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mmu_circAtp11b_1306
Basic information of circular RNA
PanCircBase ID:
mmu_circAtp11b_1306
mm39_Chr. Position ID:
chr3|35863505|35882852|+
Gene name:
Atp11b
Transcript:
ENSMUST00000200445.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
13,14,15,16,17,18,19,20,21
Exon/intron offsets:
0,764,1289,2706,2856,4687,10552,17588,19244
Genomic length:
19347
Exon/intron sizes in nt:
240,176,69,74,104,182,204,154,103
Flanking exon/introns:
chr3:35861114-35863505|chr3:35882852-35883565
Splice length:
1306
Other database IDs:
circBase: mmu_circ_0010645, CIRCpedia: MMU_CIRCpedia_17887, circAtlas: mmu-Atp11b_0032
Human Ortholog IDs:
Mature spliced Sequence:
GTGGAATATGTATTTACAGATAAAACTGGAACACTGACAGAAAATGAGATGCAGTTTCGAGAATGTTCAATTAATGGCCTGAAATACCAAGAAATCAATGGTAAACTTGTACCTGAAGGACCAAGCCCAGACTCCACAGAAGGAGAAGTGCCTTTCCTTGGTAGTTTATCCCATCTCAGCAACTCAGCCCATCTCACAGCCACTTCTCTTAGAACCAGTCCTGAAAGTGAAACTGAGCTAATCAAAGAACACGATCTGTTCTTTAAAGCAGTCAGTCTTTGCCATACTGTACAGATCAGCAATGTTCAAACTGACGGCATCGGGGATGGTCCCTGGCAGCCCAACCTGGCACCTGCACAGCTGGAGTACTATGCATCTTCACCAGATGAAAAGGCTCTGGTGGAAGCTGCGGCAAGAGCTGGTATTATATTTGTAGGCATTTCTGAAGAAACTATGGAGGTTAAAGTACTTGGGAGATTGGAAAGGTACAAATTGCTTCATATTCTGGAATTTGATTCAGATCGTAGGAGAATGAGTGTAATTGTTCAGGCACCTTCAGGTGAGAAGCTTTTATTTGCTAAAGGAGCAGAATCTTCAATTCTCCCTAAATGTATAGGTGGAGAAATAGCAAAAACCAGAATTCATGTTGATGAGTTTGCTTTGAAAGGACTGCGGACACTGTGTATAGCTTACAGACAGTTTACAGCTAAAGAGTATGAAGATGTAGACAGGCGCCTGTTTGAGGCCAGAACTGCCTTGCAGCATCGGGAAGAGAAATTGGCTGATGCCTTCCAGTACATTGAGAAAGACCTGATATTGCTAGGAGCTACAGCAGTGGAAGACAGACTACAAGATAAAGTTCGAGAAACTATTGAAGCACTGAGAATGGCTGGTATTAAAGTATGGGTACTTACTGGAGACAAACATGAAACAGCTGTTAGTGTGAGTTTATCTTGTGGACATTTTCATAGAACTATGAATATCCTGGAACTTATCAACCAGAAGTCAGATAGTGGATGTGCTGAACAGTTGAGGCAGCTTGCCAGAAGAATTACAGAGGACCATGTGATTCAGCATGGGCTAGTAGTAGATGGGACCAGCTTATCTCTTGCACTCAGGGAACATGAAAAGCTCTTTATGGAAGTTTGCAGAAACTGTTCAGCTGTATTATGTTGTCGCATGGCACCTTTACAGAAAGCAAAAGTAATAAGACTGATAAAAATCTCTCCTGAGAAACCGATAACACTGGCTGTTGGTGATGGTGCTAATGATGTAAGCATGATACAAGAAGCGCATGTTGGCATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTGTTGGTGATGGTGCTA
60.32
TGATTTCTTGGTATTTCAGGCCA
58.33
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGGCTGTTGGTGATGGTG
60.54
TGATTTCTTGGTATTTCAGGCCA
58.33
159
PCR template sequence:
ATAAGACTGATAAAAATCTCTCCTGAGAAACCGATAACACTGGCTGTTGGTGATGGTGCTAATGATGTAAGCATGATACAAGAAGCGCATGTTGGCATAGGTGGAATATGTATTTACAGATAAAACTGGAACACTGACAGAAAATGAGATGCAGTTTCGAGAATGTTCAATTAATGGCCTGAAATACCAAGAAATCAATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-223-3p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-128-3p(1), mmu-miR-130b-3p(1), mmu-miR-369-3p(1), mmu-miR-335-3p(1), mmu-miR-670-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CATGTTGGCATAGGTGGAATATGTAT
siRNA sets
ATACATATTCCACCTATGC, TACATATTCCACCTATGCC, ACATATTCCACCTATGCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATP11B_1306_ORF_1
1.0307
0.013332543
0.997298443
1281
ORF sequence:
ATGCAGTTTCGAGAATGTTCAATTAATGGCCTGAAATACCAAGAAATCAATGGTAAACTTGTACCTGAAGGACCAAGCCCAGACTCCACAGAAGGAGAAGTGCCTTTCCTTGGTAGTTTATCCCATCTCAGCAACTCAGCCCATCTCACAGCCACTTCTCTTAGAACCAGTCCTGAAAGTGAAACTGAGCTAATCAAAGAACACGATCTGTTCTTTAAAGCAGTCAGTCTTTGCCATACTGTACAGATCAGCAATGTTCAAACTGACGGCATCGGGGATGGTCCCTGGCAGCCCAACCTGGCACCTGCACAGCTGGAGTACTATGCATCTTCACCAGATGAAAAGGCTCTGGTGGAAGCTGCGGCAAGAGCTGGTATTATATTTGTAGGCATTTCTGAAGAAACTATGGAGGTTAAAGTACTTGGGAGATTGGAAAGGTACAAATTGCTTCATATTCTGGAATTTGATTCAGATCGTAGGAGAATGAGTGTAATTGTTCAGGCACCTTCAGGTGAGAAGCTTTTATTTGCTAAAGGAGCAGAATCTTCAATTCTCCCTAAATGTATAGGTGGAGAAATAGCAAAAACCAGAATTCATGTTGATGAGTTTGCTTTGAAAGGACTGCGGACACTGTGTATAGCTTACAGACAGTTTACAGCTAAAGAGTATGAAGATGTAGACAGGCGCCTGTTTGAGGCCAGAACTGCCTTGCAGCATCGGGAAGAGAAATTGGCTGATGCCTTCCAGTACATTGAGAAAGACCTGATATTGCTAGGAGCTACAGCAGTGGAAGACAGACTACAAGATAAAGTTCGAGAAACTATTGAAGCACTGAGAATGGCTGGTATTAAAGTATGGGTACTTACTGGAGACAAACATGAAACAGCTGTTAGTGTGAGTTTATCTTGTGGACATTTTCATAGAACTATGAATATCCTGGAACTTATCAACCAGAAGTCAGATAGTGGATGTGCTGAACAGTTGAGGCAGCTTGCCAGAAGAATTACAGAGGACCATGTGATTCAGCATGGGCTAGTAGTAGATGGGACCAGCTTATCTCTTGCACTCAGGGAACATGAAAAGCTCTTTATGGAAGTTTGCAGAAACTGTTCAGCTGTATTATGTTGTCGCATGGCACCTTTACAGAAAGCAAAAGTAATAAGACTGATAAAAATCTCTCCTGAGAAACCGATAACACTGGCTGTTGGTGATGGTGCTAATGATGTAAGCATGATACAAGAAGCGCATGTTGGCATAGGTGGAATATGTATTTACAGATAA
Peptide sequence:
MQFRECSINGLKYQEINGKLVPEGPSPDSTEGEVPFLGSLSHLSNSAHLTATSLRTSPESETELIKEHDLFFKAVSLCHTVQISNVQTDGIGDGPWQPNLAPAQLEYYASSPDEKALVEAAARAGIIFVGISEETMEVKVLGRLERYKLLHILEFDSDRRRMSVIVQAPSGEKLLFAKGAESSILPKCIGGEIAKTRIHVDEFALKGLRTLCIAYRQFTAKEYEDVDRRLFEARTALQHREEKLADAFQYIEKDLILLGATAVEDRLQDKVRETIEALRMAGIKVWVLTGDKHETAVSVSLSCGHFHRTMNILELINQKSDSGCAEQLRQLARRITEDHVIQHGLVVDGTSLSLALREHEKLFMEVCRNCSAVLCCRMAPLQKAKVIRLIKISPEKPITLAVGDGANDVSMIQEAHVGIGGICIYR
IRESfinder result
IRESfinder score
0.646741586
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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