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mmu_circRabep1_1176
Basic information of circular RNA
PanCircBase ID:
mmu_circRabep1_1176
mm39_Chr. Position ID:
chr11|70808140|70826008|+
Gene name:
Rabep1
Transcript:
ENSMUST00000076270.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
9,10,11,12,13,14,15
Exon/intron offsets:
0,1862,3537,5828,8457,17090,17812
Genomic length:
17868
Exon/intron sizes in nt:
468,105,117,99,141,190,56
Flanking exon/introns:
chr11:70799343-70808140|chr11:70826008-70828349
Splice length:
1176
Other database IDs:
CIRCpedia: MMU_CIRCpedia_27654, circAtlas: mmu-Rabep1_0030
circBase: hsa_circ_0107114, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_77576
Human Ortholog IDs:
Mature spliced Sequence:
GAGCATTTAGACAGCACCCATGGGTCAGTCCATTCCTTGGATGCAGACTTGATGTTACCATCTGGAGATCCATTTAGTAAATCGGACAATGACATGTTTAAAGATGGACTCAGGAGAGCTCAGTCTACAGACAGCTTGGGAACCTCAAGCTCATTGCAATCCAAAGCTTTAGGCTATAACTACAAAGCGAAATCTGCTGGAAATTTGGATGAGTCGGATTTTGGACCACTGGTTGGAGCAGATTCTGTGTCTGAGAACTTTGATACTGTGTCCCTTGGGTCACTGCAGATGCCAAGTGGATTTATGTTAACCAAAGATCAAGAAAGAGCAATTAAGGCAATGACACCTGAGCAGGAGGAGACAGCATCCCTCCTCTCCAGTGTCACCCAGGGTATGGAGAGTGCATATGTATCTCCCAGTGGTTACCGCTTAGTGAGTGAGACGGAATGGAATCTCCTGCAGAAAGAGGTACATAATGCTGGAAATAAGCTTGGTAGACGTTGTGATATGTGTTCCAATTATGAAAAACAGTTACAAGGAATTCAGATTCAGGAAGCTGAAACAAGAGACCAGGTGAAAAAACTGCAGTTAATGCTCAGGCAAGCTAATGACCAGCTTGAGAAGACGATGAAAGAGAAGCAGGAGCTGGAGGACTTCCTCAAGCAGAGTGCGGAGGACTCAAGCCACCAGATATCTGCACTTGTTTTAAGAGCCCAAGCCTCTGAGGTCTTACTTGAAGAGTTACAACAGAGCTTTTCCCAAGCAAAGAGGGACGTTCAGGAGCAGATGGCGGTGCTGATGCAGTCACGTGAACAGGTTTCAGAAGAGTTGGTGAGGTTACAGAAAGACAACGACAGCCTCCAGGGGAAGCACAGCTTGCATGTGTCATTACAGCTAGCAGAAGACTTCATTCTTCCAGACACTGTGGAGGTGCTCCGGGAACTGGTTTTAAAATATCGTGAGAACATTGTTCATGTGCGCACAGCAGCAGACCACATGGAAGAGAAGCTGAAGGCGGAAATACTTTTCCTAAAAGAGCAAATTCAAGCGGAACAGTGTTTAAAAGAAAACCTGGAAGAGACACTACAGCTGGAAATAGAAAACTGCAAGGAGGAAATAGCTTCCATTTCTAGTCTAAAAGCTGAATTAGAAAGAATAAAGGTTGAAAAGGGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGCTGGAAATAGAAAACTGCA
58.86
ACATCAAGTCTGCATCCAAGGA
59.69
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGACACTACAGCTGGAAA
55.81
ACATCAAGTCTGCATCCAAGGA
59.69
155
PCR template sequence:
AGAGACACTACAGCTGGAAATAGAAAACTGCAAGGAGGAAATAGCTTCCATTTCTAGTCTAAAAGCTGAATTAGAAAGAATAAAGGTTGAAAAGGGACAGGAGCATTTAGACAGCACCCATGGGTCAGTCCATTCCTTGGATGCAGACTTGATGTTACCATCTGGAGATCCATTTAGTAAATCGGACAATGACATGTTTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-217-5p(2), mmu-miR-9-5p(1), mmu-miR-141-3p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-26a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-26b-5p(1), mmu-miR-125a-5p(1), mmu-miR-466d-3p(1), mmu-miR-680(1), mmu-miR-335-3p(1), mmu-miR-1904(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAAAAGGGACAGGAGCATTTAGACA
siRNA sets
TGTCTAAATGCTCCTGTCC, GTCTAAATGCTCCTGTCCC, TCTAAATGCTCCTGTCCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRABEP1_1176_ORF_1
1.0304
0.188092197
0.999999162
2301
ORF sequence:
ATGTTACCATCTGGAGATCCATTTAGTAAATCGGACAATGACATGTTTAAAGATGGACTCAGGAGAGCTCAGTCTACAGACAGCTTGGGAACCTCAAGCTCATTGCAATCCAAAGCTTTAGGCTATAACTACAAAGCGAAATCTGCTGGAAATTTGGATGAGTCGGATTTTGGACCACTGGTTGGAGCAGATTCTGTGTCTGAGAACTTTGATACTGTGTCCCTTGGGTCACTGCAGATGCCAAGTGGATTTATGTTAACCAAAGATCAAGAAAGAGCAATTAAGGCAATGACACCTGAGCAGGAGGAGACAGCATCCCTCCTCTCCAGTGTCACCCAGGGTATGGAGAGTGCATATGTATCTCCCAGTGGTTACCGCTTAGTGAGTGAGACGGAATGGAATCTCCTGCAGAAAGAGGTACATAATGCTGGAAATAAGCTTGGTAGACGTTGTGATATGTGTTCCAATTATGAAAAACAGTTACAAGGAATTCAGATTCAGGAAGCTGAAACAAGAGACCAGGTGAAAAAACTGCAGTTAATGCTCAGGCAAGCTAATGACCAGCTTGAGAAGACGATGAAAGAGAAGCAGGAGCTGGAGGACTTCCTCAAGCAGAGTGCGGAGGACTCAAGCCACCAGATATCTGCACTTGTTTTAAGAGCCCAAGCCTCTGAGGTCTTACTTGAAGAGTTACAACAGAGCTTTTCCCAAGCAAAGAGGGACGTTCAGGAGCAGATGGCGGTGCTGATGCAGTCACGTGAACAGGTTTCAGAAGAGTTGGTGAGGTTACAGAAAGACAACGACAGCCTCCAGGGGAAGCACAGCTTGCATGTGTCATTACAGCTAGCAGAAGACTTCATTCTTCCAGACACTGTGGAGGTGCTCCGGGAACTGGTTTTAAAATATCGTGAGAACATTGTTCATGTGCGCACAGCAGCAGACCACATGGAAGAGAAGCTGAAGGCGGAAATACTTTTCCTAAAAGAGCAAATTCAAGCGGAACAGTGTTTAAAAGAAAACCTGGAAGAGACACTACAGCTGGAAATAGAAAACTGCAAGGAGGAAATAGCTTCCATTTCTAGTCTAAAAGCTGAATTAGAAAGAATAAAGGTTGAAAAGGGACAGGAGCATTTAGACAGCACCCATGGGTCAGTCCATTCCTTGGATGCAGACTTGATGTTACCATCTGGAGATCCATTTAGTAAATCGGACAATGACATGTTTAAAGATGGACTCAGGAGAGCTCAGTCTACAGACAGCTTGGGAACCTCAAGCTCATTGCAATCCAAAGCTTTAGGCTATAACTACAAAGCGAAATCTGCTGGAAATTTGGATGAGTCGGATTTTGGACCACTGGTTGGAGCAGATTCTGTGTCTGAGAACTTTGATACTGTGTCCCTTGGGTCACTGCAGATGCCAAGTGGATTTATGTTAACCAAAGATCAAGAAAGAGCAATTAAGGCAATGACACCTGAGCAGGAGGAGACAGCATCCCTCCTCTCCAGTGTCACCCAGGGTATGGAGAGTGCATATGTATCTCCCAGTGGTTACCGCTTAGTGAGTGAGACGGAATGGAATCTCCTGCAGAAAGAGGTACATAATGCTGGAAATAAGCTTGGTAGACGTTGTGATATGTGTTCCAATTATGAAAAACAGTTACAAGGAATTCAGATTCAGGAAGCTGAAACAAGAGACCAGGTGAAAAAACTGCAGTTAATGCTCAGGCAAGCTAATGACCAGCTTGAGAAGACGATGAAAGAGAAGCAGGAGCTGGAGGACTTCCTCAAGCAGAGTGCGGAGGACTCAAGCCACCAGATATCTGCACTTGTTTTAAGAGCCCAAGCCTCTGAGGTCTTACTTGAAGAGTTACAACAGAGCTTTTCCCAAGCAAAGAGGGACGTTCAGGAGCAGATGGCGGTGCTGATGCAGTCACGTGAACAGGTTTCAGAAGAGTTGGTGAGGTTACAGAAAGACAACGACAGCCTCCAGGGGAAGCACAGCTTGCATGTGTCATTACAGCTAGCAGAAGACTTCATTCTTCCAGACACTGTGGAGGTGCTCCGGGAACTGGTTTTAAAATATCGTGAGAACATTGTTCATGTGCGCACAGCAGCAGACCACATGGAAGAGAAGCTGAAGGCGGAAATACTTTTCCTAAAAGAGCAAATTCAAGCGGAACAGTGTTTAAAAGAAAACCTGGAAGAGACACTACAGCTGGAAATAGAAAACTGCAAGGAGGAAATAGCTTCCATTTCTAGTCTAAAAGCTGAATTAGAAAGAATAAAGGTTGAAAAGGGACAG
Peptide sequence:
MLPSGDPFSKSDNDMFKDGLRRAQSTDSLGTSSSLQSKALGYNYKAKSAGNLDESDFGPLVGADSVSENFDTVSLGSLQMPSGFMLTKDQERAIKAMTPEQEETASLLSSVTQGMESAYVSPSGYRLVSETEWNLLQKEVHNAGNKLGRRCDMCSNYEKQLQGIQIQEAETRDQVKKLQLMLRQANDQLEKTMKEKQELEDFLKQSAEDSSHQISALVLRAQASEVLLEELQQSFSQAKRDVQEQMAVLMQSREQVSEELVRLQKDNDSLQGKHSLHVSLQLAEDFILPDTVEVLRELVLKYRENIVHVRTAADHMEEKLKAEILFLKEQIQAEQCLKENLEETLQLEIENCKEEIASISSLKAELERIKVEKGQEHLDSTHGSVHSLDADLMLPSGDPFSKSDNDMFKDGLRRAQSTDSLGTSSSLQSKALGYNYKAKSAGNLDESDFGPLVGADSVSENFDTVSLGSLQMPSGFMLTKDQERAIKAMTPEQEETASLLSSVTQGMESAYVSPSGYRLVSETEWNLLQKEVHNAGNKLGRRCDMCSNYEKQLQGIQIQEAETRDQVKKLQLMLRQANDQLEKTMKEKQELEDFLKQSAEDSSHQISALVLRAQASEVLLEELQQSFSQAKRDVQEQMAVLMQSREQVSEELVRLQKDNDSLQGKHSLHVSLQLAEDFILPDTVEVLRELVLKYRENIVHVRTAADHMEEKLKAEILFLKEQIQAEQCLKENLEETLQLEIENCKEEIASISSLKAELERIKVEKGQ
IRESfinder result
IRESfinder score
0.529432467
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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