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mmu_circAbcc1_390
Basic information of circular RNA
PanCircBase ID:
mmu_circAbcc1_390
mm39_Chr. Position ID:
chr16|14209181|14214340|+
Gene name:
Abcc1
Transcript:
ENSMUST00000130671.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
3,4,5
Exon/intron offsets:
0,2635,5033
Genomic length:
5159
Exon/intron sizes in nt:
126,138,126
Flanking exon/introns:
chr16:14207847-14209181|chr16:14214340-14221853
Splice length:
390
Other database IDs:
circAtlas: mmu-Abcc1_0001
circBase: hsa_circ_0038082, circAtlas: hsa-ABCC1_0001, CIRCpedia: HSA_CIRCpedia_16563
Human Ortholog IDs:
Mature spliced Sequence:
GCCTTAGGATTCTTTCTGTGGATCATCTGCTGGGCAGACCTCTTCTACTCTTTCTGGGAAAGAAGTCAGGGAGTGCTCCGAGCCCCAGTGTTACTGGTCAGCCCAACACTGCTGGGCATCACCATGCTGCTCGCCACCTTTTTGATACAGCTTGAACGGAGGAAGGGAGTCCAATCCTCGGGAATTATGCTTACTTTCTGGCTCGTAGCCCTACTCTGTGCCCTTGCCATCTTGAGATCTAAGATCATCTCTGCCTTAAAAAAGGATGCTCATGTGGACGTGTTTCGAGATTCCACGTTCTATCTGTACTTCACCCTTGTGCTTGTTCAGCTCGTGCTGTCCTGCTTCTCAGACTGCTCACCCCTGTTCTCTGAAACTGTCCATGACCGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTCAGACTGCTCACCCCT
60.18
CAGTAACACTGGGGCTCGG
60.08
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTTCTCAGACTGCTCACCCC
59.75
CAGTAACACTGGGGCTCGG
60.08
142
PCR template sequence:
TTCCACGTTCTATCTGTACTTCACCCTTGTGCTTGTTCAGCTCGTGCTGTCCTGCTTCTCAGACTGCTCACCCCTGTTCTCTGAAACTGTCCATGACCGGGCCTTAGGATTCTTTCTGTGGATCATCTGCTGGGCAGACCTCTTCTACTCTTTCTGGGAAAGAAGTCAGGGAGTGCTCCGAGCCCCAGTGTTACTGGTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(1), mmu-miR-107-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGTCCATGACCGGGCCTTAGGATTCT
siRNA sets
AGAATCCTAAGGCCCGGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCC1_390_ORF_1
0.9537
0.156397591
0.869069775
657
ORF sequence:
ATGCTGCTCGCCACCTTTTTGATACAGCTTGAACGGAGGAAGGGAGTCCAATCCTCGGGAATTATGCTTACTTTCTGGCTCGTAGCCCTACTCTGTGCCCTTGCCATCTTGAGATCTAAGATCATCTCTGCCTTAAAAAAGGATGCTCATGTGGACGTGTTTCGAGATTCCACGTTCTATCTGTACTTCACCCTTGTGCTTGTTCAGCTCGTGCTGTCCTGCTTCTCAGACTGCTCACCCCTGTTCTCTGAAACTGTCCATGACCGGGCCTTAGGATTCTTTCTGTGGATCATCTGCTGGGCAGACCTCTTCTACTCTTTCTGGGAAAGAAGTCAGGGAGTGCTCCGAGCCCCAGTGTTACTGGTCAGCCCAACACTGCTGGGCATCACCATGCTGCTCGCCACCTTTTTGATACAGCTTGAACGGAGGAAGGGAGTCCAATCCTCGGGAATTATGCTTACTTTCTGGCTCGTAGCCCTACTCTGTGCCCTTGCCATCTTGAGATCTAAGATCATCTCTGCCTTAAAAAAGGATGCTCATGTGGACGTGTTTCGAGATTCCACGTTCTATCTGTACTTCACCCTTGTGCTTGTTCAGCTCGTGCTGTCCTGCTTCTCAGACTGCTCACCCCTGTTCTCTGAAACTGTCCATGACCGG
Peptide sequence:
MLLATFLIQLERRKGVQSSGIMLTFWLVALLCALAILRSKIISALKKDAHVDVFRDSTFYLYFTLVLVQLVLSCFSDCSPLFSETVHDRALGFFLWIICWADLFYSFWERSQGVLRAPVLLVSPTLLGITMLLATFLIQLERRKGVQSSGIMLTFWLVALLCALAILRSKIISALKKDAHVDVFRDSTFYLYFTLVLVQLVLSCFSDCSPLFSETVHDR
IRESfinder result
IRESfinder score
0.832287301
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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