top of page
mmu_circZcchc4_556
Basic information of circular RNA
PanCircBase ID:
mmu_circZcchc4_556
mm39_Chr. Position ID:
chr5|52941330|52954001|+
Gene name:
Zcchc4
Transcript:
ENSMUST00000031077.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,1109,11988,12593
Genomic length:
12671
Exon/intron sizes in nt:
119,83,276,78
Flanking exon/introns:
chr5:52940556-52941330|chr5:52954001-52961720
Splice length:
556
Other database IDs:
circAtlas: mmu-Zcchc4_0013
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_102925
Human Ortholog IDs:
Mature spliced Sequence:
GGCCTACTCTTCTCTTTGTAAAAGTGAACCAAGGGAAGGAAGAAACACGAAAGTTTTATGCCTGCTCAGCCTGTAGAGATAGAAAAGACTGTAACTTTTTTCAGTGGGAAGATGAAAAGTTGTCAGAAGCTAGACTTGCTGCCCGAGAAATTCATAATCAAAAATGCCAGCCTCCTCTATCCCGGGCACAATGCATAGAAAGGTACCTGAGTTTCATTCAGTTGCCCTTGGCTCAAAGAAAGTTCTGTCAAAGTTGCCAGCAGTTGCTGTTACCTGCAGACTGGAGGGAGCACGGCACGCATCAGCTGTCAGCTGACATTTCTGTCGCCCAGCTTGGAAGGCCCAGTCAGCTGCTCTACCCACTGGAGAACAAGAAGACGCACGCCCAGTACCTGTTTGCTGACAGGAGCTGCCAGTTTCTGGCAGGCCTCCTTGCTACCCTCGGATTCAGCAGAGTGTTGTGTGTTGGAGCACCAAGGCTCCACGAGCAGATCAGGCTAACAGCATCAGGTGAGAGGTCCGGCATGAGGAGCCTTTTATTGGACATTGACTTTCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTTGTGTGTTGGAGCACCA
60.32
ATCTCTACAGGCTGAGCAGG
58.59
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCACGAGCAGATCAGGCTA
60.4
ATCTCTACAGGCTGAGCAGG
58.59
156
PCR template sequence:
TGTTGTGTGTTGGAGCACCAAGGCTCCACGAGCAGATCAGGCTAACAGCATCAGGTGAGAGGTCCGGCATGAGGAGCCTTTTATTGGACATTGACTTTCGGGCCTACTCTTCTCTTTGTAAAAGTGAACCAAGGGAAGGAAGAAACACGAAAGTTTTATGCCTGCTCAGCCTGTAGAGATAGAAAAGACTGTAACTTTTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-216a-5p(1), mmu-miR-194-5p(1), mmu-miR-335-3p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
ACATTGACTTTCGGGCCTACTCTTCT
siRNA sets
AAGAGTAGGCCCGAAAGTC, AGAGTAGGCCCGAAAGTCA, GAAGAGTAGGCCCGAAAGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCZCCHC4_556_ORF_5
0.6016
-0.164209749
0.017252721
108
ORF sequence:
ATGAGGAGCCTTTTATTGGACATTGACTTTCGGGCCTACTCTTCTCTTTGTAAAAGTGAACCAAGGGAAGGAAGAAACACGAAAGTTTTATGCCTGCTCAGCCTGTAG
Peptide sequence:
MRSLLLDIDFRAYSSLCKSEPREGRNTKVLCLLSL
IRESfinder result
IRESfinder score
0.574566162
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page