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mmu_circRabgap1_1039
Basic information of circular RNA
PanCircBase ID:
mmu_circRabgap1_1039
mm39_Chr. Position ID:
chr2|37362306|37379845|+
Gene name:
Rabgap1
Transcript:
ENSMUST00000133434.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
3,4,5,6,7,8,9
Exon/intron offsets:
0,1284,2997,11433,14771,15217,17436
Genomic length:
17539
Exon/intron sizes in nt:
2,20,20,51,75,15,81,11,00,000
Flanking exon/introns:
chr2:37359588-37362306|chr2:37379845-37381921
Splice length:
1039
Other database IDs:
CIRCpedia: MMU_CIRCpedia_18585, circAtlas: mmu-Rabgap1_0029
Human Ortholog IDs:
Mature spliced Sequence:
ATTGTAGGAAATGGAAGTGAGCAGCAGCTTCAGAAAGAGCTAGCAGATGTGCTGATGGATCCTCCCATGGACGACCAGCCAGGGGAAAGGTCACAACTGGATGGTGAAGGAGATGGGCCTCTTTCTAATCAACTCTCAGCTTCATCCACCATTAATCCTGTGCCTCTGGTAGGGCTTCCGAAACCAGAGATGAGCCTGCCAGTGAAACCTGGACAAGGAGATTCTGAAGTATCAAGTCCTTTTACACCAGTGGCTGATGAGGATAGTGTGGTTTTCAATAAACTAACTTACTTAGGCTGTGCTTCAGTAAATGCTCCCCGGAGTGAAGTGGAAGCCTTGAGGATGATGTCCATCTTGAGAAGTCAGTGTCAGATTTCTCTGGATGTAACCCTCTCAGTGCCGAATGTATCTGAAGGAACTGTGAGACTTTTAGATCCTCAAACAAACACTGAAATAGCAAACTACCCTATCTACAAAATCCTCTTCTGTGTCAGAGGACATGATGGGACTCCTGAGAGTGACTGTTTTGCATTCACTGAAAGTCACTACAACGCAGAGCTCTTCAGGATACATGTCTTTCGCTGTGAAATACAAGAAGCTGTGAGCCGGATACTTTACAGTTTTGCCACCGCCTTCCGCCGCTCTGCCAAGCAGACCCCACTCTCAGCCACAGCTGCACCACAGACTCCTGACAGCGACATCTTTACCTTCTCTGTGTCTTTAGAAATAAAAGAAGATGATGGTAAAGGTTATTTTAGTGCTGTTCCCAAAGACAAGGACAGGCAATGCTTTAAACTTCGACAAGGAATTGATAAGAAGATTGTTATCTGTGTGCAGCAAACAGCTAACAAAGAACTTGCCATTGAAAGGTGCTTTGGTCTTCTCCTTAGCCCAGGAAAAGATGTCCGAAACAGTGATATGCACTTGCTGGATTTGGAGTCTATGGGCAAAAGTTCAGATGGAAAATCATATGTTATTACTGGAAGCTGGAACCCGAAATCCCCACATTTTCAAGTTGTGAATGAAGAAACTCCTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAACCCGAAATCCCCACAT
60.03
AGTTGTGACCTTTCCCCTGG
59.52
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAACCCGAAATCCCCACAT
60.03
CCAGTTGTGACCTTTCCCCT
59.52
151
PCR template sequence:
TCTATGGGCAAAAGTTCAGATGGAAAATCATATGTTATTACTGGAAGCTGGAACCCGAAATCCCCACATTTTCAAGTTGTGAATGAAGAAACTCCTAAAGATTGTAGGAAATGGAAGTGAGCAGCAGCTTCAGAAAGAGCTAGCAGATGTGCTGATGGATCCTCCCATGGACGACCAGCCAGGGGAAAGGTCACAACTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-101a-3p(1), mmu-miR-127-5p(1), mmu-miR-758-3p(1), mmu-miR-325-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAACTCCTAAAGATTGTAGGAAATG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRABGAP1_1039_ORF_1
0.9374
0.121901682
0.989752254
1056
ORF sequence:
ATGAAGAAACTCCTAAAGATTGTAGGAAATGGAAGTGAGCAGCAGCTTCAGAAAGAGCTAGCAGATGTGCTGATGGATCCTCCCATGGACGACCAGCCAGGGGAAAGGTCACAACTGGATGGTGAAGGAGATGGGCCTCTTTCTAATCAACTCTCAGCTTCATCCACCATTAATCCTGTGCCTCTGGTAGGGCTTCCGAAACCAGAGATGAGCCTGCCAGTGAAACCTGGACAAGGAGATTCTGAAGTATCAAGTCCTTTTACACCAGTGGCTGATGAGGATAGTGTGGTTTTCAATAAACTAACTTACTTAGGCTGTGCTTCAGTAAATGCTCCCCGGAGTGAAGTGGAAGCCTTGAGGATGATGTCCATCTTGAGAAGTCAGTGTCAGATTTCTCTGGATGTAACCCTCTCAGTGCCGAATGTATCTGAAGGAACTGTGAGACTTTTAGATCCTCAAACAAACACTGAAATAGCAAACTACCCTATCTACAAAATCCTCTTCTGTGTCAGAGGACATGATGGGACTCCTGAGAGTGACTGTTTTGCATTCACTGAAAGTCACTACAACGCAGAGCTCTTCAGGATACATGTCTTTCGCTGTGAAATACAAGAAGCTGTGAGCCGGATACTTTACAGTTTTGCCACCGCCTTCCGCCGCTCTGCCAAGCAGACCCCACTCTCAGCCACAGCTGCACCACAGACTCCTGACAGCGACATCTTTACCTTCTCTGTGTCTTTAGAAATAAAAGAAGATGATGGTAAAGGTTATTTTAGTGCTGTTCCCAAAGACAAGGACAGGCAATGCTTTAAACTTCGACAAGGAATTGATAAGAAGATTGTTATCTGTGTGCAGCAAACAGCTAACAAAGAACTTGCCATTGAAAGGTGCTTTGGTCTTCTCCTTAGCCCAGGAAAAGATGTCCGAAACAGTGATATGCACTTGCTGGATTTGGAGTCTATGGGCAAAAGTTCAGATGGAAAATCATATGTTATTACTGGAAGCTGGAACCCGAAATCCCCACATTTTCAAGTTGTGAATGAAGAAACTCCTAAA
Peptide sequence:
MKKLLKIVGNGSEQQLQKELADVLMDPPMDDQPGERSQLDGEGDGPLSNQLSASSTINPVPLVGLPKPEMSLPVKPGQGDSEVSSPFTPVADEDSVVFNKLTYLGCASVNAPRSEVEALRMMSILRSQCQISLDVTLSVPNVSEGTVRLLDPQTNTEIANYPIYKILFCVRGHDGTPESDCFAFTESHYNAELFRIHVFRCEIQEAVSRILYSFATAFRRSAKQTPLSATAAPQTPDSDIFTFSVSLEIKEDDGKGYFSAVPKDKDRQCFKLRQGIDKKIVICVQQTANKELAIERCFGLLLSPGKDVRNSDMHLLDLESMGKSSDGKSYVITGSWNPKSPHFQVVNEETPK
IRESfinder result
IRESfinder score
0.649972126
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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