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mmu_circRabgap1_1258
Basic information of circular RNA
PanCircBase ID:
mmu_circRabgap1_1258
mm39_Chr. Position ID:
chr2|37363590|37392973|+
Gene name:
Rabgap1
Transcript:
ENSMUST00000061179.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
4,5,6,7,8,9,10,11,12
Exon/intron offsets:
0,1713,10149,13487,13933,16152,18331,22004,29289
Genomic length:
29383
Exon/intron sizes in nt:
205,175,158,111,67,103,170,175,94
Flanking exon/introns:
chr2:37362526-37363590|chr2:37392973-37398939
Splice length:
1258
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATTCTGAAGTATCAAGTCCTTTTACACCAGTGGCTGATGAGGATAGTGTGGTTTTCAATAAACTAACTTACTTAGGCTGTGCTTCAGTAAATGCTCCCCGGAGTGAAGTGGAAGCCTTGAGGATGATGTCCATCTTGAGAAGTCAGTGTCAGATTTCTCTGGATGTAACCCTCTCAGTGCCGAATGTATCTGAAGGAACTGTGAGACTTTTAGATCCTCAAACAAACACTGAAATAGCAAACTACCCTATCTACAAAATCCTCTTCTGTGTCAGAGGACATGATGGGACTCCTGAGAGTGACTGTTTTGCATTCACTGAAAGTCACTACAACGCAGAGCTCTTCAGGATACATGTCTTTCGCTGTGAAATACAAGAAGCTGTGAGCCGGATACTTTACAGTTTTGCCACCGCCTTCCGCCGCTCTGCCAAGCAGACCCCACTCTCAGCCACAGCTGCACCACAGACTCCTGACAGCGACATCTTTACCTTCTCTGTGTCTTTAGAAATAAAAGAAGATGATGGTAAAGGTTATTTTAGTGCTGTTCCCAAAGACAAGGACAGGCAATGCTTTAAACTTCGACAAGGAATTGATAAGAAGATTGTTATCTGTGTGCAGCAAACAGCTAACAAAGAACTTGCCATTGAAAGGTGCTTTGGTCTTCTCCTTAGCCCAGGAAAAGATGTCCGAAACAGTGATATGCACTTGCTGGATTTGGAGTCTATGGGCAAAAGTTCAGATGGAAAATCATATGTTATTACTGGAAGCTGGAACCCGAAATCCCCACATTTTCAAGTTGTGAATGAAGAAACTCCTAAAGATAAAGTGCTGTTCATGACAACAGCTGTGGATTTGGTGATAACTGAAGTACAGGAACCTGTTCGATTTCTTCTAGAGACAAAAGTTCGAGTGTGCTCACCTAATGAAAGGTTATTCTGGCCCTTCAGCAAACGAAGCACTACTGAAAACTTCTTTCTGAAACTGAAGCAGATAAAGCAAAAGGAGAAAAAGAATAATGCTGACACTTTATATGAAGTTGTGTGTTTGGAGAGTGAGTCAGAGAGAGAGAGGAGGAAAACCACAGCCAGTCCTTCAGTTCGCCTGCCACAGTCTGGATCCCAGAGCTCCATGATCCCCTCTCCCCCAGAAGATGATGAAGAAGAAGATAATGATGAACCTCTCTTGAGTGGATTTGGGGATGTATCCAAAGAATGTGCAGAAAAAATTCTTGAAACATGGGGAGAACTGCTGTCAAAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTTGAGTGGATTTGGGGATGT
59.35
CGGGGAGCATTTACTGAAGC
58.98
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTTGAGTGGATTTGGGGATGT
57.91
CGGGGAGCATTTACTGAAGC
58.98
178
PCR template sequence:
AAGAAGATAATGATGAACCTCTCTTGAGTGGATTTGGGGATGTATCCAAAGAATGTGCAGAAAAAATTCTTGAAACATGGGGAGAACTGCTGTCAAAATGATTCTGAAGTATCAAGTCCTTTTACACCAGTGGCTGATGAGGATAGTGTGGTTTTCAATAAACTAACTTACTTAGGCTGTGCTTCAGTAAATGCTCCCCG
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-101a-3p(1), mmu-miR-322-5p(1), mmu-miR-325-3p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCTGTCAAAATGATTCTGAAGTATC
siRNA sets
ATACTTCAGAATCATTTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRABGAP1_1258_ORF_1
0.805
0.106531533
0.997837997
1317
ORF sequence:
ATGTATCCAAAGAATGTGCAGAAAAAATTCTTGAAACATGGGGAGAACTGCTGTCAAAATGATTCTGAAGTATCAAGTCCTTTTACACCAGTGGCTGATGAGGATAGTGTGGTTTTCAATAAACTAACTTACTTAGGCTGTGCTTCAGTAAATGCTCCCCGGAGTGAAGTGGAAGCCTTGAGGATGATGTCCATCTTGAGAAGTCAGTGTCAGATTTCTCTGGATGTAACCCTCTCAGTGCCGAATGTATCTGAAGGAACTGTGAGACTTTTAGATCCTCAAACAAACACTGAAATAGCAAACTACCCTATCTACAAAATCCTCTTCTGTGTCAGAGGACATGATGGGACTCCTGAGAGTGACTGTTTTGCATTCACTGAAAGTCACTACAACGCAGAGCTCTTCAGGATACATGTCTTTCGCTGTGAAATACAAGAAGCTGTGAGCCGGATACTTTACAGTTTTGCCACCGCCTTCCGCCGCTCTGCCAAGCAGACCCCACTCTCAGCCACAGCTGCACCACAGACTCCTGACAGCGACATCTTTACCTTCTCTGTGTCTTTAGAAATAAAAGAAGATGATGGTAAAGGTTATTTTAGTGCTGTTCCCAAAGACAAGGACAGGCAATGCTTTAAACTTCGACAAGGAATTGATAAGAAGATTGTTATCTGTGTGCAGCAAACAGCTAACAAAGAACTTGCCATTGAAAGGTGCTTTGGTCTTCTCCTTAGCCCAGGAAAAGATGTCCGAAACAGTGATATGCACTTGCTGGATTTGGAGTCTATGGGCAAAAGTTCAGATGGAAAATCATATGTTATTACTGGAAGCTGGAACCCGAAATCCCCACATTTTCAAGTTGTGAATGAAGAAACTCCTAAAGATAAAGTGCTGTTCATGACAACAGCTGTGGATTTGGTGATAACTGAAGTACAGGAACCTGTTCGATTTCTTCTAGAGACAAAAGTTCGAGTGTGCTCACCTAATGAAAGGTTATTCTGGCCCTTCAGCAAACGAAGCACTACTGAAAACTTCTTTCTGAAACTGAAGCAGATAAAGCAAAAGGAGAAAAAGAATAATGCTGACACTTTATATGAAGTTGTGTGTTTGGAGAGTGAGTCAGAGAGAGAGAGGAGGAAAACCACAGCCAGTCCTTCAGTTCGCCTGCCACAGTCTGGATCCCAGAGCTCCATGATCCCCTCTCCCCCAGAAGATGATGAAGAAGAAGATAATGATGAACCTCTCTTGAGTGGATTTGGGGATGTATCCAAAGAATGTGCAGAAAAAATTCTTGAAACATGGGGAGAACTGCTGTCAAAA
Peptide sequence:
MYPKNVQKKFLKHGENCCQNDSEVSSPFTPVADEDSVVFNKLTYLGCASVNAPRSEVEALRMMSILRSQCQISLDVTLSVPNVSEGTVRLLDPQTNTEIANYPIYKILFCVRGHDGTPESDCFAFTESHYNAELFRIHVFRCEIQEAVSRILYSFATAFRRSAKQTPLSATAAPQTPDSDIFTFSVSLEIKEDDGKGYFSAVPKDKDRQCFKLRQGIDKKIVICVQQTANKELAIERCFGLLLSPGKDVRNSDMHLLDLESMGKSSDGKSYVITGSWNPKSPHFQVVNEETPKDKVLFMTTAVDLVITEVQEPVRFLLETKVRVCSPNERLFWPFSKRSTTENFFLKLKQIKQKEKKNNADTLYEVVCLESESERERRKTTASPSVRLPQSGSQSSMIPSPPEDDEEEDNDEPLLSGFGDVSKECAEKILETWGELLSK
IRESfinder result
IRESfinder score
0.654938516
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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