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mmu_circStk38_703
Basic information of circular RNA
PanCircBase ID:
mmu_circStk38_703
mm39_Chr. Position ID:
chr17|29196513|29211442|-
Gene name:
Stk38
Transcript:
ENSMUST00000009138.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
9,8,7,6,5,4,3
Exon/intron offsets:
0,1663,4492,6537,10638,13758,14877
Genomic length:
14929
Exon/intron sizes in nt:
62,103,155,124,84,123,52
Flanking exon/introns:
chr17:29194910-29196513|chr17:29211442-29218982
Splice length:
703
Other database IDs:
circAtlas: mmu-Stk38_0005
circAtlas: hsa-STK38_0004, CIRCpedia: HSA_CIRCpedia_150737
Human Ortholog IDs:
Mature spliced Sequence:
ACAAAAGAAGTTAGAAAAGGTGATGGAAGAAGAAGGCCTGAAAGACGAAGAGAAACGACTCAGAAGATCCGCGCACGCTCGGAAGGAAACAGAGTTTCTTCGATTAAAGAGAACAAGGCTTGGACTGGAAGATTTTGAGTCTTTAAAAGTCATAGGCCGAGGAGCATTTGGTGAGGTGCGGCTTGTTCAGAAGAAAGACACAGGGCATGTGTACGCAATGAAAATCCTGCGCAAAGCAGACATGCTCGAGAAGGAGCAGGTTGGCCACATTCGTGCGGAGCGTGACATTCTAGTGGAGGCAGACAGTTTGTGGGTTGTGAAAATGTTCTATAGTTTTCAGGATAAGCTAAACCTCTACCTAATCATGGAGTTCCTGCCTGGAGGGGACATGATGACTTTATTGATGAAAAAAGATACTCTGACAGAAGAGGAGACTCAGTTTTATATAGCAGAGACAGTATTAGCCATAGACTCCATTCACCAGCTGGGATTCATCCACAGAGATATCAAGCCAGACAACCTTCTCTTGGACAGCAAGGGCCATGTGAAACTTTCCGACTTTGGCCTTTGCACAGGCCTGAAAAAAGCACACAGGACAGAATTTTATAGGAACCTGAACCACAGCCTGCCCAGTGATTTCACTTTTCAGAACATGAATTCCAAAAGGAAAGCAGAGACCTGGAAAAGAAACAGACGCCAGCTA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCCTGCCCAGTGATTTCA
60.61
CTCTGTTTCCTTCCGAGCGT
60.04
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCCTGCCCAGTGATTTCA
60.61
ACTCTGTTTCCTTCCGAGCG
60.04
177
PCR template sequence:
TTATAGGAACCTGAACCACAGCCTGCCCAGTGATTTCACTTTTCAGAACATGAATTCCAAAAGGAAAGCAGAGACCTGGAAAAGAAACAGACGCCAGCTAACAAAAGAAGTTAGAAAAGGTGATGGAAGAAGAAGGCCTGAAAGACGAAGAGAAACGACTCAGAAGATCCGCGCACGCTCGGAAGGAAACAGAGTTTCTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-328-3p(1), mmu-miR-216a-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGACGCCAGCTAACAAAAGAAGTTA
siRNA sets
TTCTTTTGTTAGCTGGCGT, CTTCTTTTGTTAGCTGGCG, ACTTCTTTTGTTAGCTGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSTK38_703_ORF_1
0.8835
0.161175339
0.949605219
819
ORF sequence:
ATGGAAGAAGAAGGCCTGAAAGACGAAGAGAAACGACTCAGAAGATCCGCGCACGCTCGGAAGGAAACAGAGTTTCTTCGATTAAAGAGAACAAGGCTTGGACTGGAAGATTTTGAGTCTTTAAAAGTCATAGGCCGAGGAGCATTTGGTGAGGTGCGGCTTGTTCAGAAGAAAGACACAGGGCATGTGTACGCAATGAAAATCCTGCGCAAAGCAGACATGCTCGAGAAGGAGCAGGTTGGCCACATTCGTGCGGAGCGTGACATTCTAGTGGAGGCAGACAGTTTGTGGGTTGTGAAAATGTTCTATAGTTTTCAGGATAAGCTAAACCTCTACCTAATCATGGAGTTCCTGCCTGGAGGGGACATGATGACTTTATTGATGAAAAAAGATACTCTGACAGAAGAGGAGACTCAGTTTTATATAGCAGAGACAGTATTAGCCATAGACTCCATTCACCAGCTGGGATTCATCCACAGAGATATCAAGCCAGACAACCTTCTCTTGGACAGCAAGGGCCATGTGAAACTTTCCGACTTTGGCCTTTGCACAGGCCTGAAAAAAGCACACAGGACAGAATTTTATAGGAACCTGAACCACAGCCTGCCCAGTGATTTCACTTTTCAGAACATGAATTCCAAAAGGAAAGCAGAGACCTGGAAAAGAAACAGACGCCAGCTAACAAAAGAAGTTAGAAAAGGTGATGGAAGAAGAAGGCCTGAAAGACGAAGAGAAACGACTCAGAAGATCCGCGCACGCTCGGAAGGAAACAGAGTTTCTTCGATTAAAGAGAACAAGGCTTGGACTGGAAGATTTTGA
Peptide sequence:
MEEEGLKDEEKRLRRSAHARKETEFLRLKRTRLGLEDFESLKVIGRGAFGEVRLVQKKDTGHVYAMKILRKADMLEKEQVGHIRAERDILVEADSLWVVKMFYSFQDKLNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYIAETVLAIDSIHQLGFIHRDIKPDNLLLDSKGHVKLSDFGLCTGLKKAHRTEFYRNLNHSLPSDFTFQNMNSKRKAETWKRNRRQLTKEVRKGDGRRRPERRRETTQKIRARSEGNRVSSIKENKAWTGRF
IRESfinder result
IRESfinder score
0.541070426
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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