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mmu_circShtn1_1137
Basic information of circular RNA
PanCircBase ID:
mmu_circShtn1_1137
mm39_Chr. Position ID:
chr19|58998196|59049115|-
Gene name:
Shtn1
Transcript:
ENSMUST00000163821.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
12,11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,5762,9040,12411,18390,22408,25279,28457,32097,41069,50866
Genomic length:
50919
Exon/intron sizes in nt:
83,100,154,147,95,82,98,169,95,61,53
Flanking exon/introns:
chr19:58992381-58998196|chr19:59049115-59063886
Splice length:
1137
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
CCATTGGCGAATATGAAGACCTTCGAGCAGAGAACCAGAAAACAAAGGAGAAGTGTGACAAAATTAGGCAAGAACGAGATGAAGCTGTTAAAAAACTGGAAGAGTTTCAGAAAATTTCACATATGGTTATAGAGGAGGTGAATTTCATGCAGAACCATCTTGAAATAGAGAAGACATGTCGAGAGAGCGCTGAAGCCTTGGCGACAAAGCTAAATAAAGAAAATAAAACACTGAAAAGAATCAGCATGCTATACATGGCCAAACTGGGGCCAGACGTAATTACAGAGGAGATAAACATTGATGATGATGACCCAGCCACCGACACAGATGCTGCGGCTGAGACCTGTGTGTCTGTTCAGTGTCAGAAGCAAATCAAAGAACTTCGAGATCAAATTGTGTCTGTTCAGGAAGAAAAGAAGGTGTTAGCCATCGAGCTGGAAAACCTCAAGAGCAAACTCGGGGAGGTGATGGAGGAGGTAAATAAAGTTAAGCAAGAAAAAGCTGTTTTAAATTCAGAAGTCCTTGAGCAGAGGAAAGTCTTAGAAAAATGCAACAGAGTGTCCATGTTGGCTGTTGAAGAGTATGAGGAACTGCAAGTGAACCTGGAACTGGAGAAGGACCTTCGCAAGAAAGCAGAGTCTTTTGCACAAGAGATGTTCATTGAACAAAACAAACTGAAGAGACAAAGCCACCTTCTGCTGCAGAGCTCCCTTCCTGACCAGCAGCTTTTGAAAGCTTTAGACGAAAACGCAAAACTTATCCAGCAGCTTGAAGAAGAGAGGATCCAGCATCAGAAAAAGGTCAAAGAGCTGGAGGAGCGGCTGGAGAATGAAGCACTTCACAAAGAGATCCATAACCTCAGACAACAGCTGGAGCTTCTGGAAGACGACAAGAGGGAGCTAGAGCAGAAATACCAGAGCTCGGAGGAGAAGGCCCGGAACCTGAAGCATTCAGTGGATGAACTTCAGAAGCGAGTGAACCAGTCTGAGAATTCGGTACCTCCCCCGCCTCCTCCTCCTCCACCTCTCCCCCCTCCACCTCCCAATCCAATCCGGTCCCTCATGTCTATGATCCGGAAGCGATCTCACCCCAGTGGCAATAGTGCTAAGAAAGAAAAGACAACTCAGCCAGAGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCCCAATCCAATCCGGTC
60.18
TTCTGGTTCTCTGCTCGAAGG
59.73
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAATCCGGTCCCTCATGTC
60.18
AGCTTCATCTCGTTCTTGCCT
59.72
177
PCR template sequence:
CCTCCCAATCCAATCCGGTCCCTCATGTCTATGATCCGGAAGCGATCTCACCCCAGTGGCAATAGTGCTAAGAAAGAAAAGACAACTCAGCCAGAGACAGCCATTGGCGAATATGAAGACCTTCGAGCAGAGAACCAGAAAACAAAGGAGAAGTGTGACAAAATTAGGCAAGAACGAGATGAAGCTGTTAAAAAACTGGA
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(3), 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
CAGCCAGAGACAGCCATTGGCGAATA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSHTN1_1137_ORF_1
1.2248
0.380301969
0.999999216
2151
ORF sequence:
ATGGTTATAGAGGAGGTGAATTTCATGCAGAACCATCTTGAAATAGAGAAGACATGTCGAGAGAGCGCTGAAGCCTTGGCGACAAAGCTAAATAAAGAAAATAAAACACTGAAAAGAATCAGCATGCTATACATGGCCAAACTGGGGCCAGACGTAATTACAGAGGAGATAAACATTGATGATGATGACCCAGCCACCGACACAGATGCTGCGGCTGAGACCTGTGTGTCTGTTCAGTGTCAGAAGCAAATCAAAGAACTTCGAGATCAAATTGTGTCTGTTCAGGAAGAAAAGAAGGTGTTAGCCATCGAGCTGGAAAACCTCAAGAGCAAACTCGGGGAGGTGATGGAGGAGGTAAATAAAGTTAAGCAAGAAAAAGCTGTTTTAAATTCAGAAGTCCTTGAGCAGAGGAAAGTCTTAGAAAAATGCAACAGAGTGTCCATGTTGGCTGTTGAAGAGTATGAGGAACTGCAAGTGAACCTGGAACTGGAGAAGGACCTTCGCAAGAAAGCAGAGTCTTTTGCACAAGAGATGTTCATTGAACAAAACAAACTGAAGAGACAAAGCCACCTTCTGCTGCAGAGCTCCCTTCCTGACCAGCAGCTTTTGAAAGCTTTAGACGAAAACGCAAAACTTATCCAGCAGCTTGAAGAAGAGAGGATCCAGCATCAGAAAAAGGTCAAAGAGCTGGAGGAGCGGCTGGAGAATGAAGCACTTCACAAAGAGATCCATAACCTCAGACAACAGCTGGAGCTTCTGGAAGACGACAAGAGGGAGCTAGAGCAGAAATACCAGAGCTCGGAGGAGAAGGCCCGGAACCTGAAGCATTCAGTGGATGAACTTCAGAAGCGAGTGAACCAGTCTGAGAATTCGGTACCTCCCCCGCCTCCTCCTCCTCCACCTCTCCCCCCTCCACCTCCCAATCCAATCCGGTCCCTCATGTCTATGATCCGGAAGCGATCTCACCCCAGTGGCAATAGTGCTAAGAAAGAAAAGACAACTCAGCCAGAGACAGCCATTGGCGAATATGAAGACCTTCGAGCAGAGAACCAGAAAACAAAGGAGAAGTGTGACAAAATTAGGCAAGAACGAGATGAAGCTGTTAAAAAACTGGAAGAGTTTCAGAAAATTTCACATATGGTTATAGAGGAGGTGAATTTCATGCAGAACCATCTTGAAATAGAGAAGACATGTCGAGAGAGCGCTGAAGCCTTGGCGACAAAGCTAAATAAAGAAAATAAAACACTGAAAAGAATCAGCATGCTATACATGGCCAAACTGGGGCCAGACGTAATTACAGAGGAGATAAACATTGATGATGATGACCCAGCCACCGACACAGATGCTGCGGCTGAGACCTGTGTGTCTGTTCAGTGTCAGAAGCAAATCAAAGAACTTCGAGATCAAATTGTGTCTGTTCAGGAAGAAAAGAAGGTGTTAGCCATCGAGCTGGAAAACCTCAAGAGCAAACTCGGGGAGGTGATGGAGGAGGTAAATAAAGTTAAGCAAGAAAAAGCTGTTTTAAATTCAGAAGTCCTTGAGCAGAGGAAAGTCTTAGAAAAATGCAACAGAGTGTCCATGTTGGCTGTTGAAGAGTATGAGGAACTGCAAGTGAACCTGGAACTGGAGAAGGACCTTCGCAAGAAAGCAGAGTCTTTTGCACAAGAGATGTTCATTGAACAAAACAAACTGAAGAGACAAAGCCACCTTCTGCTGCAGAGCTCCCTTCCTGACCAGCAGCTTTTGAAAGCTTTAGACGAAAACGCAAAACTTATCCAGCAGCTTGAAGAAGAGAGGATCCAGCATCAGAAAAAGGTCAAAGAGCTGGAGGAGCGGCTGGAGAATGAAGCACTTCACAAAGAGATCCATAACCTCAGACAACAGCTGGAGCTTCTGGAAGACGACAAGAGGGAGCTAGAGCAGAAATACCAGAGCTCGGAGGAGAAGGCCCGGAACCTGAAGCATTCAGTGGATGAACTTCAGAAGCGAGTGAACCAGTCTGAGAATTCGGTACCTCCCCCGCCTCCTCCTCCTCCACCTCTCCCCCCTCCACCTCCCAATCCAATCCGGTCCCTCATGTCTATGATCCGGAAGCGATCTCACCCCAGTGGCAATAGTGCTAAGAAAGAAAAGACAACTCAGCCAGAGACA
Peptide sequence:
MVIEEVNFMQNHLEIEKTCRESAEALATKLNKENKTLKRISMLYMAKLGPDVITEEINIDDDDPATDTDAAAETCVSVQCQKQIKELRDQIVSVQEEKKVLAIELENLKSKLGEVMEEVNKVKQEKAVLNSEVLEQRKVLEKCNRVSMLAVEEYEELQVNLELEKDLRKKAESFAQEMFIEQNKLKRQSHLLLQSSLPDQQLLKALDENAKLIQQLEEERIQHQKKVKELEERLENEALHKEIHNLRQQLELLEDDKRELEQKYQSSEEKARNLKHSVDELQKRVNQSENSVPPPPPPPPPLPPPPPNPIRSLMSMIRKRSHPSGNSAKKEKTTQPETAIGEYEDLRAENQKTKEKCDKIRQERDEAVKKLEEFQKISHMVIEEVNFMQNHLEIEKTCRESAEALATKLNKENKTLKRISMLYMAKLGPDVITEEINIDDDDPATDTDAAAETCVSVQCQKQIKELRDQIVSVQEEKKVLAIELENLKSKLGEVMEEVNKVKQEKAVLNSEVLEQRKVLEKCNRVSMLAVEEYEELQVNLELEKDLRKKAESFAQEMFIEQNKLKRQSHLLLQSSLPDQQLLKALDENAKLIQQLEEERIQHQKKVKELEERLENEALHKEIHNLRQQLELLEDDKRELEQKYQSSEEKARNLKHSVDELQKRVNQSENSVPPPPPPPPPLPPPPPNPIRSLMSMIRKRSHPSGNSAKKEKTTQPET
IRESfinder result
IRESfinder score
0.419223401
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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