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mmu_circMap4_537
Basic information of circular RNA
PanCircBase ID:
mmu_circMap4_537
mm39_Chr. Position ID:
chr9|109896552|109898053|+
Gene name:
Map4
Transcript:
ENSMUST00000035055.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
11,12,13
Exon/intron offsets:
0,1039,1208
Genomic length:
1501
Exon/intron sizes in nt:
1,84,60,293
Flanking exon/introns:
chr9:109893517-109896552|chr9:109898053-109900093
Splice length:
537
Other database IDs:
CIRCpedia: MMU_CIRCpedia_40161, circAtlas: mmu-Map4_0013
circBase: hsa_circ_0123979, circAtlas: hsa-MAP4_0016, CIRCpedia: HSA_CIRCpedia_45982
Human Ortholog IDs:
Mature spliced Sequence:
CCAATTACAGAAGCTAAGGTTGCCGAAAAGCGGACCTCTCCATCCAAGCCTTCATCTGCCCCAGCCCTCAAACCTGGACCTAAAACCACCCCAACCGTTTCAAAAGCCACATCTCCCTCAACTCTTGTTTCCACTGGACCAAGTAGTAGAAGTCCAGCTACAACTCTGCCTAAGAGGCCAACCAGCATCAAGACTGAGGGGAAACCTGCTGATGTCAAAAGGATGACTGCTAAGTCTGCCTCAGCTGACTTGAGTCGCTCAAAGACCACCTCTGCCAGTTCTGTGAAGAGAAACACCACTCCCACTGGGGCAGCACCCCCAGCAGGGATGACTTCCACTCGAGTCAAGCCCATGTCTGCACCTAGCCGCTCTTCTGGGGCTCTTTCTGTGGACAAGAAGCCCACTTCCACTAAGCCTAGCTCCTCTGCTCCCAGGGTGAGCCGCCTGGCCACAACTGTTTCTGCCCCTGACCTGAAGAGTGTTCGCTCCAAGGTCGGCTCTACAGAAAACATCAAACACCAGCCTGGAGGAGGCCGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCAAGGTCGGCTCTACAGA
59.96
GGGGTGGTTTTAGGTCCAGG
59.96
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGCCACAACTGTTTCTGC
59.97
GGGCAGATGAAGGCTTGGAT
60.11
154
PCR template sequence:
GAGCCGCCTGGCCACAACTGTTTCTGCCCCTGACCTGAAGAGTGTTCGCTCCAAGGTCGGCTCTACAGAAAACATCAAACACCAGCCTGGAGGAGGCCGGCCAATTACAGAAGCTAAGGTTGCCGAAAAGCGGACCTCTCCATCCAAGCCTTCATCTGCCCCAGCCCTCAAACCTGGACCTAAAACCACCCCAACCGTTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(2), mmu-miR-709(1), mmu-miR-138-5p(1), mmu-miR-370-3p(1), mmu-miR-342-5p(1), mmu-miR-705(1)
siRNAs for circular RNA silencing
Junction sequence
TGGAGGAGGCCGGCCAATTACAGAAG
siRNA sets
CTTCTGTAATTGGCCGGCC,TAATTGGCCGGCCTCCTCC,CTGTAATTGGCCGGCCTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMAP4_537_ORF_1
1.1677
0.220827791
0.981191903
852
ORF sequence:
ATGACTGCTAAGTCTGCCTCAGCTGACTTGAGTCGCTCAAAGACCACCTCTGCCAGTTCTGTGAAGAGAAACACCACTCCCACTGGGGCAGCACCCCCAGCAGGGATGACTTCCACTCGAGTCAAGCCCATGTCTGCACCTAGCCGCTCTTCTGGGGCTCTTTCTGTGGACAAGAAGCCCACTTCCACTAAGCCTAGCTCCTCTGCTCCCAGGGTGAGCCGCCTGGCCACAACTGTTTCTGCCCCTGACCTGAAGAGTGTTCGCTCCAAGGTCGGCTCTACAGAAAACATCAAACACCAGCCTGGAGGAGGCCGGCCAATTACAGAAGCTAAGGTTGCCGAAAAGCGGACCTCTCCATCCAAGCCTTCATCTGCCCCAGCCCTCAAACCTGGACCTAAAACCACCCCAACCGTTTCAAAAGCCACATCTCCCTCAACTCTTGTTTCCACTGGACCAAGTAGTAGAAGTCCAGCTACAACTCTGCCTAAGAGGCCAACCAGCATCAAGACTGAGGGGAAACCTGCTGATGTCAAAAGGATGACTGCTAAGTCTGCCTCAGCTGACTTGAGTCGCTCAAAGACCACCTCTGCCAGTTCTGTGAAGAGAAACACCACTCCCACTGGGGCAGCACCCCCAGCAGGGATGACTTCCACTCGAGTCAAGCCCATGTCTGCACCTAGCCGCTCTTCTGGGGCTCTTTCTGTGGACAAGAAGCCCACTTCCACTAAGCCTAGCTCCTCTGCTCCCAGGGTGAGCCGCCTGGCCACAACTGTTTCTGCCCCTGACCTGAAGAGTGTTCGCTCCAAGGTCGGCTCTACAGAAAACATCAAACACCAGCCTGGAGGAGGCCGG
Peptide sequence:
MTAKSASADLSRSKTTSASSVKRNTTPTGAAPPAGMTSTRVKPMSAPSRSSGALSVDKKPTSTKPSSSAPRVSRLATTVSAPDLKSVRSKVGSTENIKHQPGGGRPITEAKVAEKRTSPSKPSSAPALKPGPKTTPTVSKATSPSTLVSTGPSSRSPATTLPKRPTSIKTEGKPADVKRMTAKSASADLSRSKTTSASSVKRNTTPTGAAPPAGMTSTRVKPMSAPSRSSGALSVDKKPTSTKPSSSAPRVSRLATTVSAPDLKSVRSKVGSTENIKHQPGGGR
IRESfinder result
IRESfinder score
0.513687664
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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