top of page
mmu_circDennd1b_861
Basic information of circular RNA
PanCircBase ID:
mmu_circDennd1b_861
mm39_Chr. Position ID:
chr1|138967737|139029831|+
Gene name:
Dennd1b
Transcript:
ENSMUST00000168527.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
4,5,6,7,8,9,10,11,12,13
Exon/intron offsets:
0,1924,13346,14541,20275,22861,41173,45883,50454,61968
Genomic length:
62094
Exon/intron sizes in nt:
50,12,07,08,15,41,11,10,00,00,00,000
Flanking exon/introns:
chr1:138950886-138967737|chr1:139029831-139038121
Splice length:
861
Other database IDs:
circAtlas: mmu-Dennd1b_0043
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_140243
Human Ortholog IDs:
Mature spliced Sequence:
GAAGTTCTGCAGAGCGTGCCCAAGTTCTGTTTTCCCTTCGATGTGGAAAGGGTGTCTCAGAATCAAGTTGGACAGCACTTTACCTTCGTCCTGACAGACATGGAAAGTAAGCAGCGATTTGGGTTCTGCAGGCTCACATCTGGAGGCAGAATTTGTTTATGTATTCTTAGTTACTTGCCATGGTTTGAAGTATATTATAAACTTCTAAATACTCTGGCAGATTACTTGGCCAAGGAACTGGAAGAGGATTTGAATGAAACTCTTAAATCACTCTATAACCACCCAGTACCAAAGGCAAACACTCCTGTCAACTTGAGTGTGCACTCCTGTTTCATCACACCTGACATAACTGGACTCCCAACGATACCGGAGAGTAGAAACCTGACCGAGTACTTTGTTGCCGTGGATGTCAACAACATGCTGCGACTGTACGCCAGCATGCTGCATGAGAGGCGCATCATTATTACCTCGAGCAAATTAAGCACTTTAACTGCCTGTCTCCATGGATCGGCTGCGCTACTCTACCCGATGTACTGGCAACACATATATATCCCCGTGCTTCCTCCACACCTGCTGGACTACTGCTGTGCCCCAATGCCATACCTGATTGGAATACACTCCAGTCTCATAGAGAGAGTGAAAAATAAATCATTGGAAGATGTGGTTGTGTTAAATGTTGACACAAACACGTTAGAATCACCATTTAATGACTTGAGCAGCCTGCCCAGTGATGTGGTCTCGGCCTTGAAAAATAAGCTGAAGAAGCAGTCCACAGCTACGGGAGATGGAGTGGCTCGGGCCTTTCTGAGGGCTCAGGCGGCTTTGTTTGGCTCCTACCGAGATGCTCTGAGATACAAGCCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGCTACGGGAGATGGAGT
60.03
TGAGACACCCTTTCCACATCG
60
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCCACAGCTACGGGAGAT
60.03
TGAGACACCCTTTCCACATCG
60
154
PCR template sequence:
GAAGCAGTCCACAGCTACGGGAGATGGAGTGGCTCGGGCCTTTCTGAGGGCTCAGGCGGCTTTGTTTGGCTCCTACCGAGATGCTCTGAGATACAAGCCTGAAGTTCTGCAGAGCGTGCCCAAGTTCTGTTTTCCCTTCGATGTGGAAAGGGTGTCTCAGAATCAAGTTGGACAGCACTTTACCTTCGTCCTGACAGACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-93-5p(2), mmu-miR-17-5p(2), mmu-miR-122-5p(2), mmu-miR-106b-5p(2), mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-20a-5p(1), mmu-miR-26b-5p(1), mmu-miR-382-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-297a-5p(1), mmu-miR-466d-3p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGATACAAGCCTGAAGTTCTGCAGA
siRNA sets
AACTTCAGGCTTGTATCTC, GAACTTCAGGCTTGTATCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDENND1B_861_ORF_1
0.7844
0.150950215
0.999797507
1623
ORF sequence:
ATGGAAAGTAAGCAGCGATTTGGGTTCTGCAGGCTCACATCTGGAGGCAGAATTTGTTTATGTATTCTTAGTTACTTGCCATGGTTTGAAGTATATTATAAACTTCTAAATACTCTGGCAGATTACTTGGCCAAGGAACTGGAAGAGGATTTGAATGAAACTCTTAAATCACTCTATAACCACCCAGTACCAAAGGCAAACACTCCTGTCAACTTGAGTGTGCACTCCTGTTTCATCACACCTGACATAACTGGACTCCCAACGATACCGGAGAGTAGAAACCTGACCGAGTACTTTGTTGCCGTGGATGTCAACAACATGCTGCGACTGTACGCCAGCATGCTGCATGAGAGGCGCATCATTATTACCTCGAGCAAATTAAGCACTTTAACTGCCTGTCTCCATGGATCGGCTGCGCTACTCTACCCGATGTACTGGCAACACATATATATCCCCGTGCTTCCTCCACACCTGCTGGACTACTGCTGTGCCCCAATGCCATACCTGATTGGAATACACTCCAGTCTCATAGAGAGAGTGAAAAATAAATCATTGGAAGATGTGGTTGTGTTAAATGTTGACACAAACACGTTAGAATCACCATTTAATGACTTGAGCAGCCTGCCCAGTGATGTGGTCTCGGCCTTGAAAAATAAGCTGAAGAAGCAGTCCACAGCTACGGGAGATGGAGTGGCTCGGGCCTTTCTGAGGGCTCAGGCGGCTTTGTTTGGCTCCTACCGAGATGCTCTGAGATACAAGCCTGAAGTTCTGCAGAGCGTGCCCAAGTTCTGTTTTCCCTTCGATGTGGAAAGGGTGTCTCAGAATCAAGTTGGACAGCACTTTACCTTCGTCCTGACAGACATGGAAAGTAAGCAGCGATTTGGGTTCTGCAGGCTCACATCTGGAGGCAGAATTTGTTTATGTATTCTTAGTTACTTGCCATGGTTTGAAGTATATTATAAACTTCTAAATACTCTGGCAGATTACTTGGCCAAGGAACTGGAAGAGGATTTGAATGAAACTCTTAAATCACTCTATAACCACCCAGTACCAAAGGCAAACACTCCTGTCAACTTGAGTGTGCACTCCTGTTTCATCACACCTGACATAACTGGACTCCCAACGATACCGGAGAGTAGAAACCTGACCGAGTACTTTGTTGCCGTGGATGTCAACAACATGCTGCGACTGTACGCCAGCATGCTGCATGAGAGGCGCATCATTATTACCTCGAGCAAATTAAGCACTTTAACTGCCTGTCTCCATGGATCGGCTGCGCTACTCTACCCGATGTACTGGCAACACATATATATCCCCGTGCTTCCTCCACACCTGCTGGACTACTGCTGTGCCCCAATGCCATACCTGATTGGAATACACTCCAGTCTCATAGAGAGAGTGAAAAATAAATCATTGGAAGATGTGGTTGTGTTAAATGTTGACACAAACACGTTAGAATCACCATTTAATGACTTGAGCAGCCTGCCCAGTGATGTGGTCTCGGCCTTGAAAAATAAGCTGAAGAAGCAGTCCACAGCTACGGGAGATGGAGTGGCTCGGGCCTTTCTGAGGGCTCAGGCGGCTTTGTTTGGCTCCTACCGAGATGCTCTGAGATACAAGCCT
Peptide sequence:
MESKQRFGFCRLTSGGRICLCILSYLPWFEVYYKLLNTLADYLAKELEEDLNETLKSLYNHPVPKANTPVNLSVHSCFITPDITGLPTIPESRNLTEYFVAVDVNNMLRLYASMLHERRIIITSSKLSTLTACLHGSAALLYPMYWQHIYIPVLPPHLLDYCCAPMPYLIGIHSSLIERVKNKSLEDVVVLNVDTNTLESPFNDLSSLPSDVVSALKNKLKKQSTATGDGVARAFLRAQAALFGSYRDALRYKPEVLQSVPKFCFPFDVERVSQNQVGQHFTFVLTDMESKQRFGFCRLTSGGRICLCILSYLPWFEVYYKLLNTLADYLAKELEEDLNETLKSLYNHPVPKANTPVNLSVHSCFITPDITGLPTIPESRNLTEYFVAVDVNNMLRLYASMLHERRIIITSSKLSTLTACLHGSAALLYPMYWQHIYIPVLPPHLLDYCCAPMPYLIGIHSSLIERVKNKSLEDVVVLNVDTNTLESPFNDLSSLPSDVVSALKNKLKKQSTATGDGVARAFLRAQAALFGSYRDALRYKP
IRESfinder result
IRESfinder score
0.66725301
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page