top of page
mmu_circPgap1_511
Basic information of circular RNA
PanCircBase ID:
mmu_circPgap1_511
mm39_Chr. Position ID:
chr1|54536692|54554071|-
Gene name:
Pgap1
Transcript:
ENSMUST00000097739.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
20,19,18,17,16,15,14
Exon/intron offsets:
0,12494,13860,14367,15063,15238,17303
Genomic length:
17379
Exon/intron sizes in nt:
94,39,109,67,52,74,76
Flanking exon/introns:
chr1:54534050-54536692|chr1:54554071-54560450
Splice length:
511
Other database IDs:
circAtlas: mmu-Pgap1_0018
Human Ortholog IDs:
Mature spliced Sequence:
TTTGTTGTCGACTGTGAATTCTTTAAGAAAGAAGCGAGATCCATGCAGCTCCCTGTGACTCACCTTTTTTCCTTTGGACTGTCTTCCAGGAAGGTGACGTTAAATACAAACGGCCTATACTACAACATAGAGCTGCTGAACTTTGGACAGATATACCAAGCTTTTAAAGTCAACGTGGTCAGCAAGTGCACTGGAAGCAAAGAAGAAATAACCAGTATCTATAAACTTCATATCCCCTGGTCCTATGAAGATTCACTAACCATCGCACAGGTTCCATCTTCCACAGACATTTCTCTGAAGCTTCATGTTGCTCAGCCAGAAAATGACAGCCATGTGGCACTGTTAAAAATGTACACGTCGTCAGACTGTCAGTATGAGGTGACAATTAAGACTTCCTTCCCACAAATACTTGGACAGGTAGTTAGGTTTCATGGTGGAGCCCTTCCTGCCTACGTTGTATCTAGCATCCTTCTTGCGTATGGAGGACAGTTATACTCACTCCTCTCAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTTCATGGTGGAGCCCTTCC
59.96
CAGGGAGCTGCATGGATCTC
60.25
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTTCATGGTGGAGCCCTTCC
59.96
AAAGGTGAGTCACAGGGAGC
59.6
152
PCR template sequence:
GGACAGGTAGTTAGGTTTCATGGTGGAGCCCTTCCTGCCTACGTTGTATCTAGCATCCTTCTTGCGTATGGAGGACAGTTATACTCACTCCTCTCAACAGTTTGTTGTCGACTGTGAATTCTTTAAGAAAGAAGCGAGATCCATGCAGCTCCCTGTGACTCACCTTTTTTCCTTTGGACTGTCTTCCAGGAAGGTGACGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-148a-3p(1), mmu-miR-127-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCCTCTCAACAGTTTGTTGTCGACT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPGAP1_511_ORF_1
0.7362
0.071686914
0.659259119
591
ORF sequence:
ATGGTGGAGCCCTTCCTGCCTACGTTGTATCTAGCATCCTTCTTGCGTATGGAGGACAGTTATACTCACTCCTCTCAACAGTTTGTTGTCGACTGTGAATTCTTTAAGAAAGAAGCGAGATCCATGCAGCTCCCTGTGACTCACCTTTTTTCCTTTGGACTGTCTTCCAGGAAGGTGACGTTAAATACAAACGGCCTATACTACAACATAGAGCTGCTGAACTTTGGACAGATATACCAAGCTTTTAAAGTCAACGTGGTCAGCAAGTGCACTGGAAGCAAAGAAGAAATAACCAGTATCTATAAACTTCATATCCCCTGGTCCTATGAAGATTCACTAACCATCGCACAGGTTCCATCTTCCACAGACATTTCTCTGAAGCTTCATGTTGCTCAGCCAGAAAATGACAGCCATGTGGCACTGTTAAAAATGTACACGTCGTCAGACTGTCAGTATGAGGTGACAATTAAGACTTCCTTCCCACAAATACTTGGACAGGTAGTTAGGTTTCATGGTGGAGCCCTTCCTGCCTACGTTGTATCTAGCATCCTTCTTGCGTATGGAGGACAGTTATACTCACTCCTCTCAACA
Peptide sequence:
MVEPFLPTLYLASFLRMEDSYTHSSQQFVVDCEFFKKEARSMQLPVTHLFSFGLSSRKVTLNTNGLYYNIELLNFGQIYQAFKVNVVSKCTGSKEEITSIYKLHIPWSYEDSLTIAQVPSSTDISLKLHVAQPENDSHVALLKMYTSSDCQYEVTIKTSFPQILGQVVRFHGGALPAYVVSSILLAYGGQLYSLLST
IRESfinder result
IRESfinder score
0.747127457
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page