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mmu_circPgap1_758
Basic information of circular RNA
PanCircBase ID:
mmu_circPgap1_758
mm39_Chr. Position ID:
chr1|54525628|54536786|-
Gene name:
Pgap1
Transcript:
ENSMUST00000097739.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
25,24,23,22,21,20
Exon/intron offsets:
0,3751,5559,6739,8331,11064
Genomic length:
11158
Exon/intron sizes in nt:
188,51,136,198,91,94
Flanking exon/introns:
chr1:54521115-54525628|chr1:54536786-54549186
Splice length:
758
Other database IDs:
circBase: mmu_circ_0008789, CIRCpedia: MMU_CIRCpedia_215538, circAtlas: mmu-Pgap1_0016
circBase: hsa_circ_0118483, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_135202
Human Ortholog IDs:
Mature spliced Sequence:
GTAGTTAGGTTTCATGGTGGAGCCCTTCCTGCCTACGTTGTATCTAGCATCCTTCTTGCGTATGGAGGACAGTTATACTCACTCCTCTCAACAGGTTATTGCTTAGAATATTCTACCATATTGGATAAAGAAGCCAAACCATACAAAGTTGACCCATTTGTAATTATGATTAAGTTTTTGTTGGGGTATAAATGGTTTAAGGAATTATGGGATGCAGTGTTATTACCGGAATTAGATGCCATCGTTTTGACTAGCCAGAGTATGTGTTTCCCTCTTGTATCCTTGATTCTCTTTCTGTTTGGAACATGTACTGCATACTGGAGTGGTCTACTCTCTTCTACATCTGTGCAGCTTCTTTCTTCATTGTGGCTAGCTCTGAAAAGACCTGCTGAACTTCCTAAAGATATCAAGGTGATGTCACCAGACTTGCCTGTTTTGACAGTTGTCTTTCTCATAGTGAGTTGGACAACTTGTGGAGCACTTGCCATACTTCTGTCTTATCTGTACTATGTGTTTAAGGTTGTTCATCTGCAAGCCAGCCTAACTACATTTAAAAATAATCAGCCAGTGAATCCCAAACACTCTAGAAGAAGTGAAAAAAAGTCCAACCACCATAAAGACTCTGCTGTACAAAGTCTTCGCTTATGTGCTAATGATGCTGAAGACAGTCTTCGCATGCACAGCACCGTGATTAACTTGCTGACGTGGGTTGTGCTGCTCAGCATGCCGTCTCTAATCTACTGGTTAAAGAACCTTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGACAGTCTTCGCATGCACA
59.97
TGTCCTCCATACGCAAGAAGG
59.79
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGACAGTCTTCGCATGCACA
59.97
GTCCTCCATACGCAAGAAGGA
59.52
166
PCR template sequence:
CTGAAGACAGTCTTCGCATGCACAGCACCGTGATTAACTTGCTGACGTGGGTTGTGCTGCTCAGCATGCCGTCTCTAATCTACTGGTTAAAGAACCTTAGGTAGTTAGGTTTCATGGTGGAGCCCTTCCTGCCTACGTTGTATCTAGCATCCTTCTTGCGTATGGAGGACAGTTATACTCACTCCTCTCAACAGGTTATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-199a-5p(1), mmu-miR-135a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-324-5p(1), mmu-miR-381-3p(1), mmu-miR-3087-3p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TAAAGAACCTTAGGTAGTTAGGTTTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPGAP1_758_ORF_1
0.679
-0.097781883
0.473150503
597
ORF sequence:
ATGATTAAGTTTTTGTTGGGGTATAAATGGTTTAAGGAATTATGGGATGCAGTGTTATTACCGGAATTAGATGCCATCGTTTTGACTAGCCAGAGTATGTGTTTCCCTCTTGTATCCTTGATTCTCTTTCTGTTTGGAACATGTACTGCATACTGGAGTGGTCTACTCTCTTCTACATCTGTGCAGCTTCTTTCTTCATTGTGGCTAGCTCTGAAAAGACCTGCTGAACTTCCTAAAGATATCAAGGTGATGTCACCAGACTTGCCTGTTTTGACAGTTGTCTTTCTCATAGTGAGTTGGACAACTTGTGGAGCACTTGCCATACTTCTGTCTTATCTGTACTATGTGTTTAAGGTTGTTCATCTGCAAGCCAGCCTAACTACATTTAAAAATAATCAGCCAGTGAATCCCAAACACTCTAGAAGAAGTGAAAAAAAGTCCAACCACCATAAAGACTCTGCTGTACAAAGTCTTCGCTTATGTGCTAATGATGCTGAAGACAGTCTTCGCATGCACAGCACCGTGATTAACTTGCTGACGTGGGTTGTGCTGCTCAGCATGCCGTCTCTAATCTACTGGTTAAAGAACCTTAGGTAG
Peptide sequence:
MIKFLLGYKWFKELWDAVLLPELDAIVLTSQSMCFPLVSLILFLFGTCTAYWSGLLSSTSVQLLSSLWLALKRPAELPKDIKVMSPDLPVLTVVFLIVSWTTCGALAILLSYLYYVFKVVHLQASLTTFKNNQPVNPKHSRRSEKKSNHHKDSAVQSLRLCANDAEDSLRMHSTVINLLTWVVLLSMPSLIYWLKNLR
IRESfinder result
IRESfinder score
0.809360117
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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