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mmu_circShtn1_940
Basic information of circular RNA
PanCircBase ID:
mmu_circShtn1_940
mm39_Chr. Position ID:
chr19|59003958|59030388|-
Gene name:
Shtn1
Transcript:
ENSMUST00000163821.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
11,10,9,8,7,6,5,4
Exon/intron offsets:
0,3278,6649,12628,16646,19517,22695,26335
Genomic length:
26430
Exon/intron sizes in nt:
100,154,147,95,82,98,169,95
Flanking exon/introns:
chr19:58998279-59003958|chr19:59030388-59039265
Splice length:
940
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TTTCACATATGGTTATAGAGGAGGTGAATTTCATGCAGAACCATCTTGAAATAGAGAAGACATGTCGAGAGAGCGCTGAAGCCTTGGCGACAAAGCTAAATAAAGAAAATAAAACACTGAAAAGAATCAGCATGCTATACATGGCCAAACTGGGGCCAGACGTAATTACAGAGGAGATAAACATTGATGATGATGACCCAGCCACCGACACAGATGCTGCGGCTGAGACCTGTGTGTCTGTTCAGTGTCAGAAGCAAATCAAAGAACTTCGAGATCAAATTGTGTCTGTTCAGGAAGAAAAGAAGGTGTTAGCCATCGAGCTGGAAAACCTCAAGAGCAAACTCGGGGAGGTGATGGAGGAGGTAAATAAAGTTAAGCAAGAAAAAGCTGTTTTAAATTCAGAAGTCCTTGAGCAGAGGAAAGTCTTAGAAAAATGCAACAGAGTGTCCATGTTGGCTGTTGAAGAGTATGAGGAACTGCAAGTGAACCTGGAACTGGAGAAGGACCTTCGCAAGAAAGCAGAGTCTTTTGCACAAGAGATGTTCATTGAACAAAACAAACTGAAGAGACAAAGCCACCTTCTGCTGCAGAGCTCCCTTCCTGACCAGCAGCTTTTGAAAGCTTTAGACGAAAACGCAAAACTTATCCAGCAGCTTGAAGAAGAGAGGATCCAGCATCAGAAAAAGGTCAAAGAGCTGGAGGAGCGGCTGGAGAATGAAGCACTTCACAAAGAGATCCATAACCTCAGACAACAGCTGGAGCTTCTGGAAGACGACAAGAGGGAGCTAGAGCAGAAATACCAGAGCTCGGAGGAGAAGGCCCGGAACCTGAAGCATTCAGTGGATGAACTTCAGAAGCGAGTGAACCAGTCTGAGAATTCGGTACCTCCCCCGCCTCCTCCTCCTCCACCTCTCCCCCCTCCACCTCCCAATCCAATCCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCCTCCTCCTCCACCTCTC
60.11
CTTTGTCGCCAAGGCTTCAG
59.76
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCGAGTGAACCAGTCTGAGA
59.4
CTTCAGCGCTCTCTCGACAT
59.9
165
PCR template sequence:
TGGATGAACTTCAGAAGCGAGTGAACCAGTCTGAGAATTCGGTACCTCCCCCGCCTCCTCCTCCTCCACCTCTCCCCCCTCCACCTCCCAATCCAATCCGTTTCACATATGGTTATAGAGGAGGTGAATTTCATGCAGAACCATCTTGAAATAGAGAAGACATGTCGAGAGAGCGCTGAAGCCTTGGCGACAAAGCTAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-207(2), mmu-miR-103-3p(1), mmu-miR-298-5p(1), mmu-miR-320-3p(1), mmu-miR-107-3p(1), mmu-miR-705(1)
siRNAs for circular RNA silencing
Junction sequence
CCAATCCAATCCGTTTCACATATGGT
siRNA sets
ATATGTGAAACGGATTGGA, TATGTGAAACGGATTGGAT, CATATGTGAAACGGATTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSHTN1_940_ORF_1
1.2359
0.346401966
0.995957335
981
ORF sequence:
ATGGTTATAGAGGAGGTGAATTTCATGCAGAACCATCTTGAAATAGAGAAGACATGTCGAGAGAGCGCTGAAGCCTTGGCGACAAAGCTAAATAAAGAAAATAAAACACTGAAAAGAATCAGCATGCTATACATGGCCAAACTGGGGCCAGACGTAATTACAGAGGAGATAAACATTGATGATGATGACCCAGCCACCGACACAGATGCTGCGGCTGAGACCTGTGTGTCTGTTCAGTGTCAGAAGCAAATCAAAGAACTTCGAGATCAAATTGTGTCTGTTCAGGAAGAAAAGAAGGTGTTAGCCATCGAGCTGGAAAACCTCAAGAGCAAACTCGGGGAGGTGATGGAGGAGGTAAATAAAGTTAAGCAAGAAAAAGCTGTTTTAAATTCAGAAGTCCTTGAGCAGAGGAAAGTCTTAGAAAAATGCAACAGAGTGTCCATGTTGGCTGTTGAAGAGTATGAGGAACTGCAAGTGAACCTGGAACTGGAGAAGGACCTTCGCAAGAAAGCAGAGTCTTTTGCACAAGAGATGTTCATTGAACAAAACAAACTGAAGAGACAAAGCCACCTTCTGCTGCAGAGCTCCCTTCCTGACCAGCAGCTTTTGAAAGCTTTAGACGAAAACGCAAAACTTATCCAGCAGCTTGAAGAAGAGAGGATCCAGCATCAGAAAAAGGTCAAAGAGCTGGAGGAGCGGCTGGAGAATGAAGCACTTCACAAAGAGATCCATAACCTCAGACAACAGCTGGAGCTTCTGGAAGACGACAAGAGGGAGCTAGAGCAGAAATACCAGAGCTCGGAGGAGAAGGCCCGGAACCTGAAGCATTCAGTGGATGAACTTCAGAAGCGAGTGAACCAGTCTGAGAATTCGGTACCTCCCCCGCCTCCTCCTCCTCCACCTCTCCCCCCTCCACCTCCCAATCCAATCCGTTTCACATATGGTTATAGAGGAGGTGAATTTCATGCAGAACCATCTTGA
Peptide sequence:
MVIEEVNFMQNHLEIEKTCRESAEALATKLNKENKTLKRISMLYMAKLGPDVITEEINIDDDDPATDTDAAAETCVSVQCQKQIKELRDQIVSVQEEKKVLAIELENLKSKLGEVMEEVNKVKQEKAVLNSEVLEQRKVLEKCNRVSMLAVEEYEELQVNLELEKDLRKKAESFAQEMFIEQNKLKRQSHLLLQSSLPDQQLLKALDENAKLIQQLEEERIQHQKKVKELEERLENEALHKEIHNLRQQLELLEDDKRELEQKYQSSEEKARNLKHSVDELQKRVNQSENSVPPPPPPPPPLPPPPPNPIRFTYGYRGGEFHAEPS
IRESfinder result
IRESfinder score
0.446924556
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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