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mmu_circHectd4_1351
Basic information of circular RNA
PanCircBase ID:
mmu_circHectd4_1351
mm39_Chr. Position ID:
chr5|121391923|121411862|+
Gene name:
Hectd4
Transcript:
ENSMUST00000042614.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
2,3,4,5,6,7,8
Exon/intron offsets:
0,4838,5944,8638,10024,12374,19746
Genomic length:
19939
Exon/intron sizes in nt:
5,18,90,13,11,09,13,91,00,000
Flanking exon/introns:
chr5:121358720-121391923|chr5:121411862-121415737
Splice length:
1351
Other database IDs:
circAtlas: mmu-Gm15800_0017
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_350569
Human Ortholog IDs:
Mature spliced Sequence:
ATTTTAACATTCGAGACCAAGAACCCAACAGAATTAGCAGAACGTTTGCGCTCTGTTTGTGGGAACCAGAGCAATGCCTATGCCCGCCTGCTGGAATACCGCCTGAATGCCTTGCGTGGACTATGGAATGCCCAGCGCCAGCTGGCCCTGGAGGAGCAACATGAAAGGGAAGGCTCAGGTGACGAAGAGACCTTGGCCCTGCTCAAGCGCCAGGGCTTGTTGCAGCAGCCTGAACAAGCCCCCTTCACGTCCCGGGTGGGCCTCCTGTTGGTCTTCCCCCTTATTCAGTCCCAGAGTAGAACAGACCCTTCCCTCTGTAACATAACTGCTGAGGTGCTATTAAACTGCCTGCGAGACTGTCAGCCTTTGAGCTTGACCAAGGAGCCTGCTGATTGTCTCAATGGGATAGAAACCTTGCTGTGCTCTTGGCTAGAGGAGACCTCGGACACAGGCCGACACATCCCACACAAGCAGAAGGAGAACGCTGCTGCTGCCCTGGTGGCTTTGGCGTGTGCCAGGGGGTCACTGAAGACCTTTGTCCACACAGTTCACCTGCTGCAGAGACAGACTGAGCTGGGCTCCCTGCCTGTCGCCGATGTTTTATATAGGTTGCTGCTTTTGGAAGGGGGACCTGGATCCCCATCCTGTTTGCTTGGGGGCAAACACATAGTATCTTGGGGATATGAGGACATGCTGCCAGCACCAGACAGCAACACTGGCTCCAGCTCTGAAAACAAAGATGCTGACTTGGGCCGCTGTCTCACCGCAGATGGGCATTACCTGTACACTACCAACTCAGCCGGAAGAGGAGTGAGCAAGCTGGGCTCTGGACTGCATGGCACGCTCAGAGGGTTTGTGTACTGTCGCAATGAGGAGCTAGAGCCAGGGTGGGTGGCGTACGGCAATGGCCACCTACTCCATCGGCCTGTGTCTTTTGACAATAAACCTCACTCCCTTTTCCAGGTCATAGACCAGAACACCCTGCAGGTGTGCCAGACAGTGCCCATGCCCGCCAGCCCCCTTCCTGTGGGCAGCACCATGAGCACTGTGCACCTTTCCTCAGATGGCACTTACTTCTACTGGATCTGGTCCCCTGCCAGTTTAAATGAGAAAACCCCAAAGGGACACTCTGTCTTCATGGACATTTTTGAACTTGTGGTGGAAAATGGGGTATTTGTAGCCAACCCGCTTCAGGAACGCACAATCCTAATGAGAAAAGAGGGTGAGTCTGCTAAAAGCATTAATGAGATGCTCCTGAGCAGACTGTCTCGGTACAGAGCCTCTCCATCGGCGACTCTCGCGGCCCTGACTGGCTCCACCATCTCCAACACGCTGAAGGAGGATCAAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCGGTACAGAGCCTCTCC
60.11
CACAAACAGAGCGCAAACGT
60.25
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCGGTACAGAGCCTCTCC
60.11
TAGGCATTGCTCTGGTTCCC
59.74
165
PCR template sequence:
CTCCTGAGCAGACTGTCTCGGTACAGAGCCTCTCCATCGGCGACTCTCGCGGCCCTGACTGGCTCCACCATCTCCAACACGCTGAAGGAGGATCAAGCAGATTTTAACATTCGAGACCAAGAACCCAACAGAATTAGCAGAACGTTTGCGCTCTGTTTGTGGGAACCAGAGCAATGCCTATGCCCGCCTGCTGGAATACC
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-210-3p(1), mmu-miR-16-5p(1), mmu-miR-199a-5p(1), mmu-miR-322-5p(1), mmu-miR-335-5p(1), mmu-miR-18a-5p(1), mmu-miR-298-5p(1), mmu-miR-214-3p(1), mmu-miR-149-5p(1), mmu-miR-431-5p(1), mmu-miR-666-5p(1), mmu-miR-335-3p(1), mmu-miR-669d-5p(1), mmu-miR-188-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GAGGATCAAGCAGATTTTAACATTCG
siRNA sets
ATGTTAAAATCTGCTTGAT, TTAAAATCTGCTTGATCCT, TGTTAAAATCTGCTTGATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHECTD4_1351_ORF_1
0.7799
0.191948862
0.946965777
825
ORF sequence:
ATGCTGCCAGCACCAGACAGCAACACTGGCTCCAGCTCTGAAAACAAAGATGCTGACTTGGGCCGCTGTCTCACCGCAGATGGGCATTACCTGTACACTACCAACTCAGCCGGAAGAGGAGTGAGCAAGCTGGGCTCTGGACTGCATGGCACGCTCAGAGGGTTTGTGTACTGTCGCAATGAGGAGCTAGAGCCAGGGTGGGTGGCGTACGGCAATGGCCACCTACTCCATCGGCCTGTGTCTTTTGACAATAAACCTCACTCCCTTTTCCAGGTCATAGACCAGAACACCCTGCAGGTGTGCCAGACAGTGCCCATGCCCGCCAGCCCCCTTCCTGTGGGCAGCACCATGAGCACTGTGCACCTTTCCTCAGATGGCACTTACTTCTACTGGATCTGGTCCCCTGCCAGTTTAAATGAGAAAACCCCAAAGGGACACTCTGTCTTCATGGACATTTTTGAACTTGTGGTGGAAAATGGGGTATTTGTAGCCAACCCGCTTCAGGAACGCACAATCCTAATGAGAAAAGAGGGTGAGTCTGCTAAAAGCATTAATGAGATGCTCCTGAGCAGACTGTCTCGGTACAGAGCCTCTCCATCGGCGACTCTCGCGGCCCTGACTGGCTCCACCATCTCCAACACGCTGAAGGAGGATCAAGCAGATTTTAACATTCGAGACCAAGAACCCAACAGAATTAGCAGAACGTTTGCGCTCTGTTTGTGGGAACCAGAGCAATGCCTATGCCCGCCTGCTGGAATACCGCCTGAATGCCTTGCGTGGACTATGGAATGCCCAGCGCCAGCTGGCCCTGGAGGAGCAACATGA
Peptide sequence:
MLPAPDSNTGSSSENKDADLGRCLTADGHYLYTTNSAGRGVSKLGSGLHGTLRGFVYCRNEELEPGWVAYGNGHLLHRPVSFDNKPHSLFQVIDQNTLQVCQTVPMPASPLPVGSTMSTVHLSSDGTYFYWIWSPASLNEKTPKGHSVFMDIFELVVENGVFVANPLQERTILMRKEGESAKSINEMLLSRLSRYRASPSATLAALTGSTISNTLKEDQADFNIRDQEPNRISRTFALCLWEPEQCLCPPAGIPPECLAWTMECPAPAGPGGAT
IRESfinder result
IRESfinder score
0.442447735
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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