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mmu_circRabgap1_958
Basic information of circular RNA
PanCircBase ID:
mmu_circRabgap1_958
mm39_Chr. Position ID:
chr2|37359388|37373897|+
Gene name:
Rabgap1
Transcript:
ENSMUST00000133434.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
2,3,4,5,6
Exon/intron offsets:
0,2918,4202,5915,14351
Genomic length:
14509
Exon/intron sizes in nt:
20,02,20,20,51,75,158
Flanking exon/introns:
chr2:37333468-37359388|chr2:37373897-37377077
Splice length:
958
Other database IDs:
CIRCpedia: MMU_CIRCpedia_213860, circAtlas: mmu-Rabgap1_0021
circBase: hsa_circ_0008917, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_62626
Human Ortholog IDs:
Mature spliced Sequence:
GCATTAAAAAAATATTTAACCATTCATGAGTTGAGCCTCATTCTTGAGTTATGGATGACAAGGCCTCTGTTGGAAAAATCAGTGTCTCATCAGACTCAGTGTCTACTCTTAATAGTGAAGATTTTGTCTTGGTTTCCAGGCAAGGAGATGAGACACCATCTACAAATAATGGGAGTGATGATGAGAAGACGGGACTCAAGATTGTAGGAAATGGAAGTGAGCAGCAGCTTCAGAAAGAGCTAGCAGATGTGCTGATGGATCCTCCCATGGACGACCAGCCAGGGGAAAGGTCACAACTGGATGGTGAAGGAGATGGGCCTCTTTCTAATCAACTCTCAGCTTCATCCACCATTAATCCTGTGCCTCTGGTAGGGCTTCCGAAACCAGAGATGAGCCTGCCAGTGAAACCTGGACAAGGAGATTCTGAAGTATCAAGTCCTTTTACACCAGTGGCTGATGAGGATAGTGTGGTTTTCAATAAACTAACTTACTTAGGCTGTGCTTCAGTAAATGCTCCCCGGAGTGAAGTGGAAGCCTTGAGGATGATGTCCATCTTGAGAAGTCAGTGTCAGATTTCTCTGGATGTAACCCTCTCAGTGCCGAATGTATCTGAAGGAACTGTGAGACTTTTAGATCCTCAAACAAACACTGAAATAGCAAACTACCCTATCTACAAAATCCTCTTCTGTGTCAGAGGACATGATGGGACTCCTGAGAGTGACTGTTTTGCATTCACTGAAAGTCACTACAACGCAGAGCTCTTCAGGATACATGTCTTTCGCTGTGAAATACAAGAAGCTGTGAGCCGGATACTTTACAGTTTTGCCACCGCCTTCCGCCGCTCTGCCAAGCAGACCCCACTCTCAGCCACAGCTGCACCACAGACTCCTGACAGCGACATCTTTACCTTCTCTGTGTCTTTAGAAATAAAAGAAGATGATGGTAAAGGTTATTTTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACCACAGACTCCTGACAGC
60.32
TTCCAACAGAGGCCTTGTCA
59.16
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCACCACAGACTCCTGACAG
60.32
TTCCAACAGAGGCCTTGTCA
59.16
158
PCR template sequence:
CACTCTCAGCCACAGCTGCACCACAGACTCCTGACAGCGACATCTTTACCTTCTCTGTGTCTTTAGAAATAAAAGAAGATGATGGTAAAGGTTATTTTAGGCATTAAAAAAATATTTAACCATTCATGAGTTGAGCCTCATTCTTGAGTTATGGATGACAAGGCCTCTGTTGGAAAAATCAGTGTCTCATCAGACTCAGT
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-434-5p(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), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGGTTATTTTAGGCATTAAAAAAAT
siRNA sets
TTTTTTAATGCCTAAAATA, TAATGCCTAAAATAACCTT, TTTTTAATGCCTAAAATAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRABGAP1_958_ORF_1
1.0091
0.131589359
0.976560874
915
ORF sequence:
ATGGATGACAAGGCCTCTGTTGGAAAAATCAGTGTCTCATCAGACTCAGTGTCTACTCTTAATAGTGAAGATTTTGTCTTGGTTTCCAGGCAAGGAGATGAGACACCATCTACAAATAATGGGAGTGATGATGAGAAGACGGGACTCAAGATTGTAGGAAATGGAAGTGAGCAGCAGCTTCAGAAAGAGCTAGCAGATGTGCTGATGGATCCTCCCATGGACGACCAGCCAGGGGAAAGGTCACAACTGGATGGTGAAGGAGATGGGCCTCTTTCTAATCAACTCTCAGCTTCATCCACCATTAATCCTGTGCCTCTGGTAGGGCTTCCGAAACCAGAGATGAGCCTGCCAGTGAAACCTGGACAAGGAGATTCTGAAGTATCAAGTCCTTTTACACCAGTGGCTGATGAGGATAGTGTGGTTTTCAATAAACTAACTTACTTAGGCTGTGCTTCAGTAAATGCTCCCCGGAGTGAAGTGGAAGCCTTGAGGATGATGTCCATCTTGAGAAGTCAGTGTCAGATTTCTCTGGATGTAACCCTCTCAGTGCCGAATGTATCTGAAGGAACTGTGAGACTTTTAGATCCTCAAACAAACACTGAAATAGCAAACTACCCTATCTACAAAATCCTCTTCTGTGTCAGAGGACATGATGGGACTCCTGAGAGTGACTGTTTTGCATTCACTGAAAGTCACTACAACGCAGAGCTCTTCAGGATACATGTCTTTCGCTGTGAAATACAAGAAGCTGTGAGCCGGATACTTTACAGTTTTGCCACCGCCTTCCGCCGCTCTGCCAAGCAGACCCCACTCTCAGCCACAGCTGCACCACAGACTCCTGACAGCGACATCTTTACCTTCTCTGTGTCTTTAGAAATAAAAGAAGATGATGGTAAAGGTTATTTTAGGCATTAA
Peptide sequence:
MDDKASVGKISVSSDSVSTLNSEDFVLVSRQGDETPSTNNGSDDEKTGLKIVGNGSEQQLQKELADVLMDPPMDDQPGERSQLDGEGDGPLSNQLSASSTINPVPLVGLPKPEMSLPVKPGQGDSEVSSPFTPVADEDSVVFNKLTYLGCASVNAPRSEVEALRMMSILRSQCQISLDVTLSVPNVSEGTVRLLDPQTNTEIANYPIYKILFCVRGHDGTPESDCFAFTESHYNAELFRIHVFRCEIQEAVSRILYSFATAFRRSAKQTPLSATAAPQTPDSDIFTFSVSLEIKEDDGKGYFRH
IRESfinder result
IRESfinder score
0.677525805
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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