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mmu_circHadha_716
Basic information of circular RNA
PanCircBase ID:
mmu_circHadha_716
mm39_Chr. Position ID:
chr5|30331562|30340099|-
Gene name:
Hadha
Transcript:
ENSMUST00000156859.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
13,12,11,10,9,8
Exon/intron offsets:
0,2235,3256,5675,7493,8414
Genomic length:
8537
Exon/intron sizes in nt:
17,21,35,11,05,71,19,100
Flanking exon/introns:
chr5:30328692-30331562|chr5:30340099-30345946
Splice length:
716
Other database IDs:
circAtlas: mmu-Hadha_0004
circBase: hsa_circ_0053060, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_40517
Human Ortholog IDs:
Mature spliced Sequence:
GACCAGGAATAAAATCACCAGAAGAAAGGACAATTGAATACCTAGAGGAAGTTGCAGTTAATTTTGCCAAAGGCCTGGCTGATCGGAAAGTCTCTGCAAAGCAGAGCAAAGGCCTTGTGGAAAAGCTGACAACGTATGCCATGACTGTCCCATTTGTCAGACAACAGGTTTACAAAACAGTTGAAGAAAAAGTGAAGAAGCAGACTAAAGGCCTTTATCCTGCCCCTTTGAAAATAATTGATGCTGTGAAGGCTGGACTTGAGCAAGGCAGTGACGCTGGTTATCTTGCTGAATCGCAGAAATTTGGAGAGCTTGCATTGACCAAAGAATCGAAGGCCCTGATGGGGCTTTATAACGGCCAGGTCCTGTGCAAGAAAAATAAATTTGGAGCACCACAGAAGAACGTTCAGCAGCTAGCCATCCTTGGCGCAGGGCTGATGGGGGCTGGCATTGCCCAGGTCTCTGTGGATAAGGGACTGAAAACTCTTCTTAAAGACACCACAGTGACGGGGCTGGGCCGGGGACAGCAGCAAGTGTTCAAAGGGCTGAACGACAAAGTGAAGAAGAAAGCTCTCACATCATTTGAAAGGGATTCCATCTTCAGCAACTTGATTGGGCAGCTGGATTACAAAGGCTTTGAGAAGGCCGACATGGTGATTGAGGCTGTGTTTGAGGACCTCGGTGTAAAGCACAAAGTGTTAAAGGAAGTGGAAAGC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGTTTGAGGACCTCGGTG
59.89
AGACTTTCCGATCAGCCAGG
59.46
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGTTTGAGGACCTCGGTGT
59.89
AGACTTTCCGATCAGCCAGG
59.46
144
PCR template sequence:
GCAGCTGGATTACAAAGGCTTTGAGAAGGCCGACATGGTGATTGAGGCTGTGTTTGAGGACCTCGGTGTAAAGCACAAAGTGTTAAAGGAAGTGGAAAGCGACCAGGAATAAAATCACCAGAAGAAAGGACAATTGAATACCTAGAGGAAGTTGCAGTTAATTTTGCCAAAGGCCTGGCTGATCGGAAAGTCTCTGCAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-22-3p(1), mmu-miR-382-5p(1), mmu-miR-452-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAAGTGGAAAGCGACCAGGAATAAA
siRNA sets
TTATTCCTGGTCGCTTTCC, TATTCCTGGTCGCTTTCCA, TTTATTCCTGGTCGCTTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHADHA_716_ORF_1
1.1759
0.277880756
0.908005037
588
ORF sequence:
ATGACTGTCCCATTTGTCAGACAACAGGTTTACAAAACAGTTGAAGAAAAAGTGAAGAAGCAGACTAAAGGCCTTTATCCTGCCCCTTTGAAAATAATTGATGCTGTGAAGGCTGGACTTGAGCAAGGCAGTGACGCTGGTTATCTTGCTGAATCGCAGAAATTTGGAGAGCTTGCATTGACCAAAGAATCGAAGGCCCTGATGGGGCTTTATAACGGCCAGGTCCTGTGCAAGAAAAATAAATTTGGAGCACCACAGAAGAACGTTCAGCAGCTAGCCATCCTTGGCGCAGGGCTGATGGGGGCTGGCATTGCCCAGGTCTCTGTGGATAAGGGACTGAAAACTCTTCTTAAAGACACCACAGTGACGGGGCTGGGCCGGGGACAGCAGCAAGTGTTCAAAGGGCTGAACGACAAAGTGAAGAAGAAAGCTCTCACATCATTTGAAAGGGATTCCATCTTCAGCAACTTGATTGGGCAGCTGGATTACAAAGGCTTTGAGAAGGCCGACATGGTGATTGAGGCTGTGTTTGAGGACCTCGGTGTAAAGCACAAAGTGTTAAAGGAAGTGGAAAGCGACCAGGAATAA
Peptide sequence:
MTVPFVRQQVYKTVEEKVKKQTKGLYPAPLKIIDAVKAGLEQGSDAGYLAESQKFGELALTKESKALMGLYNGQVLCKKNKFGAPQKNVQQLAILGAGLMGAGIAQVSVDKGLKTLLKDTTVTGLGRGQQQVFKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLGVKHKVLKEVESDQE
IRESfinder result
IRESfinder score
0.545838683
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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