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mmu_circAbcc4_631
Basic information of circular RNA
PanCircBase ID:
mmu_circAbcc4_631
mm39_Chr. Position ID:
chr14|118832173|118836935|-
Gene name:
Abcc4
Transcript:
ENSMUST00000036554.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
19,18,17,16,15
Exon/intron offsets:
0,1918,2377,2732,4552
Genomic length:
4762
Exon/intron sizes in nt:
147,95,38,141,210
Flanking exon/introns:
chr14:118790775-118832173|chr14:118836935-118841568
Splice length:
631
Other database IDs:
circAtlas: mmu-Abcc4_0024
circBase: hsa_circ_0007470, circAtlas: hsa-ABCC4_0029, CIRCpedia: HSA_CIRCpedia_11219
Human Ortholog IDs:
Mature spliced Sequence:
GGTGAGATGGTGCAGAAGGGGACTTACACGGAGTTTCTGAAATCTGGTGTAGATTTTGGCTCCCTGTTAAAGAAAGAAAACGAGGAAGCAGAGCCCTCCACAGCCCCAGGAACCCCGACACTCAGGAAACGAACCTTCTCCGAGGCCTCAATTTGGTCTCAGCAGTCATCCAGACCCTCGTTGAAAGACGGGGCCCCAGAGGGCCAAGACGCAGAGAACACGCAGGCAGTGCAACCCGAGGAGAGCCGTTCGGAAGGGAGAATCGGCTTCAAGGCCTACAAGAATTACTTCTCGGCGGGCGCATCCTGGTTCTTCATCATTTTCCTTGTGCTGCTTAACATGGTGGGCCAGGTTTTCTATGTTCTTCAGGACTGGTGGCTTTCCCACTGGGCGAACAAGCAAGGTGCACTGAACAACACCAGAAATGCGAATGGAAATATAACGGAGACCCTAGACCTCAGCTGGTACTTAGGAATTTACGCAGGTCTAACTGCGGTCACCGTCCTTTTTGGCATAGCGAGATCCCTACTGGTGTTCTATATCCTTGTGAACGCTTCCCAGACTTTGCACAACAGGATGTTTGAGTCCATACTGAAGGCTCCCGTGTTGTTCTTCGACAGAAATCCAATCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCATACTGAAGGCTCCCG
59.89
GGGCTCTGCTTCCTCGTTTT
60.61
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCATACTGAAGGCTCCCGTG
60.18
GGGCTCTGCTTCCTCGTTTT
60.61
141
PCR template sequence:
GTGTTCTATATCCTTGTGAACGCTTCCCAGACTTTGCACAACAGGATGTTTGAGTCCATACTGAAGGCTCCCGTGTTGTTCTTCGACAGAAATCCAATCGGGTGAGATGGTGCAGAAGGGGACTTACACGGAGTTTCTGAAATCTGGTGTAGATTTTGGCTCCCTGTTAAAGAAAGAAAACGAGGAAGCAGAGCCCTCCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-375-3p(1), mmu-miR-15b-5p(1), mmu-miR-328-3p(1), mmu-miR-326-3p(1), mmu-miR-22-3p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAATCCAATCGGGTGAGATGGTGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCC4_631_ORF_1
1.1893
0.211813932
0.913043821
630
ORF sequence:
ATGGTGCAGAAGGGGACTTACACGGAGTTTCTGAAATCTGGTGTAGATTTTGGCTCCCTGTTAAAGAAAGAAAACGAGGAAGCAGAGCCCTCCACAGCCCCAGGAACCCCGACACTCAGGAAACGAACCTTCTCCGAGGCCTCAATTTGGTCTCAGCAGTCATCCAGACCCTCGTTGAAAGACGGGGCCCCAGAGGGCCAAGACGCAGAGAACACGCAGGCAGTGCAACCCGAGGAGAGCCGTTCGGAAGGGAGAATCGGCTTCAAGGCCTACAAGAATTACTTCTCGGCGGGCGCATCCTGGTTCTTCATCATTTTCCTTGTGCTGCTTAACATGGTGGGCCAGGTTTTCTATGTTCTTCAGGACTGGTGGCTTTCCCACTGGGCGAACAAGCAAGGTGCACTGAACAACACCAGAAATGCGAATGGAAATATAACGGAGACCCTAGACCTCAGCTGGTACTTAGGAATTTACGCAGGTCTAACTGCGGTCACCGTCCTTTTTGGCATAGCGAGATCCCTACTGGTGTTCTATATCCTTGTGAACGCTTCCCAGACTTTGCACAACAGGATGTTTGAGTCCATACTGAAGGCTCCCGTGTTGTTCTTCGACAGAAATCCAATCGGGTGA
Peptide sequence:
MVQKGTYTEFLKSGVDFGSLLKKENEEAEPSTAPGTPTLRKRTFSEASIWSQQSSRPSLKDGAPEGQDAENTQAVQPEESRSEGRIGFKAYKNYFSAGASWFFIIFLVLLNMVGQVFYVLQDWWLSHWANKQGALNNTRNANGNITETLDLSWYLGIYAGLTAVTVLFGIARSLLVFYILVNASQTLHNRMFESILKAPVLFFDRNPIG
IRESfinder result
IRESfinder score
0.533309577
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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