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mmu_circLtn1_1875
Basic information of circular RNA
PanCircBase ID:
mmu_circLtn1_1875
mm39_Chr. Position ID:
chr16|87212438|87223232|-
Gene name:
Ltn1
Transcript:
ENSMUST00000039449.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
10,9,8,7,6,5,4,3
Exon/intron offsets:
0,2884,4622,5258,7847,9278,10017,10695
Genomic length:
10794
Exon/intron sizes in nt:
810,136,191,174,181,53,231,99
Flanking exon/introns:
chr16:87212083-87212438|chr16:87223232-87224476
Splice length:
1875
Other database IDs:
circAtlas: mmu-Ltn1_0027
Human Ortholog IDs:
Mature spliced Sequence:
GCAATGCAAGAATTTGGAATTATGTGCACAGAGAGAGACACAGAAGCCGTCAAAGGGGTTCTTCCATACTGGCCAAGAATCTTCTGCAAAATCTCCCTTGATCATGATCGCCGTGTTCGAGAGGCGACGCAGCAAGCTTTTGAAAAACTTATCCTTAAAGTAAAGAAGCACTTAGCTCCCTATTTAAAAAGCGTGATGGGCTATTGGTTGATGGCTCAGTGTGACACATATCCACCAGCTGCACTGGCAGCAAAAGATGCATTCGAAGCCGCTTTCCCTCCAAGCAAGCAACCTGAAGCCATAGCGTTTTGCAAGGAAGAAATTACAACTGTGTTACAGGACCATCTTCTGAAGGAGACTCCTGACACACTCAGTGACCCTCAAACTGTGCCAGAGGAAGAGAGAGAGGCTAAGTTCCACCGAGTCGTGACGTGCTCTTTATTGGCACTGAAGAGATTGCTTTGTTTCTTACCTAACAATGAGCTTGATTCTCTGGAGGAGAAATTTAAATCACTTTTATCACAGAATAAATTTTGGAAGTATGGAAAACACAGTGTACCTCAGGTCCGCTCAGCATATTTTGAGTTAGTTTCTGCTTTGTGCCAGCACGTTCCCCAGGTGATGAAAGAGGAAGCTGCCAAAGTGAGTCCATCTGTCCTGCTCAGCATTGATGACAGTGACCCTGTGGTCTGCCCAGCTCTCTGGGAGGCTGTGCTCTACACGCTGACAACTATTGAGGACTGTTGGTTTCATGTAAATGCCAAGAAAAGTGTGTTTCCGAAGCTGATGGCCATGATCCGAGAGGGTGGCCGGGGCCTAGCTGCTGTTATGTATCCTTACCTCTTACCGTTCATCAGCAAACTCCCTCAGTCCATCACAGAGCCAAAGCTGGACTTCTTCAAAAACTTCCTCACCTCTCTAGTTACCGGGCTGTCAACTGAGAGGACCAAATCGAGCTCTTCTGAGTGCTCAGCTGTCATCTCGGCATTTTTTGAATGCTTGCGGTTTATAATGCAGCAGAACTTAGGCGAGGAGGAGATGGTGCAGATGCTTATCAATGAGCAGTTGATCCCATTTATTGATACAGTTCTCAAAGACTCAGGACTGCACCACGGACCGATGTTTGACCATTTAGCAGACACATTGAGCTCTTGGGAAGCCAAAGCAGATGCAGAGCGAGACCCTGGAGCTGTTTACAACTTGGAGAACGTTCTGCTAAGCTTCTGGGGAAGACTGTCAGAGATCTGCACCGAGAAAATCCGCCAGCCAGAAGCAGATGTGAAGTCCGTTCTGTGTGTGTCTAGCCTAGTAGGGGTCCTTCAGAGGCCAAGGAGCTCACTGAAGTTACACAGAAAGAAAACTGCTCAGGTCAGGTTTGCCATCAATATACCTGAAGCTCATAAAGGGGATGAAAAGTCCATGTCTTCAGAAGGAGAGAACAGCGAGGGCTCTGACGGAGGGGCTCAGTCTCCTCTCAGTAATACATCTTCAGACTTAGTATCTCCTTTAAGGAAAAAACCTCTGGAAGACTTAGTCTGTAAGCTGGCAGAGGTGAGCATTAGCTTTGTCAACGAGCGGAAGTCAGAGCAGCACCTGCAGTTTCTCTCCACGCTGCTCGACTCCTTCTCCTCCGTCCAAGTATTTAACATTCTCCTCAGTGACAAACAGAAGAATGTCGTCAAAGCCAAACCTCTGGAAATAACCAAACTTGCAGAAAAAAATCCTGCAGTTAAGTTCTTATATCATAAATTGATAGGCTGGCTAAATGACAGCCAGAAAGAGGACGGGGGCTTCCTGGTGGACATCTTGTATAGTGCCCTCCGATGCTGTGACAGTGGTGTGGAAAGGAAAGAAGTCTTGGATGATCTAACCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTTCCTGGTGGACATCTT
59.67
TGGAAGAACCCCTTTGACGG
59.89
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTTCCTGGTGGACATCTT
59.67
AAGAACCCCTTTGACGGCTT
59.81
150
PCR template sequence:
GAAAGAGGACGGGGGCTTCCTGGTGGACATCTTGTATAGTGCCCTCCGATGCTGTGACAGTGGTGTGGAAAGGAAAGAAGTCTTGGATGATCTAACCAAGGCAATGCAAGAATTTGGAATTATGTGCACAGAGAGAGACACAGAAGCCGTCAAAGGGGTTCTTCCATACTGGCCAAGAATCTTCTGCAAAATCTCCCTTG
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-155-5p(1), mmu-miR-135a-5p(1), mmu-miR-146a-5p(1), mmu-miR-30c-5p(1), mmu-miR-184-3p(1), mmu-miR-132-3p(1), mmu-miR-138-5p(1), mmu-miR-185-5p(1), mmu-miR-30d-5p(1), mmu-miR-503-5p(1), mmu-miR-212-3p(1), mmu-miR-182-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-190b-5p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGATCTAACCAAGGCAATGCAAGAAT
siRNA sets
ATTCTTGCATTGCCTTGGT, TTGCATTGCCTTGGTTAGA, TTCTTGCATTGCCTTGGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLTN1_1875_ORF_1
0.8938
0.178477836
1
3747
ORF sequence:
ATGCAAGAATTTGGAATTATGTGCACAGAGAGAGACACAGAAGCCGTCAAAGGGGTTCTTCCATACTGGCCAAGAATCTTCTGCAAAATCTCCCTTGATCATGATCGCCGTGTTCGAGAGGCGACGCAGCAAGCTTTTGAAAAACTTATCCTTAAAGTAAAGAAGCACTTAGCTCCCTATTTAAAAAGCGTGATGGGCTATTGGTTGATGGCTCAGTGTGACACATATCCACCAGCTGCACTGGCAGCAAAAGATGCATTCGAAGCCGCTTTCCCTCCAAGCAAGCAACCTGAAGCCATAGCGTTTTGCAAGGAAGAAATTACAACTGTGTTACAGGACCATCTTCTGAAGGAGACTCCTGACACACTCAGTGACCCTCAAACTGTGCCAGAGGAAGAGAGAGAGGCTAAGTTCCACCGAGTCGTGACGTGCTCTTTATTGGCACTGAAGAGATTGCTTTGTTTCTTACCTAACAATGAGCTTGATTCTCTGGAGGAGAAATTTAAATCACTTTTATCACAGAATAAATTTTGGAAGTATGGAAAACACAGTGTACCTCAGGTCCGCTCAGCATATTTTGAGTTAGTTTCTGCTTTGTGCCAGCACGTTCCCCAGGTGATGAAAGAGGAAGCTGCCAAAGTGAGTCCATCTGTCCTGCTCAGCATTGATGACAGTGACCCTGTGGTCTGCCCAGCTCTCTGGGAGGCTGTGCTCTACACGCTGACAACTATTGAGGACTGTTGGTTTCATGTAAATGCCAAGAAAAGTGTGTTTCCGAAGCTGATGGCCATGATCCGAGAGGGTGGCCGGGGCCTAGCTGCTGTTATGTATCCTTACCTCTTACCGTTCATCAGCAAACTCCCTCAGTCCATCACAGAGCCAAAGCTGGACTTCTTCAAAAACTTCCTCACCTCTCTAGTTACCGGGCTGTCAACTGAGAGGACCAAATCGAGCTCTTCTGAGTGCTCAGCTGTCATCTCGGCATTTTTTGAATGCTTGCGGTTTATAATGCAGCAGAACTTAGGCGAGGAGGAGATGGTGCAGATGCTTATCAATGAGCAGTTGATCCCATTTATTGATACAGTTCTCAAAGACTCAGGACTGCACCACGGACCGATGTTTGACCATTTAGCAGACACATTGAGCTCTTGGGAAGCCAAAGCAGATGCAGAGCGAGACCCTGGAGCTGTTTACAACTTGGAGAACGTTCTGCTAAGCTTCTGGGGAAGACTGTCAGAGATCTGCACCGAGAAAATCCGCCAGCCAGAAGCAGATGTGAAGTCCGTTCTGTGTGTGTCTAGCCTAGTAGGGGTCCTTCAGAGGCCAAGGAGCTCACTGAAGTTACACAGAAAGAAAACTGCTCAGGTCAGGTTTGCCATCAATATACCTGAAGCTCATAAAGGGGATGAAAAGTCCATGTCTTCAGAAGGAGAGAACAGCGAGGGCTCTGACGGAGGGGCTCAGTCTCCTCTCAGTAATACATCTTCAGACTTAGTATCTCCTTTAAGGAAAAAACCTCTGGAAGACTTAGTCTGTAAGCTGGCAGAGGTGAGCATTAGCTTTGTCAACGAGCGGAAGTCAGAGCAGCACCTGCAGTTTCTCTCCACGCTGCTCGACTCCTTCTCCTCCGTCCAAGTATTTAACATTCTCCTCAGTGACAAACAGAAGAATGTCGTCAAAGCCAAACCTCTGGAAATAACCAAACTTGCAGAAAAAAATCCTGCAGTTAAGTTCTTATATCATAAATTGATAGGCTGGCTAAATGACAGCCAGAAAGAGGACGGGGGCTTCCTGGTGGACATCTTGTATAGTGCCCTCCGATGCTGTGACAGTGGTGTGGAAAGGAAAGAAGTCTTGGATGATCTAACCAAGGCAATGCAAGAATTTGGAATTATGTGCACAGAGAGAGACACAGAAGCCGTCAAAGGGGTTCTTCCATACTGGCCAAGAATCTTCTGCAAAATCTCCCTTGATCATGATCGCCGTGTTCGAGAGGCGACGCAGCAAGCTTTTGAAAAACTTATCCTTAAAGTAAAGAAGCACTTAGCTCCCTATTTAAAAAGCGTGATGGGCTATTGGTTGATGGCTCAGTGTGACACATATCCACCAGCTGCACTGGCAGCAAAAGATGCATTCGAAGCCGCTTTCCCTCCAAGCAAGCAACCTGAAGCCATAGCGTTTTGCAAGGAAGAAATTACAACTGTGTTACAGGACCATCTTCTGAAGGAGACTCCTGACACACTCAGTGACCCTCAAACTGTGCCAGAGGAAGAGAGAGAGGCTAAGTTCCACCGAGTCGTGACGTGCTCTTTATTGGCACTGAAGAGATTGCTTTGTTTCTTACCTAACAATGAGCTTGATTCTCTGGAGGAGAAATTTAAATCACTTTTATCACAGAATAAATTTTGGAAGTATGGAAAACACAGTGTACCTCAGGTCCGCTCAGCATATTTTGAGTTAGTTTCTGCTTTGTGCCAGCACGTTCCCCAGGTGATGAAAGAGGAAGCTGCCAAAGTGAGTCCATCTGTCCTGCTCAGCATTGATGACAGTGACCCTGTGGTCTGCCCAGCTCTCTGGGAGGCTGTGCTCTACACGCTGACAACTATTGAGGACTGTTGGTTTCATGTAAATGCCAAGAAAAGTGTGTTTCCGAAGCTGATGGCCATGATCCGAGAGGGTGGCCGGGGCCTAGCTGCTGTTATGTATCCTTACCTCTTACCGTTCATCAGCAAACTCCCTCAGTCCATCACAGAGCCAAAGCTGGACTTCTTCAAAAACTTCCTCACCTCTCTAGTTACCGGGCTGTCAACTGAGAGGACCAAATCGAGCTCTTCTGAGTGCTCAGCTGTCATCTCGGCATTTTTTGAATGCTTGCGGTTTATAATGCAGCAGAACTTAGGCGAGGAGGAGATGGTGCAGATGCTTATCAATGAGCAGTTGATCCCATTTATTGATACAGTTCTCAAAGACTCAGGACTGCACCACGGACCGATGTTTGACCATTTAGCAGACACATTGAGCTCTTGGGAAGCCAAAGCAGATGCAGAGCGAGACCCTGGAGCTGTTTACAACTTGGAGAACGTTCTGCTAAGCTTCTGGGGAAGACTGTCAGAGATCTGCACCGAGAAAATCCGCCAGCCAGAAGCAGATGTGAAGTCCGTTCTGTGTGTGTCTAGCCTAGTAGGGGTCCTTCAGAGGCCAAGGAGCTCACTGAAGTTACACAGAAAGAAAACTGCTCAGGTCAGGTTTGCCATCAATATACCTGAAGCTCATAAAGGGGATGAAAAGTCCATGTCTTCAGAAGGAGAGAACAGCGAGGGCTCTGACGGAGGGGCTCAGTCTCCTCTCAGTAATACATCTTCAGACTTAGTATCTCCTTTAAGGAAAAAACCTCTGGAAGACTTAGTCTGTAAGCTGGCAGAGGTGAGCATTAGCTTTGTCAACGAGCGGAAGTCAGAGCAGCACCTGCAGTTTCTCTCCACGCTGCTCGACTCCTTCTCCTCCGTCCAAGTATTTAACATTCTCCTCAGTGACAAACAGAAGAATGTCGTCAAAGCCAAACCTCTGGAAATAACCAAACTTGCAGAAAAAAATCCTGCAGTTAAGTTCTTATATCATAAATTGATAGGCTGGCTAAATGACAGCCAGAAAGAGGACGGGGGCTTCCTGGTGGACATCTTGTATAGTGCCCTCCGATGCTGTGACAGTGGTGTGGAAAGGAAAGAAGTCTTGGATGATCTAACCAAG
Peptide sequence:
MQEFGIMCTERDTEAVKGVLPYWPRIFCKISLDHDRRVREATQQAFEKLILKVKKHLAPYLKSVMGYWLMAQCDTYPPAALAAKDAFEAAFPPSKQPEAIAFCKEEITTVLQDHLLKETPDTLSDPQTVPEEEREAKFHRVVTCSLLALKRLLCFLPNNELDSLEEKFKSLLSQNKFWKYGKHSVPQVRSAYFELVSALCQHVPQVMKEEAAKVSPSVLLSIDDSDPVVCPALWEAVLYTLTTIEDCWFHVNAKKSVFPKLMAMIREGGRGLAAVMYPYLLPFISKLPQSITEPKLDFFKNFLTSLVTGLSTERTKSSSSECSAVISAFFECLRFIMQQNLGEEEMVQMLINEQLIPFIDTVLKDSGLHHGPMFDHLADTLSSWEAKADAERDPGAVYNLENVLLSFWGRLSEICTEKIRQPEADVKSVLCVSSLVGVLQRPRSSLKLHRKKTAQVRFAINIPEAHKGDEKSMSSEGENSEGSDGGAQSPLSNTSSDLVSPLRKKPLEDLVCKLAEVSISFVNERKSEQHLQFLSTLLDSFSSVQVFNILLSDKQKNVVKAKPLEITKLAEKNPAVKFLYHKLIGWLNDSQKEDGGFLVDILYSALRCCDSGVERKEVLDDLTKAMQEFGIMCTERDTEAVKGVLPYWPRIFCKISLDHDRRVREATQQAFEKLILKVKKHLAPYLKSVMGYWLMAQCDTYPPAALAAKDAFEAAFPPSKQPEAIAFCKEEITTVLQDHLLKETPDTLSDPQTVPEEEREAKFHRVVTCSLLALKRLLCFLPNNELDSLEEKFKSLLSQNKFWKYGKHSVPQVRSAYFELVSALCQHVPQVMKEEAAKVSPSVLLSIDDSDPVVCPALWEAVLYTLTTIEDCWFHVNAKKSVFPKLMAMIREGGRGLAAVMYPYLLPFISKLPQSITEPKLDFFKNFLTSLVTGLSTERTKSSSSECSAVISAFFECLRFIMQQNLGEEEMVQMLINEQLIPFIDTVLKDSGLHHGPMFDHLADTLSSWEAKADAERDPGAVYNLENVLLSFWGRLSEICTEKIRQPEADVKSVLCVSSLVGVLQRPRSSLKLHRKKTAQVRFAINIPEAHKGDEKSMSSEGENSEGSDGGAQSPLSNTSSDLVSPLRKKPLEDLVCKLAEVSISFVNERKSEQHLQFLSTLLDSFSSVQVFNILLSDKQKNVVKAKPLEITKLAEKNPAVKFLYHKLIGWLNDSQKEDGGFLVDILYSALRCCDSGVERKEVLDDLTK
IRESfinder result
IRESfinder score
0.609905676
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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