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mmu_circMap3k4_2023
Basic information of circular RNA
PanCircBase ID:
mmu_circMap3k4_2023
mm39_Chr. Position ID:
chr17|12476800|12491107|-
Gene name:
Map3k4
Transcript:
ENSMUST00000233755.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,6,5,4,3
Exon/intron offsets:
0,2537,3330,5992,12949
Genomic length:
14307
Exon/intron sizes in nt:
1,17,15,81,47,24,31,350
Flanking exon/introns:
chr17:12475748-12476800|chr17:12491107-12496807
Splice length:
2023
Other database IDs:
CIRCpedia: MMU_CIRCpedia_224836, circAtlas: mmu-Map3k4_0010
Human Ortholog IDs:
Mature spliced Sequence:
AAAAAATGAACACACCGAGTCAGTCTCCACATAAAGATTTGGGGAAGGGAGTGGAGACCGTGGAAGAATACAGCTACAAGCAGGAGAAGAAGATTCGAGCAACTCTGAGAACAACGGAGCGAGACCATAAGAAAAATGCACAGTGCTCGTTCATGTTGGACTCGGTGGCTGGGTCTTTGCCAAAAAAATCGATTCCAGATGTGGATCTCAATAAGCCTTACCTCAGTCTCGGCTGTAGCAATGCCAAGCTGCCCGTCTCGATGCCCATGCCGATAGCCAGAACTGCACGGCAGACTTCCCGGACTGACTGCCCCGCAGATCGCTTAAAGTTCTTTGAAACACTGCGCCTTTTGCTAAAGCTTACCTCAGTCTCGAAGAAGAAGGACAGGGAGCAGAGGGGACAAGAAAACACGGCTGCTTTCTGGTTCAACCGATCGAACGAACTGATCTGGTTAGAACTGCAGGCCTGGCACGCGGGCCGCACCATCAATGACCAGGACCTCTTTCTCTACACAGCCCGCCAGGCCATCCCAGACATCATCAATGAGATCCTCACCTTCAAAGTTAACTACGGGAGCATTGCCTTCTCCAGCAATGGAGCCGGTTTCAACGGGCCCTTGGTAGAAGGCCAGTGCAGAACCCCTCAGGAGACAAACCGTGTGGGCTGCTCATCGTACCACGAGCACCTCCAGCGCCAGAGGGTCTCGTTTGAGCAGGTGAAGCGGATAATGGAGCTGCTGGAGTACATGGAGGCACTTTACCCATCCTTGCAGGCTCTGCAGAAGGACTATGAACGGTACGCCGCCAAGGACTTTGAGGACAGAGTGCAGGCGCTCTGCCTGTGGCTCAACATCACGAAAGATCTAAATCAGAAGCTGCGGATCATGGGCACCGTGCTGGGCATCAAGAACCTATCAGACATTGGCTGGCCAGTGTTTGAAATCCCCTCCCCTCGGCCGTCCAAGGGCTACGAGCCAGAGGACGAGGTCGAGGACACGGAGGTTGAGCTGAGGGAGCTGGAGAGCGGGACGGAGGAGAGTGACGAGGAGCCAACCCCCAGTCCGAGGGTGCCAGAGCTCAGGCTGTCCACAGACGCCATCTTGGACAGTCGCTCCCAGGGCTGCGTCTCCAGGAAGCTGGAGAGGCTCGAGTCAGAGGAAGATTCCATAGGCTGGGGGACAGCGGACTGTGGCCCTGAAGCCAGCAGGCATTGTTTGACTTCTATCTATAGACCATTCGTGGACAAAGCACTGAAGCAAATGGGGCTAAGAAAGTTAATTTTACGACTTCATAAGCTTATGAATGGGTCCTTGCAAAGAGCTCGTGTAGCTCTGGTGAAGGACGACCGTCCAGTGGAGTTCTCTGACTTTCCAGGTCCCATGTGGGGCTCGGATTATGTGCAGTTGTCGGGAACACCTCCTTCCTCAGAGCAGAAGTGTAGCGCTGTGTCCTGGGAAGAACTGAGAGCCATGGACCTGCCTTCCTTTGAGCCCGCCTTCCTGGTGCTCTGTCGGGTCCTGCTGAACGTGATCCACGAGTGCCTGAAGCTGCGGCTGGAACAGAGGCCTGCCGGGGAGCCTTCCCTCTTGAGTATCAAACAGCTAGTGCGAGAGTGTAAAGAGGTCCTAAAGGGCGGGCTCCTGATGAAGCAGTATTACCAGTTCATGCTGCAGGAGGTCCTGGGCGGACTGGAGAAGACCGACTGCAACATGGATGCCTTTGAGGAGGACCTGCAGAAGATGCTGATGGTGTATTTTGATTACATGAGAAGCTGGATCCAAATGCTACAGCAGTTACCTCAGGCTTCCCATAGCTTAAAAAACCTGCTAGAAGAGGAATGGAATTTCACCAAAGAAATAACCCATTATATCCGTGGCGGAGAAGCGCAGGCTGGAAAGCTTTTCTGTGACATCGCAGGGATGCTGCTGAAATCCACAGGGAGCTTTCTGGAATCCGGCCTGCAGGAGAGCTGTGCTGAGCTGTGGACCAGCGCCGACGACAACGGTGCTGCCGACGAGCTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCACAGGGAGCTTTCTGGAA
59.6
TCTCCACTCCCTTCCCCAAA
60.1
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAGCTTTCTGGAATCCGG
60.46
TCTCCACTCCCTTCCCCAAA
60.1
143
PCR template sequence:
TGCTGAAATCCACAGGGAGCTTTCTGGAATCCGGCCTGCAGGAGAGCTGTGCTGAGCTGTGGACCAGCGCCGACGACAACGGTGCTGCCGACGAGCTAAGAAAAAATGAACACACCGAGTCAGTCTCCACATAAAGATTTGGGGAAGGGAGTGGAGACCGTGGAAGAATACAGCTACAAGCAGGAGAAGAAGATTCGAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
27
Interacting miRNAs (#binding sites)
mmu-miR-207(2), mmu-miR-193b-3p(2), mmu-miR-20b-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-103-3p(1), mmu-miR-221-3p(1), mmu-miR-200c-3p(1), mmu-miR-322-5p(1), mmu-miR-106b-5p(1), mmu-miR-146a-5p(1), mmu-miR-339-5p(1), mmu-miR-139-5p(1), mmu-miR-214-3p(1), mmu-miR-149-5p(1), mmu-miR-136-5p(1), mmu-miR-182-5p(1), mmu-miR-467b-5p(1), mmu-miR-107-3p(1), mmu-miR-325-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CCGACGAGCTAAGAAAAAATGAACAC
siRNA sets
GTTCATTTTTTCTTAGCTC, TTCATTTTTTCTTAGCTCG, GTGTTCATTTTTTCTTAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMAP3K4_2023_ORF_1
1.2417
0.376954213
0.99999836
2052
ORF sequence:
ATGAACACACCGAGTCAGTCTCCACATAAAGATTTGGGGAAGGGAGTGGAGACCGTGGAAGAATACAGCTACAAGCAGGAGAAGAAGATTCGAGCAACTCTGAGAACAACGGAGCGAGACCATAAGAAAAATGCACAGTGCTCGTTCATGTTGGACTCGGTGGCTGGGTCTTTGCCAAAAAAATCGATTCCAGATGTGGATCTCAATAAGCCTTACCTCAGTCTCGGCTGTAGCAATGCCAAGCTGCCCGTCTCGATGCCCATGCCGATAGCCAGAACTGCACGGCAGACTTCCCGGACTGACTGCCCCGCAGATCGCTTAAAGTTCTTTGAAACACTGCGCCTTTTGCTAAAGCTTACCTCAGTCTCGAAGAAGAAGGACAGGGAGCAGAGGGGACAAGAAAACACGGCTGCTTTCTGGTTCAACCGATCGAACGAACTGATCTGGTTAGAACTGCAGGCCTGGCACGCGGGCCGCACCATCAATGACCAGGACCTCTTTCTCTACACAGCCCGCCAGGCCATCCCAGACATCATCAATGAGATCCTCACCTTCAAAGTTAACTACGGGAGCATTGCCTTCTCCAGCAATGGAGCCGGTTTCAACGGGCCCTTGGTAGAAGGCCAGTGCAGAACCCCTCAGGAGACAAACCGTGTGGGCTGCTCATCGTACCACGAGCACCTCCAGCGCCAGAGGGTCTCGTTTGAGCAGGTGAAGCGGATAATGGAGCTGCTGGAGTACATGGAGGCACTTTACCCATCCTTGCAGGCTCTGCAGAAGGACTATGAACGGTACGCCGCCAAGGACTTTGAGGACAGAGTGCAGGCGCTCTGCCTGTGGCTCAACATCACGAAAGATCTAAATCAGAAGCTGCGGATCATGGGCACCGTGCTGGGCATCAAGAACCTATCAGACATTGGCTGGCCAGTGTTTGAAATCCCCTCCCCTCGGCCGTCCAAGGGCTACGAGCCAGAGGACGAGGTCGAGGACACGGAGGTTGAGCTGAGGGAGCTGGAGAGCGGGACGGAGGAGAGTGACGAGGAGCCAACCCCCAGTCCGAGGGTGCCAGAGCTCAGGCTGTCCACAGACGCCATCTTGGACAGTCGCTCCCAGGGCTGCGTCTCCAGGAAGCTGGAGAGGCTCGAGTCAGAGGAAGATTCCATAGGCTGGGGGACAGCGGACTGTGGCCCTGAAGCCAGCAGGCATTGTTTGACTTCTATCTATAGACCATTCGTGGACAAAGCACTGAAGCAAATGGGGCTAAGAAAGTTAATTTTACGACTTCATAAGCTTATGAATGGGTCCTTGCAAAGAGCTCGTGTAGCTCTGGTGAAGGACGACCGTCCAGTGGAGTTCTCTGACTTTCCAGGTCCCATGTGGGGCTCGGATTATGTGCAGTTGTCGGGAACACCTCCTTCCTCAGAGCAGAAGTGTAGCGCTGTGTCCTGGGAAGAACTGAGAGCCATGGACCTGCCTTCCTTTGAGCCCGCCTTCCTGGTGCTCTGTCGGGTCCTGCTGAACGTGATCCACGAGTGCCTGAAGCTGCGGCTGGAACAGAGGCCTGCCGGGGAGCCTTCCCTCTTGAGTATCAAACAGCTAGTGCGAGAGTGTAAAGAGGTCCTAAAGGGCGGGCTCCTGATGAAGCAGTATTACCAGTTCATGCTGCAGGAGGTCCTGGGCGGACTGGAGAAGACCGACTGCAACATGGATGCCTTTGAGGAGGACCTGCAGAAGATGCTGATGGTGTATTTTGATTACATGAGAAGCTGGATCCAAATGCTACAGCAGTTACCTCAGGCTTCCCATAGCTTAAAAAACCTGCTAGAAGAGGAATGGAATTTCACCAAAGAAATAACCCATTATATCCGTGGCGGAGAAGCGCAGGCTGGAAAGCTTTTCTGTGACATCGCAGGGATGCTGCTGAAATCCACAGGGAGCTTTCTGGAATCCGGCCTGCAGGAGAGCTGTGCTGAGCTGTGGACCAGCGCCGACGACAACGGTGCTGCCGACGAGCTAAGAAAAAATGAACACACCGAGTCAGTCTCCACATAA
Peptide sequence:
MNTPSQSPHKDLGKGVETVEEYSYKQEKKIRATLRTTERDHKKNAQCSFMLDSVAGSLPKKSIPDVDLNKPYLSLGCSNAKLPVSMPMPIARTARQTSRTDCPADRLKFFETLRLLLKLTSVSKKKDREQRGQENTAAFWFNRSNELIWLELQAWHAGRTINDQDLFLYTARQAIPDIINEILTFKVNYGSIAFSSNGAGFNGPLVEGQCRTPQETNRVGCSSYHEHLQRQRVSFEQVKRIMELLEYMEALYPSLQALQKDYERYAAKDFEDRVQALCLWLNITKDLNQKLRIMGTVLGIKNLSDIGWPVFEIPSPRPSKGYEPEDEVEDTEVELRELESGTEESDEEPTPSPRVPELRLSTDAILDSRSQGCVSRKLERLESEEDSIGWGTADCGPEASRHCLTSIYRPFVDKALKQMGLRKLILRLHKLMNGSLQRARVALVKDDRPVEFSDFPGPMWGSDYVQLSGTPPSSEQKCSAVSWEELRAMDLPSFEPAFLVLCRVLLNVIHECLKLRLEQRPAGEPSLLSIKQLVRECKEVLKGGLLMKQYYQFMLQEVLGGLEKTDCNMDAFEEDLQKMLMVYFDYMRSWIQMLQQLPQASHSLKNLLEEEWNFTKEITHYIRGGEAQAGKLFCDIAGMLLKSTGSFLESGLQESCAELWTSADDNGAADELRKNEHTESVST
IRESfinder result
IRESfinder score
0.384561098
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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