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mmu_circShtn1_653
Basic information of circular RNA
PanCircBase ID:
mmu_circShtn1_653
mm39_Chr. Position ID:
chr19|59016586|59049115|-
Gene name:
Shtn1
Transcript:
ENSMUST00000163821.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
8,7,6,5,4,3,2
Exon/intron offsets:
0,4018,6889,10067,13707,22679,32476
Genomic length:
32529
Exon/intron sizes in nt:
95,82,98,169,95,61,53
Flanking exon/introns:
chr19:59010754-59016586|chr19:59049115-59063886
Splice length:
653
Other database IDs:
CIRCpedia: MMU_CIRCpedia_24362, circAtlas: mmu-4930506M07Rik_0004
circBase: hsa_circ_0092814, circAtlas: hsa-SHTN1_0004, CIRCpedia: HSA_CIRCpedia_152084
Human Ortholog IDs:
Mature spliced Sequence:
CCATTGGCGAATATGAAGACCTTCGAGCAGAGAACCAGAAAACAAAGGAGAAGTGTGACAAAATTAGGCAAGAACGAGATGAAGCTGTTAAAAAACTGGAAGAGTTTCAGAAAATTTCACATATGGTTATAGAGGAGGTGAATTTCATGCAGAACCATCTTGAAATAGAGAAGACATGTCGAGAGAGCGCTGAAGCCTTGGCGACAAAGCTAAATAAAGAAAATAAAACACTGAAAAGAATCAGCATGCTATACATGGCCAAACTGGGGCCAGACGTAATTACAGAGGAGATAAACATTGATGATGATGACCCAGCCACCGACACAGATGCTGCGGCTGAGACCTGTGTGTCTGTTCAGTGTCAGAAGCAAATCAAAGAACTTCGAGATCAAATTGTGTCTGTTCAGGAAGAAAAGAAGGTGTTAGCCATCGAGCTGGAAAACCTCAAGAGCAAACTCGGGGAGGTGATGGAGGAGGTAAATAAAGTTAAGCAAGAAAAAGCTGTTTTAAATTCAGAAGTCCTTGAGCAGAGGAAAGTCTTAGAAAAATGCAACAGAGTGTCCATGTTGGCTGTTGAAGAGTATGAGGAACTGCAAGTGAACCTGGAACTGGAGAAGGACCTTCGCAAGAAAGCAGAGTCTTTTGCACAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGAGTGTCCATGTTGGCTG
58.84
TTCTGGTTCTCTGCTCGAAGG
59.73
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGAGTGTCCATGTTGGCTGT
60.54
TTCTGGTTCTCTGCTCGAAGG
59.73
140
PCR template sequence:
CAGAGTGTCCATGTTGGCTGTTGAAGAGTATGAGGAACTGCAAGTGAACCTGGAACTGGAGAAGGACCTTCGCAAGAAAGCAGAGTCTTTTGCACAAGAGCCATTGGCGAATATGAAGACCTTCGAGCAGAGAACCAGAAAACAAAGGAGAAGTGTGACAAAATTAGGCAAGAACGAGATGAAGCTGTTAAAAAACTGGA
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-103-3p(1), mmu-miR-107-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTGCACAAGAGCCATTGGCGAATA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSHTN1_653_ORF_1
1.1001
0.24021245
0.926811361
663
ORF sequence:
ATGGTTATAGAGGAGGTGAATTTCATGCAGAACCATCTTGAAATAGAGAAGACATGTCGAGAGAGCGCTGAAGCCTTGGCGACAAAGCTAAATAAAGAAAATAAAACACTGAAAAGAATCAGCATGCTATACATGGCCAAACTGGGGCCAGACGTAATTACAGAGGAGATAAACATTGATGATGATGACCCAGCCACCGACACAGATGCTGCGGCTGAGACCTGTGTGTCTGTTCAGTGTCAGAAGCAAATCAAAGAACTTCGAGATCAAATTGTGTCTGTTCAGGAAGAAAAGAAGGTGTTAGCCATCGAGCTGGAAAACCTCAAGAGCAAACTCGGGGAGGTGATGGAGGAGGTAAATAAAGTTAAGCAAGAAAAAGCTGTTTTAAATTCAGAAGTCCTTGAGCAGAGGAAAGTCTTAGAAAAATGCAACAGAGTGTCCATGTTGGCTGTTGAAGAGTATGAGGAACTGCAAGTGAACCTGGAACTGGAGAAGGACCTTCGCAAGAAAGCAGAGTCTTTTGCACAAGAGCCATTGGCGAATATGAAGACCTTCGAGCAGAGAACCAGAAAACAAAGGAGAAGTGTGACAAAATTAGGCAAGAACGAGATGAAGCTGTTAAAAAACTGGAAGAGTTTCAGAAAATTTCACATATGGTTATAG
Peptide sequence:
MVIEEVNFMQNHLEIEKTCRESAEALATKLNKENKTLKRISMLYMAKLGPDVITEEINIDDDDPATDTDAAAETCVSVQCQKQIKELRDQIVSVQEEKKVLAIELENLKSKLGEVMEEVNKVKQEKAVLNSEVLEQRKVLEKCNRVSMLAVEEYEELQVNLELEKDLRKKAESFAQEPLANMKTFEQRTRKQRRSVTKLGKNEMKLLKNWKSFRKFHIWL
IRESfinder result
IRESfinder score
0.402056338
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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