGTCAGACTGTCAGTATGAGGTGACAATTAAGACTTCCTTCCCACAAATACTTGGACAGGATACAAATAGTTGGATTTTTGGCTGCATAAACAGCACTTCCATGTGCCGGCAAGGGGTTGATTTGTCATGGAAAGCTGAGCTGTTACCAACAATTAAGTCTCTGACGCTAAGACTTCAAGACTATCCATCCTTGTCGCATATTGTTGTCTATGTGCCATCTGTCCACGGAAGTAAGTTTGTTGTCGACTGTGAATTCTTTAAGAAAGAAGCGAGATCCATGCAGCTCCCTGTGACTCACCTTTTTTCCTTTGGACTGTCTTCCAGGAAGGTGACGTTAAATACAAACGGCCTATACTACAACATAGAGCTGCTGAACTTTGGACAGATATACCAAGCTTTTAAAGTCAACGTGGTCAGCAAGTGCACTGGAAGCAAAGAAGAAATAACCAGTATCTATAAACTTCATATCCCCTGGTCCTATGAAGATTCACTAACCATCGCACAGGTTCCATCTTCCACAGACATTTCTCTGAAGCTTCATGTTGCTCAGCCAGAAAATGACAGCCATGTGGCACTGTTAAAAATGTACACGTCGTCAGACTGTCAGTATGAGGTGACAATTAAGACTTCCTTCCCACAAATACTTGGACAG
Peptide sequence:
MCRQGVDLSWKAELLPTIKSLTLRLQDYPSLSHIVVYVPSVHGSKFVVDCEFFKKEARSMQLPVTHLFSFGLSSRKVTLNTNGLYYNIELLNFGQIYQAFKVNVVSKCTGSKEEITSIYKLHIPWSYEDSLTIAQVPSSTDISLKLHVAQPENDSHVALLKMYTSSDCQYEVTIKTSFPQILGQDTNSWIFGCINSTSMCRQGVDLSWKAELLPTIKSLTLRLQDYPSLSHIVVYVPSVHGSKFVVDCEFFKKEARSMQLPVTHLFSFGLSSRKVTLNTNGLYYNIELLNFGQIYQAFKVNVVSKCTGSKEEITSIYKLHIPWSYEDSLTIAQVPSSTDISLKLHVAQPENDSHVALLKMYTSSDCQYEVTIKTSFPQILGQ
IRESfinder result
IRESfinder score
0.723953798
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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