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mmu_circPgap1_463
Basic information of circular RNA
PanCircBase ID:
mmu_circPgap1_463
mm39_Chr. Position ID:
chr1|54551755|54567754|-
Gene name:
Pgap1
Transcript:
ENSMUST00000097739.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
16,15,14,13,12,11,10
Exon/intron offsets:
0,175,2240,8695,11719,12771,15915
Genomic length:
15999
Exon/intron sizes in nt:
52,74,76,78,52,47,84
Flanking exon/introns:
chr1:54551126-54551755|chr1:54567754-54569275
Splice length:
463
Other database IDs:
CIRCpedia: MMU_CIRCpedia_22859, circAtlas: mmu-Pgap1_0008
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GAATCTGATAAGATTTACTTTGCATTTCCTCTTGCAAATCATAGAAAAATCTACACTCATGCCTATTGTCAGAGCACCATGCTGGATACAAATAGTTGGATTTTTGGCTGCATAAACAGCACTTCCATGTGCCGGCAAGGGGTTGATTTGTCATGGAAAGCTGAGCTGTTACCAACAATTAAGTCTCTGACGCTAAGACTTCAAGACTATCCATCCTTGTCGCATATTGTTGTCTATGTGCCATCTGTCCACGGAAGTAAGTTTGTTGTCGACTGTGAATTCTTTAAGAAAGAAGCGAGATCCATGCAGCTCCCTGTGACTCACCTTTTTTCCTTTGGACTGTCTTCCAGGAAGGTGACGTTAAATACAAACGGCCTATACTACAACATAGAGCTGCTGAACTTTGGACAGATATACCAAGCTTTTAAAGTCAACGTGGTCAGCAAGTGCACTGGAAGCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTGCTGAACTTTGGACAGA
59.86
TGGTGCTCTGACAATAGGCA
59.02
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGCTGCTGAACTTTGGACA
59.86
TGGTGCTCTGACAATAGGCA
59.02
153
PCR template sequence:
AATACAAACGGCCTATACTACAACATAGAGCTGCTGAACTTTGGACAGATATACCAAGCTTTTAAAGTCAACGTGGTCAGCAAGTGCACTGGAAGCAAAGGAATCTGATAAGATTTACTTTGCATTTCCTCTTGCAAATCATAGAAAAATCTACACTCATGCCTATTGTCAGAGCACCATGCTGGATACAAATAGTTGGA
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-194-5p(1), mmu-miR-3065-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGGAAGCAAAGGAATCTGATAAGA
siRNA sets
TCTTATCAGATTCCTTTGC, TATCAGATTCCTTTGCTTC, TCAGATTCCTTTGCTTCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPGAP1_463_ORF_1
0.5893
0.029942825
0.229619304
393
ORF sequence:
ATGCTGGATACAAATAGTTGGATTTTTGGCTGCATAAACAGCACTTCCATGTGCCGGCAAGGGGTTGATTTGTCATGGAAAGCTGAGCTGTTACCAACAATTAAGTCTCTGACGCTAAGACTTCAAGACTATCCATCCTTGTCGCATATTGTTGTCTATGTGCCATCTGTCCACGGAAGTAAGTTTGTTGTCGACTGTGAATTCTTTAAGAAAGAAGCGAGATCCATGCAGCTCCCTGTGACTCACCTTTTTTCCTTTGGACTGTCTTCCAGGAAGGTGACGTTAAATACAAACGGCCTATACTACAACATAGAGCTGCTGAACTTTGGACAGATATACCAAGCTTTTAAAGTCAACGTGGTCAGCAAGTGCACTGGAAGCAAAGGAATCTGA
Peptide sequence:
MLDTNSWIFGCINSTSMCRQGVDLSWKAELLPTIKSLTLRLQDYPSLSHIVVYVPSVHGSKFVVDCEFFKKEARSMQLPVTHLFSFGLSSRKVTLNTNGLYYNIELLNFGQIYQAFKVNVVSKCTGSKGI
IRESfinder result
IRESfinder score
0.707253348
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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