top of page
mmu_circLmbrd1_1104
Basic information of circular RNA
PanCircBase ID:
mmu_circLmbrd1_1104
mm39_Chr. Position ID:
chr1|24745057|24801364|+
Gene name:
Lmbrd1
Transcript:
ENSMUST00000191471.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
5,6,7,8,9,10,11,12,13,14,15
Exon/intron offsets:
0,5535,8932,22569,25770,37906,38279,38889,40828,42823,56215
Genomic length:
56307
Exon/intron sizes in nt:
68,89,74,126,153,65,103,105,150,79,92
Flanking exon/introns:
chr1:24743999-24745057|chr1:24801364-24801703
Splice length:
1104
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CAAATTAAAACGGCGCTCAAGTACACTTTGGGATTTGTTGTGATCTGCGCTCTGCTGCTTCTCGTTGGTGCCTTTGTGCCTCTGCATCTGCCCAACAACAACAACTCAACAGAGTGGGAAAAGGTGAAGCTCCTGTTTGAAGACCTTGGAACTGGTCAAGGCCTGGCAGCTCTGTCCTTTTCCATCAGCTCTCTGACCTTGATTGGGATGCTGGCGGCCATAACCTACACAGCGTACGGCATGTCGGCATTACCTTTAAACCTAATCAAAGGCACTAGAAGCACTGCCTACGAGCGCCTGGAGAACACGGAGGACATCGAGGAAGTGGAGCAGCACATTCAGACGATTCGATCCAAGAGCAAAGATGGTCGACCTTTGCCAGCGAGGGATAGACGTGCCTTAAAGCAATGTGAAGAAAGACTAAGAACGCTTAGGAAAAGAGAGCGGCACTTGGAATTCATTGAAAACAGCTGGTGGACGAAATTTTGTGGTGCCCTGCGCCCCCTGAAGATCATTTGGGGAATATTTTTCATCCTCGTTGCGTTGCTGTTTGTAATTTCTCTCTTCCTGTCAAATTTGGATAAAGCTCTTCATTCAGCAGGAATAGATTCGGGTTTCATCATCTTCGGAACTAACCTGAGCAATCCACTGAACATGCTTTTGCCGTTGTTACAAACAGTGTTCCCTCTTGATTACATTCTTATAACAATTATTATTATGTACTTTATTTTTACTTCGATGGCAGGAATTCGAAACATTGGCATTTGGTTCTTTTGGATTAGGTTATATAAAATCAGAAGAGGGCGAACCAGGCCTCAGGCACTCTTATTTCTCTGCATGATCCTCCTGCTCATTGTCCTTCATACCAGCTACATGATCTACAGTCTCGCGCCTCAGTACGTGATGTACGGAAGCCAGAATTACTTAATAGAGAGCAATATAACTTCTGATGCCCATAAAGGCAATTCAACCCTCGCTGTGCCAAAAAGATGTGACGCAGATGCCCCTAAAGATCAGTGTACTGTTACCCGAACATACATTTTCCTCCACAAGTTCTGGTTCTTCAGTGCTGCATACTATTTTGGTAACTGGGCCTTTCTCGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGGTTCTTCAGTGCTGCA
59.53
TGTTGTTGGGCAGATGCAGA
60.18
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGGTTCTTCAGTGCTGCA
59.53
GTTGTTGGGCAGATGCAGAG
59.48
149
PCR template sequence:
CCCTAAAGATCAGTGTACTGTTACCCGAACATACATTTTCCTCCACAAGTTCTGGTTCTTCAGTGCTGCATACTATTTTGGTAACTGGGCCTTTCTCGTGCAAATTAAAACGGCGCTCAAGTACACTTTGGGATTTGTTGTGATCTGCGCTCTGCTGCTTCTCGTTGGTGCCTTTGTGCCTCTGCATCTGCCCAACAACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-199a-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-101a-3p(1), mmu-miR-15b-5p(1), mmu-miR-23a-3p(1), mmu-miR-22-3p(1), mmu-miR-370-3p(1), mmu-miR-34b-5p(1), mmu-miR-680(1), mmu-miR-344d-3p(1), mmu-miR-539-5p(1), mmu-miR-3470b(1), mmu-miR-540-3p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCCTTTCTCGTGCAAATTAAAACGG
siRNA sets
TTAATTTGCACGAGAAAGG, TTTAATTTGCACGAGAAAG, TAATTTGCACGAGAAAGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLMBRD1_1104_ORF_1
0.8072
0.107027195
0.999984642
2001
ORF sequence:
ATGCTGGCGGCCATAACCTACACAGCGTACGGCATGTCGGCATTACCTTTAAACCTAATCAAAGGCACTAGAAGCACTGCCTACGAGCGCCTGGAGAACACGGAGGACATCGAGGAAGTGGAGCAGCACATTCAGACGATTCGATCCAAGAGCAAAGATGGTCGACCTTTGCCAGCGAGGGATAGACGTGCCTTAAAGCAATGTGAAGAAAGACTAAGAACGCTTAGGAAAAGAGAGCGGCACTTGGAATTCATTGAAAACAGCTGGTGGACGAAATTTTGTGGTGCCCTGCGCCCCCTGAAGATCATTTGGGGAATATTTTTCATCCTCGTTGCGTTGCTGTTTGTAATTTCTCTCTTCCTGTCAAATTTGGATAAAGCTCTTCATTCAGCAGGAATAGATTCGGGTTTCATCATCTTCGGAACTAACCTGAGCAATCCACTGAACATGCTTTTGCCGTTGTTACAAACAGTGTTCCCTCTTGATTACATTCTTATAACAATTATTATTATGTACTTTATTTTTACTTCGATGGCAGGAATTCGAAACATTGGCATTTGGTTCTTTTGGATTAGGTTATATAAAATCAGAAGAGGGCGAACCAGGCCTCAGGCACTCTTATTTCTCTGCATGATCCTCCTGCTCATTGTCCTTCATACCAGCTACATGATCTACAGTCTCGCGCCTCAGTACGTGATGTACGGAAGCCAGAATTACTTAATAGAGAGCAATATAACTTCTGATGCCCATAAAGGCAATTCAACCCTCGCTGTGCCAAAAAGATGTGACGCAGATGCCCCTAAAGATCAGTGTACTGTTACCCGAACATACATTTTCCTCCACAAGTTCTGGTTCTTCAGTGCTGCATACTATTTTGGTAACTGGGCCTTTCTCGTGCAAATTAAAACGGCGCTCAAGTACACTTTGGGATTTGTTGTGATCTGCGCTCTGCTGCTTCTCGTTGGTGCCTTTGTGCCTCTGCATCTGCCCAACAACAACAACTCAACAGAGTGGGAAAAGGTGAAGCTCCTGTTTGAAGACCTTGGAACTGGTCAAGGCCTGGCAGCTCTGTCCTTTTCCATCAGCTCTCTGACCTTGATTGGGATGCTGGCGGCCATAACCTACACAGCGTACGGCATGTCGGCATTACCTTTAAACCTAATCAAAGGCACTAGAAGCACTGCCTACGAGCGCCTGGAGAACACGGAGGACATCGAGGAAGTGGAGCAGCACATTCAGACGATTCGATCCAAGAGCAAAGATGGTCGACCTTTGCCAGCGAGGGATAGACGTGCCTTAAAGCAATGTGAAGAAAGACTAAGAACGCTTAGGAAAAGAGAGCGGCACTTGGAATTCATTGAAAACAGCTGGTGGACGAAATTTTGTGGTGCCCTGCGCCCCCTGAAGATCATTTGGGGAATATTTTTCATCCTCGTTGCGTTGCTGTTTGTAATTTCTCTCTTCCTGTCAAATTTGGATAAAGCTCTTCATTCAGCAGGAATAGATTCGGGTTTCATCATCTTCGGAACTAACCTGAGCAATCCACTGAACATGCTTTTGCCGTTGTTACAAACAGTGTTCCCTCTTGATTACATTCTTATAACAATTATTATTATGTACTTTATTTTTACTTCGATGGCAGGAATTCGAAACATTGGCATTTGGTTCTTTTGGATTAGGTTATATAAAATCAGAAGAGGGCGAACCAGGCCTCAGGCACTCTTATTTCTCTGCATGATCCTCCTGCTCATTGTCCTTCATACCAGCTACATGATCTACAGTCTCGCGCCTCAGTACGTGATGTACGGAAGCCAGAATTACTTAATAGAGAGCAATATAACTTCTGATGCCCATAAAGGCAATTCAACCCTCGCTGTGCCAAAAAGATGTGACGCAGATGCCCCTAAAGATCAGTGTACTGTTACCCGAACATACATTTTCCTCCACAAGTTCTGGTTCTTCAGTGCTGCATACTATTTTGGTAACTGGGCCTTTCTCGTG
Peptide sequence:
MLAAITYTAYGMSALPLNLIKGTRSTAYERLENTEDIEEVEQHIQTIRSKSKDGRPLPARDRRALKQCEERLRTLRKRERHLEFIENSWWTKFCGALRPLKIIWGIFFILVALLFVISLFLSNLDKALHSAGIDSGFIIFGTNLSNPLNMLLPLLQTVFPLDYILITIIIMYFIFTSMAGIRNIGIWFFWIRLYKIRRGRTRPQALLFLCMILLLIVLHTSYMIYSLAPQYVMYGSQNYLIESNITSDAHKGNSTLAVPKRCDADAPKDQCTVTRTYIFLHKFWFFSAAYYFGNWAFLVQIKTALKYTLGFVVICALLLLVGAFVPLHLPNNNNSTEWEKVKLLFEDLGTGQGLAALSFSISSLTLIGMLAAITYTAYGMSALPLNLIKGTRSTAYERLENTEDIEEVEQHIQTIRSKSKDGRPLPARDRRALKQCEERLRTLRKRERHLEFIENSWWTKFCGALRPLKIIWGIFFILVALLFVISLFLSNLDKALHSAGIDSGFIIFGTNLSNPLNMLLPLLQTVFPLDYILITIIIMYFIFTSMAGIRNIGIWFFWIRLYKIRRGRTRPQALLFLCMILLLIVLHTSYMIYSLAPQYVMYGSQNYLIESNITSDAHKGNSTLAVPKRCDADAPKDQCTVTRTYIFLHKFWFFSAAYYFGNWAFLV
IRESfinder result
IRESfinder score
0.640007852
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page