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mmu_circRb1_1088
Basic information of circular RNA
PanCircBase ID:
mmu_circRb1_1088
mm39_Chr. Position ID:
chr14|73499968|73520418|-
Gene name:
Rb1
Transcript:
ENSMUST00000022701.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
17,16,15,14,13,12,11,10,9,8,7
Exon/intron offsets:
0,1764,1921,2044,2987,6582,10104,11108,15885,17593,20339
Genomic length:
20450
Exon/intron sizes in nt:
19,77,73,25,71,17,88,70,00,00,00,00,000
Flanking exon/introns:
chr14:73454219-73499968|chr14:73520418-73525042
Splice length:
1088
Other database IDs:
circBase: mmu_circ_0005426, CIRCpedia: MMU_CIRCpedia_28353, circAtlas: mmu-Rb1_0003
circBase: hsa_circ_0100638, circAtlas: hsa-RB1_0004, CIRCpedia: HSA_CIRCpedia_126837
Human Ortholog IDs:
Mature spliced Sequence:
GAGAAGTATTACAGATGGAAGATGACCTGGTAATCTCATTTCAGCTAATGTTGTGTGTAGTTGACTATTTTATTAAGTTCTCACCTCCTGCACTACTCAGAGAGCCATACAAAACAGCTGCAATCCCCATTAATGGTTCACCTCGAACACCCAGAAGAGGTCAGAACAGGAGCGCTCGGATAGCAAAACAACTAGAAAATGATACGAGGATTATCGAGGTTCTCTGTAAAGAACACGAGTGTAATATAGATGAGGTGAAAAATGTTTATTTCAAAAATTTTATCCCTTTTATAAATTCACTTGGAATTGTATCATCTAATGGACTTCCAGAGGTTGAAAGTCTTTCTAAACGCTATGAAGAAGTTTATCTTAAAAACAAAGATTTAGATGCAAGACTGTTTTTGGATCATGATAAAACACTTCAGACTGATCCTATAGACAGTTTTGAAACAGAGAGAACGCCACGAAAAAACAACCCTGATGAAGAGGCAAACGTGGTTACTCCACACACTCCAGTTAGGACTGTTATGAATACTATTCAACAATTAATGGTGATTTTAAATTCTGCAAGTGATCAGCCATCAGAAAATCTGATTTCCTACTTCAATAATTGCACAGTGAATCCAAAAGAAAATATCCTAAAGAGAGTAAAGGATGTTGGGCACATCTTTAAAGAGAAGTTTGCTAACGCTGTGGGCCAGGGCTGTGTTGACATCGGAGTACAGCGATATAAACTTGGAGTCCGATTGTATTACCGTGTGATGGAATCCATGCTTAAATCAGAAGAAGAACGTTTGTCCATTCAGAATTTTAGCAAACTCCTAAATGACAACATCTTTCATATGTCTTTACTGGCCTGTGCTCTTGAAGTTGTAATGGCTACGTATAGCAGAAGTACATTGCAGCATCTTGATTCTGGAACAGATTTGTCCTTCCCGTGGATTCTGAACGTACTTAATTTAAAAGCCTTTGATTTTTACAAAGTGATTGAAAGTTTTATCAAAGTGGAAGCCAACTTGACAAGAGAAATGATAAAACATTTAGAAAGATGTGAGCATCGAATCATGGAATCCCTTGCATGGCTTTCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGGAAGCCAACTTGACAAGA
60.09
AGTGCAGGAGGTGAGAACTT
58.57
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAAGCCAACTTGACAAGAGA
59.83
AGTGCAGGAGGTGAGAACTT
58.57
177
PCR template sequence:
TGAAAGTTTTATCAAAGTGGAAGCCAACTTGACAAGAGAAATGATAAAACATTTAGAAAGATGTGAGCATCGAATCATGGAATCCCTTGCATGGCTTTCAGAGAAGTATTACAGATGGAAGATGACCTGGTAATCTCATTTCAGCTAATGTTGTGTGTAGTTGACTATTTTATTAAGTTCTCACCTCCTGCACTACTCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-let-7e-5p(1), mmu-miR-146a-5p(1), mmu-miR-30c-5p(1), mmu-miR-541-5p(1), mmu-miR-98-5p(1), mmu-miR-300-3p(1), mmu-miR-673-5p(1), mmu-miR-574-5p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCATGGCTTTCAGAGAAGTATTACA
siRNA sets
TAATACTTCTCTGAAAGCC,AATACTTCTCTGAAAGCCA,GTAATACTTCTCTGAAAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRB1_1088_ORF_1
0.8864
0.014970508
0.987920644
1107
ORF sequence:
ATGGAAGATGACCTGGTAATCTCATTTCAGCTAATGTTGTGTGTAGTTGACTATTTTATTAAGTTCTCACCTCCTGCACTACTCAGAGAGCCATACAAAACAGCTGCAATCCCCATTAATGGTTCACCTCGAACACCCAGAAGAGGTCAGAACAGGAGCGCTCGGATAGCAAAACAACTAGAAAATGATACGAGGATTATCGAGGTTCTCTGTAAAGAACACGAGTGTAATATAGATGAGGTGAAAAATGTTTATTTCAAAAATTTTATCCCTTTTATAAATTCACTTGGAATTGTATCATCTAATGGACTTCCAGAGGTTGAAAGTCTTTCTAAACGCTATGAAGAAGTTTATCTTAAAAACAAAGATTTAGATGCAAGACTGTTTTTGGATCATGATAAAACACTTCAGACTGATCCTATAGACAGTTTTGAAACAGAGAGAACGCCACGAAAAAACAACCCTGATGAAGAGGCAAACGTGGTTACTCCACACACTCCAGTTAGGACTGTTATGAATACTATTCAACAATTAATGGTGATTTTAAATTCTGCAAGTGATCAGCCATCAGAAAATCTGATTTCCTACTTCAATAATTGCACAGTGAATCCAAAAGAAAATATCCTAAAGAGAGTAAAGGATGTTGGGCACATCTTTAAAGAGAAGTTTGCTAACGCTGTGGGCCAGGGCTGTGTTGACATCGGAGTACAGCGATATAAACTTGGAGTCCGATTGTATTACCGTGTGATGGAATCCATGCTTAAATCAGAAGAAGAACGTTTGTCCATTCAGAATTTTAGCAAACTCCTAAATGACAACATCTTTCATATGTCTTTACTGGCCTGTGCTCTTGAAGTTGTAATGGCTACGTATAGCAGAAGTACATTGCAGCATCTTGATTCTGGAACAGATTTGTCCTTCCCGTGGATTCTGAACGTACTTAATTTAAAAGCCTTTGATTTTTACAAAGTGATTGAAAGTTTTATCAAAGTGGAAGCCAACTTGACAAGAGAAATGATAAAACATTTAGAAAGATGTGAGCATCGAATCATGGAATCCCTTGCATGGCTTTCAGAGAAGTATTACAGATGGAAGATGACCTGGTAA
Peptide sequence:
MEDDLVISFQLMLCVVDYFIKFSPPALLREPYKTAAIPINGSPRTPRRGQNRSARIAKQLENDTRIIEVLCKEHECNIDEVKNVYFKNFIPFINSLGIVSSNGLPEVESLSKRYEEVYLKNKDLDARLFLDHDKTLQTDPIDSFETERTPRKNNPDEEANVVTPHTPVRTVMNTIQQLMVILNSASDQPSENLISYFNNCTVNPKENILKRVKDVGHIFKEKFANAVGQGCVDIGVQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTLQHLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKVEANLTREMIKHLERCEHRIMESLAWLSEKYYRWKMTW
IRESfinder result
IRESfinder score
0.722057096
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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