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mmu_circAbcf1_556
Basic information of circular RNA
PanCircBase ID:
mmu_circAbcf1_556
mm39_Chr. Position ID:
chr17|36269960|36270884|-
Gene name:
Abcf1
Transcript:
ENSMUST00000043757.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
18,17,16,15
Exon/intron offsets:
0,160,367,799
Genomic length:
924
Exon/intron sizes in nt:
71,75,285,125
Flanking exon/introns:
chr17:36269249-36269960|chr17:36270884-36271005
Splice length:
556
Other database IDs:
circAtlas: mmu-Abcf1_0018
Human Ortholog IDs:
Mature spliced Sequence:
CTACCTTCAGGGCTGGAGGAAGACGTTGCTGATTGTCTCCCACGACCAGGGCTTTCTGGATGACGTTTGCACTGATATCATCCACCTGGACACCCAGCGGCTCCATTACTACAGGGGCAATTACATGACCTTCAAGAAGATGTACCAGCAGAAGCAGAAAGAGCTGCTAAAGCAGTACGAGAAGCAGGAGAAGAAACTGAAGGAGCTGAAGGCTGGGGGCAAGTCCACCAAGCAAGCGGAAAAGCAAACAAAGGAAGTCCTGACTCGAAAACAGCAGAAGTGCCGACGGAAAAACCAGGATGAAGAGTCTCAGGAGCCCCCTGAGCTCCTGAAGCGTCCCAAGGAGTACACCGTGCGCTTCACCTTCCCAGACCCCCCGCCTCTCAGCCCACCTGTGCTGGGCCTGCACGGTGTGACGTTTGGCTACGAGGGGCAGAAGCCACTCTTTAAGAATCTAGATTTCGGCATCGACATGGACTCCCGGATTTGCATCGTGGGTCCCAATGGTGTGGGGAAGAGCACACTACTCCTGCTGCTGACTGGCAAGCTGACACCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGACTCCCGGATTTGCATC
60.11
ACGTCATCCAGAAAGCCCTG
60.04
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGACATGGACTCCCGGATTT
59.82
ACGTCATCCAGAAAGCCCTG
60.04
154
PCR template sequence:
AGATTTCGGCATCGACATGGACTCCCGGATTTGCATCGTGGGTCCCAATGGTGTGGGGAAGAGCACACTACTCCTGCTGCTGACTGGCAAGCTGACACCGCTACCTTCAGGGCTGGAGGAAGACGTTGCTGATTGTCTCCCACGACCAGGGCTTTCTGGATGACGTTTGCACTGATATCATCCACCTGGACACCCAGCGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-1904(2), mmu-miR-15a-5p(1), mmu-miR-19b-3p(1), mmu-miR-130a-3p(1), mmu-miR-19a-3p(1), mmu-miR-503-5p(1), mmu-miR-125a-5p(1), mmu-miR-301b-3p(1), mmu-miR-301a-3p(1), mmu-miR-207(1), mmu-miR-5101(1)
siRNAs for circular RNA silencing
Junction sequence
CAAGCTGACACCGCTACCTTCAGGGC
siRNA sets
TGAAGGTAGCGGTGTCAGC, GAAGGTAGCGGTGTCAGCT, AAGGTAGCGGTGTCAGCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCF1_556_ORF_1
1.3132
0.520980088
0.946603212
495
ORF sequence:
ATGACCTTCAAGAAGATGTACCAGCAGAAGCAGAAAGAGCTGCTAAAGCAGTACGAGAAGCAGGAGAAGAAACTGAAGGAGCTGAAGGCTGGGGGCAAGTCCACCAAGCAAGCGGAAAAGCAAACAAAGGAAGTCCTGACTCGAAAACAGCAGAAGTGCCGACGGAAAAACCAGGATGAAGAGTCTCAGGAGCCCCCTGAGCTCCTGAAGCGTCCCAAGGAGTACACCGTGCGCTTCACCTTCCCAGACCCCCCGCCTCTCAGCCCACCTGTGCTGGGCCTGCACGGTGTGACGTTTGGCTACGAGGGGCAGAAGCCACTCTTTAAGAATCTAGATTTCGGCATCGACATGGACTCCCGGATTTGCATCGTGGGTCCCAATGGTGTGGGGAAGAGCACACTACTCCTGCTGCTGACTGGCAAGCTGACACCGCTACCTTCAGGGCTGGAGGAAGACGTTGCTGATTGTCTCCCACGACCAGGGCTTTCTGGATGA
Peptide sequence:
MTFKKMYQQKQKELLKQYEKQEKKLKELKAGGKSTKQAEKQTKEVLTRKQQKCRRKNQDEESQEPPELLKRPKEYTVRFTFPDPPPLSPPVLGLHGVTFGYEGQKPLFKNLDFGIDMDSRICIVGPNGVGKSTLLLLLTGKLTPLPSGLEEDVADCLPRPGLSG
IRESfinder result
IRESfinder score
0.324135657
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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