top of page
mmu_circRabep1_1020
Basic information of circular RNA
PanCircBase ID:
mmu_circRabep1_1020
mm39_Chr. Position ID:
chr11|70791297|70810107|+
Gene name:
Rabep1
Transcript:
ENSMUST00000076270.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,7,8,9,10
Exon/intron offsets:
0,4133,7914,16843,18705
Genomic length:
18810
Exon/intron sizes in nt:
13,61,79,13,24,68,105
Flanking exon/introns:
chr11:70784514-70791297|chr11:70810107-70811677
Splice length:
1020
Other database IDs:
circAtlas: mmu-Rabep1_0047
circBase: hsa_circ_0107106, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_114411
Human Ortholog IDs:
Mature spliced Sequence:
GTTAAGGAGCTGAATCATTATCTGGAGGCCGAGAAGTCTTGCAGGACTGACCTGGAGATGTACGTAGCTGTTTTGAACACTCAGAAATCTGTGCTACAGGAAGATGCTGAGAAATTGAGGAAAGAACTGCATGAAGTTTGCCATCTCTTGGAACAAGAACGACAACAACACAACCAGTTAAAGCATACATGGCAGAAGGCCAACGACCAGTTTCTGGAATCTCAGCGTTTGCTGATGAGAGACATGCAGAGAATGGAGATTGTGTTAACTTCGGAACAGCTCCGACAAGTTGAAGAACTAAAGAAGAAAGACCAGGAGGAGGATGAACAACAAAGGGTCAATAAGAGAAAAGATAACAAGAAAACAGATACCGAAGAAGAAGTAAAAATACCAGTAGTGTGTGCTTTAACTCAAGAAGAATCTTCAACCCCATTATCAAATGAAGAGGAGCATTTAGACAGCACCCATGGGTCAGTCCATTCCTTGGATGCAGACTTGATGTTACCATCTGGAGATCCATTTAGTAAATCGGACAATGACATGTTTAAAGATGGACTCAGGAGAGCTCAGTCTACAGACAGCTTGGGAACCTCAAGCTCATTGCAATCCAAAGCTTTAGGCTATAACTACAAAGCGAAATCTGCTGGAAATTTGGATGAGTCGGATTTTGGACCACTGGTTGGAGCAGATTCTGTGTCTGAGAACTTTGATACTGTGTCCCTTGGGTCACTGCAGATGCCAAGTGGATTTATGTTAACCAAAGATCAAGAAAGAGCAATTAAGGCAATGACACCTGAGCAGGAGGAGACAGCATCCCTCCTCTCCAGTGTCACCCAGGGTATGGAGAGTGCATATGTATCTCCCAGTGGTTACCGCTTAGTGAGTGAGACGGAATGGAATCTCCTGCAGAAAGAGGTACATAATGCTGGAAATAAGCTTGGTAGACGTTGTGATATGTGTTCCAATTATGAAAAACAGTTACAAGGAATTCAGATTCAGGAAGCTGAAACAAGAGACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGGAAATAAGCTTGGTAGACG
59.69
AGTCCTGCAAGACTTCTCGG
59.39
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGGAAATAAGCTTGGTAGACG
59.69
CTGCAAGACTTCTCGGCCTC
60.74
140
PCR template sequence:
TAATGCTGGAAATAAGCTTGGTAGACGTTGTGATATGTGTTCCAATTATGAAAAACAGTTACAAGGAATTCAGATTCAGGAAGCTGAAACAAGAGACCAGGTTAAGGAGCTGAATCATTATCTGGAGGCCGAGAAGTCTTGCAGGACTGACCTGGAGATGTACGTAGCTGTTTTGAACACTCAGAAATCTGTGCTACAGG
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-9-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-217-5p(1), mmu-miR-136-5p(1), mmu-miR-125a-5p(1), mmu-miR-466d-3p(1), mmu-miR-680(1), mmu-miR-207(1), mmu-miR-335-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AACAAGAGACCAGGTTAAGGAGCTGA
siRNA sets
TCAGCTCCTTAACCTGGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRABEP1_1020_ORF_1
0.9713
0.171776167
0.999990148
1983
ORF sequence:
ATGTACGTAGCTGTTTTGAACACTCAGAAATCTGTGCTACAGGAAGATGCTGAGAAATTGAGGAAAGAACTGCATGAAGTTTGCCATCTCTTGGAACAAGAACGACAACAACACAACCAGTTAAAGCATACATGGCAGAAGGCCAACGACCAGTTTCTGGAATCTCAGCGTTTGCTGATGAGAGACATGCAGAGAATGGAGATTGTGTTAACTTCGGAACAGCTCCGACAAGTTGAAGAACTAAAGAAGAAAGACCAGGAGGAGGATGAACAACAAAGGGTCAATAAGAGAAAAGATAACAAGAAAACAGATACCGAAGAAGAAGTAAAAATACCAGTAGTGTGTGCTTTAACTCAAGAAGAATCTTCAACCCCATTATCAAATGAAGAGGAGCATTTAGACAGCACCCATGGGTCAGTCCATTCCTTGGATGCAGACTTGATGTTACCATCTGGAGATCCATTTAGTAAATCGGACAATGACATGTTTAAAGATGGACTCAGGAGAGCTCAGTCTACAGACAGCTTGGGAACCTCAAGCTCATTGCAATCCAAAGCTTTAGGCTATAACTACAAAGCGAAATCTGCTGGAAATTTGGATGAGTCGGATTTTGGACCACTGGTTGGAGCAGATTCTGTGTCTGAGAACTTTGATACTGTGTCCCTTGGGTCACTGCAGATGCCAAGTGGATTTATGTTAACCAAAGATCAAGAAAGAGCAATTAAGGCAATGACACCTGAGCAGGAGGAGACAGCATCCCTCCTCTCCAGTGTCACCCAGGGTATGGAGAGTGCATATGTATCTCCCAGTGGTTACCGCTTAGTGAGTGAGACGGAATGGAATCTCCTGCAGAAAGAGGTACATAATGCTGGAAATAAGCTTGGTAGACGTTGTGATATGTGTTCCAATTATGAAAAACAGTTACAAGGAATTCAGATTCAGGAAGCTGAAACAAGAGACCAGGTTAAGGAGCTGAATCATTATCTGGAGGCCGAGAAGTCTTGCAGGACTGACCTGGAGATGTACGTAGCTGTTTTGAACACTCAGAAATCTGTGCTACAGGAAGATGCTGAGAAATTGAGGAAAGAACTGCATGAAGTTTGCCATCTCTTGGAACAAGAACGACAACAACACAACCAGTTAAAGCATACATGGCAGAAGGCCAACGACCAGTTTCTGGAATCTCAGCGTTTGCTGATGAGAGACATGCAGAGAATGGAGATTGTGTTAACTTCGGAACAGCTCCGACAAGTTGAAGAACTAAAGAAGAAAGACCAGGAGGAGGATGAACAACAAAGGGTCAATAAGAGAAAAGATAACAAGAAAACAGATACCGAAGAAGAAGTAAAAATACCAGTAGTGTGTGCTTTAACTCAAGAAGAATCTTCAACCCCATTATCAAATGAAGAGGAGCATTTAGACAGCACCCATGGGTCAGTCCATTCCTTGGATGCAGACTTGATGTTACCATCTGGAGATCCATTTAGTAAATCGGACAATGACATGTTTAAAGATGGACTCAGGAGAGCTCAGTCTACAGACAGCTTGGGAACCTCAAGCTCATTGCAATCCAAAGCTTTAGGCTATAACTACAAAGCGAAATCTGCTGGAAATTTGGATGAGTCGGATTTTGGACCACTGGTTGGAGCAGATTCTGTGTCTGAGAACTTTGATACTGTGTCCCTTGGGTCACTGCAGATGCCAAGTGGATTTATGTTAACCAAAGATCAAGAAAGAGCAATTAAGGCAATGACACCTGAGCAGGAGGAGACAGCATCCCTCCTCTCCAGTGTCACCCAGGGTATGGAGAGTGCATATGTATCTCCCAGTGGTTACCGCTTAGTGAGTGAGACGGAATGGAATCTCCTGCAGAAAGAGGTACATAATGCTGGAAATAAGCTTGGTAGACGTTGTGATATGTGTTCCAATTATGAAAAACAGTTACAAGGAATTCAGATTCAGGAAGCTGAAACAAGAGACCAG
Peptide sequence:
MYVAVLNTQKSVLQEDAEKLRKELHEVCHLLEQERQQHNQLKHTWQKANDQFLESQRLLMRDMQRMEIVLTSEQLRQVEELKKKDQEEDEQQRVNKRKDNKKTDTEEEVKIPVVCALTQEESSTPLSNEEEHLDSTHGSVHSLDADLMLPSGDPFSKSDNDMFKDGLRRAQSTDSLGTSSSLQSKALGYNYKAKSAGNLDESDFGPLVGADSVSENFDTVSLGSLQMPSGFMLTKDQERAIKAMTPEQEETASLLSSVTQGMESAYVSPSGYRLVSETEWNLLQKEVHNAGNKLGRRCDMCSNYEKQLQGIQIQEAETRDQVKELNHYLEAEKSCRTDLEMYVAVLNTQKSVLQEDAEKLRKELHEVCHLLEQERQQHNQLKHTWQKANDQFLESQRLLMRDMQRMEIVLTSEQLRQVEELKKKDQEEDEQQRVNKRKDNKKTDTEEEVKIPVVCALTQEESSTPLSNEEEHLDSTHGSVHSLDADLMLPSGDPFSKSDNDMFKDGLRRAQSTDSLGTSSSLQSKALGYNYKAKSAGNLDESDFGPLVGADSVSENFDTVSLGSLQMPSGFMLTKDQERAIKAMTPEQEETASLLSSVTQGMESAYVSPSGYRLVSETEWNLLQKEVHNAGNKLGRRCDMCSNYEKQLQGIQIQEAETRDQ
IRESfinder result
IRESfinder score
0.543764095
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page