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mmu_circKsr1_584

Basic information of circular RNA
PanCircBase ID:

mmu_circKsr1_584

mm39_Chr. Position ID:

chr11|78919300|78931763|-

Gene name:

Ksr1

Transcript:

ENSMUST00000018478.11

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

7

Exon/intron indexes:

12,11,10,9,8,7,6

Exon/intron offsets:

0,554,4743,8020,8212,9677,12402

Genomic length:

12463

Exon/intron sizes in nt:

49,55,166,107,62,84,61

Flanking exon/introns:

chr11:78918625-78919300|chr11:78931763-78934021

Splice length:

584

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

AACTCCCTCATGGATCCCCACAGCTGGTACGAAGGGATATCGGGCTCTCGGTGACGCACAGGTTCTCCACAAAGTCATGGTTGTCACAGGTGTGCAACGTGTGCCAGAAGAGCATGATTTTTGGCGTGAAGTGCAAACACTGCAGGTTAAAATGCCATAACAAGTGCACAAAGGAAGCTCCCGCCTGCAGGATCACCTTCCTCCCACTGGCCAGGCTTCGGAGGACAGAGTCTGTCCCGTCAGATATCAACAACCCAGTGGACAGAGCAGCAGAGCCCCATTTTGGAACCCTTCCCAAGGCCCTGACAAAGAAGGAGCACCCTCCAGCCATGAACCTGGACTCCAGCAGCAACCCATCCTCCACCACGTCCTCCACACCCTCATCGCCGGCACCTTTCCTGACCTCATCTAATCCCTCCAGTGCCACCACGCCTCCCAACCCGTCACCTGGCCAGCGGGACAGCAGGTTCAGCTTCCCAGACATTTCAGCCTGTTCTCAGGCAGCCCCGCTGTCCAGCACAGCCGACAGTACACGGCTCGACGACCAGCCCAAAACAGATGTGCTAGGTGTTCACGAAGCAGAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AGCACAGCCGACAGTACAC

60.01

TTTGTGGAGAACCTGTGCGT

60.11

142

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CAGCACAGCCGACAGTACA

60.01

TTTGTGGAGAACCTGTGCGT

60.11

143

PCR template sequence:

TTCAGCCTGTTCTCAGGCAGCCCCGCTGTCCAGCACAGCCGACAGTACACGGCTCGACGACCAGCCCAAAACAGATGTGCTAGGTGTTCACGAAGCAGAGAACTCCCTCATGGATCCCCACAGCTGGTACGAAGGGATATCGGGCTCTCGGTGACGCACAGGTTCTCCACAAAGTCATGGTTGTCACAGGTGTGCAACGT

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

3

Interacting miRNAs (#binding sites)

mmu-miR-705(2), mmu-miR-203-3p(1), mmu-miR-541-5p(1)

siRNAs for circular RNA silencing
Junction sequence

TCACGAAGCAGAGAACTCCCTCATGG

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCKSR1_584_ORF_1

0.7297

0.267924118

0.725226066

525

ORF sequence:

ATGATTTTTGGCGTGAAGTGCAAACACTGCAGGTTAAAATGCCATAACAAGTGCACAAAGGAAGCTCCCGCCTGCAGGATCACCTTCCTCCCACTGGCCAGGCTTCGGAGGACAGAGTCTGTCCCGTCAGATATCAACAACCCAGTGGACAGAGCAGCAGAGCCCCATTTTGGAACCCTTCCCAAGGCCCTGACAAAGAAGGAGCACCCTCCAGCCATGAACCTGGACTCCAGCAGCAACCCATCCTCCACCACGTCCTCCACACCCTCATCGCCGGCACCTTTCCTGACCTCATCTAATCCCTCCAGTGCCACCACGCCTCCCAACCCGTCACCTGGCCAGCGGGACAGCAGGTTCAGCTTCCCAGACATTTCAGCCTGTTCTCAGGCAGCCCCGCTGTCCAGCACAGCCGACAGTACACGGCTCGACGACCAGCCCAAAACAGATGTGCTAGGTGTTCACGAAGCAGAGAACTCCCTCATGGATCCCCACAGCTGGTACGAAGGGATATCGGGCTCTCGGTGA

Peptide sequence:

MIFGVKCKHCRLKCHNKCTKEAPACRITFLPLARLRRTESVPSDINNPVDRAAEPHFGTLPKALTKKEHPPAMNLDSSSNPSSTTSSTPSSPAPFLTSSNPSSATTPPNPSPGQRDSRFSFPDISACSQAAPLSSTADSTRLDDQPKTDVLGVHEAENSLMDPHSWYEGISGSR

IRESfinder result

IRESfinder score

0.468101242

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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