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mmu_circKdm2b_1262
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm2b_1262
mm39_Chr. Position ID:
chr5|123070529|123099651|-
Gene name:
Kdm2b
Transcript:
ENSMUST00000046073.16
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
11,10,9,8,7,6,5
Exon/intron offsets:
0,2266,8486,15260,16603,28546,28943
Genomic length:
29122
Exon/intron sizes in nt:
4,85,12,71,16,15,49,41,00,000
Flanking exon/introns:
chr5:123059534-123070529|chr5:123099651-123120839
Splice length:
1262
Other database IDs:
CIRCpedia: MMU_CIRCpedia_5936, circAtlas: mmu-Kdm2b_0011
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_7209
Human Ortholog IDs:
Mature spliced Sequence:
GGAGCCGCCGTTTGGTGGATGTCATGGACGTCAACACCCAGAAGGGTACCGAGATGAGCATGTCCCAGTTTGTGCGCTACTACGAGACACCAGAGGCACAGCGGGATAAACTGTACAACGTCATCAGCCTCGAGTTCAGCCATACGAAGCTGGAGCATCTGGTCAAGCGTCCCACTGTGGTGGACCTGGTCGACTGGGTGGACAACATGTGGCCTCAGCATCTAAAGGAAAAGCAGACAGAAGCCACCAATGCCCTTGCAGAGATGAAGTACCCCAAAGTGAAAAAGTACTGTCTGATGAGCGTGAAGGGCTGTTTCACTGACTTCCACATTGACTTTGGAGGCACCTCCGTGTGGTACCATGTGTTCCGTGGTGGCAAGATCTTTTGGCTGATCCCTCCAACCCTGCACAACTTGGCTTTGTACGAGGAGTGGGTGCTGTCTGGCAAACAGAGCGACATCTTTCTGGGAGACCGCGTGGAACGCTGCCAAAGAATTGAGCTGAAGCAAGGCTACACCTTTTTCATCCCTTCCGGTTGGATCCATGCGGTTTATACGCCTGTGGACTCTCTGGTGTTCGGCGGGAACATCCTGCATAGCTTCAACGTGCCCATGCAGCTGCGGATCTACGAGATCGAGGACAGGACCCGGGTTCAGCCCAAGTTCCGTTACCCCTTCTACTATGAGATGTGCTGGTATGTCTTGGAGAGATATGTGTACTGTGTGACCCAGCGCTCCTACCTCACTCAGGAATACCAGAGAGAATTAATGCTTATTGATGCCCCAAGAAAAACCAGTGTAGACGGCTTTTCATCCGACTCCTGGCTGGACATGGAGGAGGAGTCCTGCGAGCAGCAGCCACAGGAGGAAGAGGAGGAGGAGGAGGACAAGGAGGAGGAAGGAGATGGTGCAGATAAAACACCCAAGCCACCCACCGATGACCCCACCTCACCCACCAGCACCCCGCCCGAAGACCAGGACAGCACAGGGAAGAAGCCTAAAGCCCCTGCCATACGGTTCCTCAAGAGGACGTTGTCCAATGAGTCAGAGGAAAGTGTCAAGTCGACCTCGATGCCCACGGACGATCCCAAGACGCCCACGGGCTCCCCGGCCACCGAGGTTTCTACCAAGTGGACTCACCTTACCGAATTTGAACTGAAGGGCTTGAAAGCCCTGGTTGAAAAGCTAGAGTCCCTTCCGGAGAATAAGAAGTGTGTCCCTGAGGGAATCGAGGACCCCCAGGCCCTCCTGGAAGGTGTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTAGAGTCCCTTCCGGAG
60.11
TAGCGCACAAACTGGGACAT
59.96
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTAGAGTCCCTTCCGGAGA
60.11
TAGCGCACAAACTGGGACAT
59.96
158
PCR template sequence:
CTTGAAAGCCCTGGTTGAAAAGCTAGAGTCCCTTCCGGAGAATAAGAAGTGTGTCCCTGAGGGAATCGAGGACCCCCAGGCCCTCCTGGAAGGTGTAAAGGGAGCCGCCGTTTGGTGGATGTCATGGACGTCAACACCCAGAAGGGTACCGAGATGAGCATGTCCCAGTTTGTGCGCTACTACGAGACACCAGAGGCACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-101a-3p(1), mmu-miR-205-5p(1), mmu-let-7c-5p(1), mmu-miR-128-3p(1), mmu-let-7d-5p(1), mmu-miR-127-5p(1), mmu-miR-382-5p(1), mmu-miR-342-5p(1), mmu-miR-207(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAAGGTGTAAAGGGAGCCGCCGTTT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM2B_1262_ORF_1
1.2015
0.44378535
0.999696272
1296
ORF sequence:
ATGGACGTCAACACCCAGAAGGGTACCGAGATGAGCATGTCCCAGTTTGTGCGCTACTACGAGACACCAGAGGCACAGCGGGATAAACTGTACAACGTCATCAGCCTCGAGTTCAGCCATACGAAGCTGGAGCATCTGGTCAAGCGTCCCACTGTGGTGGACCTGGTCGACTGGGTGGACAACATGTGGCCTCAGCATCTAAAGGAAAAGCAGACAGAAGCCACCAATGCCCTTGCAGAGATGAAGTACCCCAAAGTGAAAAAGTACTGTCTGATGAGCGTGAAGGGCTGTTTCACTGACTTCCACATTGACTTTGGAGGCACCTCCGTGTGGTACCATGTGTTCCGTGGTGGCAAGATCTTTTGGCTGATCCCTCCAACCCTGCACAACTTGGCTTTGTACGAGGAGTGGGTGCTGTCTGGCAAACAGAGCGACATCTTTCTGGGAGACCGCGTGGAACGCTGCCAAAGAATTGAGCTGAAGCAAGGCTACACCTTTTTCATCCCTTCCGGTTGGATCCATGCGGTTTATACGCCTGTGGACTCTCTGGTGTTCGGCGGGAACATCCTGCATAGCTTCAACGTGCCCATGCAGCTGCGGATCTACGAGATCGAGGACAGGACCCGGGTTCAGCCCAAGTTCCGTTACCCCTTCTACTATGAGATGTGCTGGTATGTCTTGGAGAGATATGTGTACTGTGTGACCCAGCGCTCCTACCTCACTCAGGAATACCAGAGAGAATTAATGCTTATTGATGCCCCAAGAAAAACCAGTGTAGACGGCTTTTCATCCGACTCCTGGCTGGACATGGAGGAGGAGTCCTGCGAGCAGCAGCCACAGGAGGAAGAGGAGGAGGAGGAGGACAAGGAGGAGGAAGGAGATGGTGCAGATAAAACACCCAAGCCACCCACCGATGACCCCACCTCACCCACCAGCACCCCGCCCGAAGACCAGGACAGCACAGGGAAGAAGCCTAAAGCCCCTGCCATACGGTTCCTCAAGAGGACGTTGTCCAATGAGTCAGAGGAAAGTGTCAAGTCGACCTCGATGCCCACGGACGATCCCAAGACGCCCACGGGCTCCCCGGCCACCGAGGTTTCTACCAAGTGGACTCACCTTACCGAATTTGAACTGAAGGGCTTGAAAGCCCTGGTTGAAAAGCTAGAGTCCCTTCCGGAGAATAAGAAGTGTGTCCCTGAGGGAATCGAGGACCCCCAGGCCCTCCTGGAAGGTGTAAAGGGAGCCGCCGTTTGGTGGATGTCATGGACGTCAACACCCAGAAGGGTACCGAGATGA
Peptide sequence:
MDVNTQKGTEMSMSQFVRYYETPEAQRDKLYNVISLEFSHTKLEHLVKRPTVVDLVDWVDNMWPQHLKEKQTEATNALAEMKYPKVKKYCLMSVKGCFTDFHIDFGGTSVWYHVFRGGKIFWLIPPTLHNLALYEEWVLSGKQSDIFLGDRVERCQRIELKQGYTFFIPSGWIHAVYTPVDSLVFGGNILHSFNVPMQLRIYEIEDRTRVQPKFRYPFYYEMCWYVLERYVYCVTQRSYLTQEYQRELMLIDAPRKTSVDGFSSDSWLDMEEESCEQQPQEEEEEEEDKEEEGDGADKTPKPPTDDPTSPTSTPPEDQDSTGKKPKAPAIRFLKRTLSNESEESVKSTSMPTDDPKTPTGSPATEVSTKWTHLTEFELKGLKALVEKLESLPENKKCVPEGIEDPQALLEGVKGAAVWWMSWTSTPRRVPR
IRESfinder result
IRESfinder score
0.317228878
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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