top of page
mmu_circKdm7a_1217
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm7a_1217
mm39_Chr. Position ID:
chr6|39125875|39147244|-
Gene name:
Kdm7a
Transcript:
ENSMUST00000002305.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
14,13,12,11,10,9,8,7,6
Exon/intron offsets:
0,345,2316,3871,9272,16155,17725,19999,21182
Genomic length:
21369
Exon/intron sizes in nt:
1,55,12,52,10,90,92,10,00,00,00,000
Flanking exon/introns:
chr6:39124735-39125875|chr6:39147244-39147702
Splice length:
1217
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AATGTCTGAATTGGTGGAGGTTCCTGATATAGCCAGAAAACTTTCATGGGTGGAAAATTACTGGCCAGATGATTCAGTCTTCCCCAAGCCCTTTGTCCAGAAATACTGCTTAATGGGAGTTCAAGATAGCTATACAGATTTCCACATTGACTTTGGTGGGACTTCAGTCTGGTACCATGTCCTTTGGGGTGAGAAGATTTTTTATTTGATAAAGCCAACAAATGAAAATTTGGCACTCTATGAATCTTGGAGTTCATCTGTGACCCAGAGTGAGGTGTTCTTTGGAGATAAAGTAGATAAATGCTACAAATGTGTGGTAAAGCAGGGACATACTTTGTTTGTTCCTACAGGGTGGATCCATGCTGTGCTCACTTCTCAGGACTGTATGGCTTTTGGAGGGAACTTTCTGCACAACCTCAACATTGGCATGCAGCTCAGGTGTTATGAGATGGAAAAAAGACTAAAAACACCAGATCTTTTCAAATTTCCTTTCTTTGAAGCCATATGCTGGTTTGTAGCCAAAAGTTTGCTGGAAACCTTGAAAGAACTGAAAGAAGATGGTTTCCAGCCTCAAAGTTACTTAGTACAGGGAGTAAAAGCACTGCATACTGCTTTAAAATTATGGATGAAAAAAGAACTTGTATCTGAACATGCCTTTGAGATTCCAGACAATGTTAGACCTGGGCATCTTATTAAGGAACTTTCTAAAGTAATTCGAGCAATAGAGGAGGAAAATGGCAAACCAGTTAAATCTCAGGGAATTCCTTCTGTGTGTCCAGTTTCACGGCCTTCAAATGAGGCATCTCCACCATATCATTCCCGGAGAAAGATGAGGAAACTTCGAGATCATAATGTCCGAACTCCTTCTAACCTTGACATTCTTGAGCTCCATACAAGGGAAGTCCTCAAAAGATTAGAGATGTGTCCATGGGAGGAGGACCTACTGAGCTCTAAACTGAATGGAAAATTCAACAAACATCTCCAGCCATCTTCCACAGTACCTGAGTGGAGAGCGAAAGATAATGATCTACGATTACTGCTGACAAATGGAAGAATAATTAAAGATGAGAGACAGCTGTTTGCAGATCGAAGTCTTTATACAGCAGATAGTGAAAATGAAGAGGACAAGAAGCCAACACAGAATGCAAACATGAAGACAGAACAGAGCTCAGGAAGAGAGGAGGCCGAAAGTCAAGGCTCTCCCAAACCACTCAACA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAGAGAGGAGGCCGAAAG
59.82
GACAAAGGGCTTGGGGAAGA
59.89
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAGAGAGGAGGCCGAAAG
59.82
AAAGGGCTTGGGGAAGACTG
59.89
140
PCR template sequence:
GAAGAGGACAAGAAGCCAACACAGAATGCAAACATGAAGACAGAACAGAGCTCAGGAAGAGAGGAGGCCGAAAGTCAAGGCTCTCCCAAACCACTCAACAAATGTCTGAATTGGTGGAGGTTCCTGATATAGCCAGAAAACTTTCATGGGTGGAAAATTACTGGCCAGATGATTCAGTCTTCCCCAAGCCCTTTGTCCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-7b-5p(1), mmu-miR-216a-5p(1), mmu-miR-7a-5p(1), mmu-miR-125b-5p(1), mmu-miR-10b-5p(1), mmu-miR-10a-5p(1), mmu-miR-495-3p(1), mmu-miR-125a-5p(1), mmu-miR-335-3p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAACCACTCAACAAATGTCTGAATTG
siRNA sets
TCAGACATTTGTTGAGTGG, CAATTCAGACATTTGTTGA, CAGACATTTGTTGAGTGGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM7A_1217_ORF_1
0.769
0.026580575
0.994752354
1248
ORF sequence:
ATGTCTGAATTGGTGGAGGTTCCTGATATAGCCAGAAAACTTTCATGGGTGGAAAATTACTGGCCAGATGATTCAGTCTTCCCCAAGCCCTTTGTCCAGAAATACTGCTTAATGGGAGTTCAAGATAGCTATACAGATTTCCACATTGACTTTGGTGGGACTTCAGTCTGGTACCATGTCCTTTGGGGTGAGAAGATTTTTTATTTGATAAAGCCAACAAATGAAAATTTGGCACTCTATGAATCTTGGAGTTCATCTGTGACCCAGAGTGAGGTGTTCTTTGGAGATAAAGTAGATAAATGCTACAAATGTGTGGTAAAGCAGGGACATACTTTGTTTGTTCCTACAGGGTGGATCCATGCTGTGCTCACTTCTCAGGACTGTATGGCTTTTGGAGGGAACTTTCTGCACAACCTCAACATTGGCATGCAGCTCAGGTGTTATGAGATGGAAAAAAGACTAAAAACACCAGATCTTTTCAAATTTCCTTTCTTTGAAGCCATATGCTGGTTTGTAGCCAAAAGTTTGCTGGAAACCTTGAAAGAACTGAAAGAAGATGGTTTCCAGCCTCAAAGTTACTTAGTACAGGGAGTAAAAGCACTGCATACTGCTTTAAAATTATGGATGAAAAAAGAACTTGTATCTGAACATGCCTTTGAGATTCCAGACAATGTTAGACCTGGGCATCTTATTAAGGAACTTTCTAAAGTAATTCGAGCAATAGAGGAGGAAAATGGCAAACCAGTTAAATCTCAGGGAATTCCTTCTGTGTGTCCAGTTTCACGGCCTTCAAATGAGGCATCTCCACCATATCATTCCCGGAGAAAGATGAGGAAACTTCGAGATCATAATGTCCGAACTCCTTCTAACCTTGACATTCTTGAGCTCCATACAAGGGAAGTCCTCAAAAGATTAGAGATGTGTCCATGGGAGGAGGACCTACTGAGCTCTAAACTGAATGGAAAATTCAACAAACATCTCCAGCCATCTTCCACAGTACCTGAGTGGAGAGCGAAAGATAATGATCTACGATTACTGCTGACAAATGGAAGAATAATTAAAGATGAGAGACAGCTGTTTGCAGATCGAAGTCTTTATACAGCAGATAGTGAAAATGAAGAGGACAAGAAGCCAACACAGAATGCAAACATGAAGACAGAACAGAGCTCAGGAAGAGAGGAGGCCGAAAGTCAAGGCTCTCCCAAACCACTCAACAAATGTCTGAATTGGTGGAGGTTCCTGATATAG
Peptide sequence:
MSELVEVPDIARKLSWVENYWPDDSVFPKPFVQKYCLMGVQDSYTDFHIDFGGTSVWYHVLWGEKIFYLIKPTNENLALYESWSSSVTQSEVFFGDKVDKCYKCVVKQGHTLFVPTGWIHAVLTSQDCMAFGGNFLHNLNIGMQLRCYEMEKRLKTPDLFKFPFFEAICWFVAKSLLETLKELKEDGFQPQSYLVQGVKALHTALKLWMKKELVSEHAFEIPDNVRPGHLIKELSKVIRAIEEENGKPVKSQGIPSVCPVSRPSNEASPPYHSRRKMRKLRDHNVRTPSNLDILELHTREVLKRLEMCPWEEDLLSSKLNGKFNKHLQPSSTVPEWRAKDNDLRLLLTNGRIIKDERQLFADRSLYTADSENEEDKKPTQNANMKTEQSSGREEAESQGSPKPLNKCLNWWRFLI
IRESfinder result
IRESfinder score
0.690601844
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page