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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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Institute of Life sciences, Bhubaneswar, India

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