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mmu_circKhdrbs3_523
Basic information of circular RNA
PanCircBase ID:
mmu_circKhdrbs3_523
mm39_Chr. Position ID:
chr15|68866900|68896688|+
Gene name:
Khdrbs3
Transcript:
ENSMUST00000022954.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,18306,22276,29648
Genomic length:
29788
Exon/intron sizes in nt:
1,19,11,71,47,140
Flanking exon/introns:
chr15:68800682-68866900|chr15:68896688-68901563
Splice length:
523
Other database IDs:
circBase: mmu_circ_0005746, CIRCpedia: MMU_CIRCpedia_27080, circAtlas: mmu-Khdrbs3_0005
circBase: hsa_circ_0135838, circAtlas: hsa-KHDRBS3_0004, CIRCpedia: HSA_CIRCpedia_69486
Human Ortholog IDs:
Mature spliced Sequence:
AAATAGAAAAGTTTCAAAAGGGAGAAGGCAAGGAGGAAGAGAAGTACATTGACGTGGTGATAAACAAGAACATGAAGCTGGGACAGAAGGTGCTGATTCCCGTGAAGCAGTTTCCCAAGTTCAACTTTGTGGGGAAGCTTTTGGGTCCGCGTGGCAATTCCCTGAAGCGCTTACAAGAAGAAACGTTGACAAAAATGTCCATCCTTGGCAAAGGTTCCATGAGAGACAAGGCAAAGGAGGAAGAGCTGAGGAAAAGTGGAGAAGCGAAGTACTTTCACCTCAATGACGACCTGCACGTGCTCATTGAAGTGTTCGCACCCCCAGCAGAAGCATATGCCCGGATGGGGCACGCCTTGGAAGAGATCAAGAAATTCCTGATCCCTGACTATAATGATGAAATCAGGCAAGCACAACTCCAGGAGTTAACATATTTGAATGGAGGTTCAGAAAATGCAGATGTCCCAGTGGTTCGAGGGAAATCTACTTTGCGTACGAGAGGTGTAACTACACCAGCAATAACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAGATGTCCCAGTGGTTC
59.96
CACCTTCTGTCCCAGCTTCA
59.6
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATGTCCCAGTGGTTCGAGG
60.11
CACCTTCTGTCCCAGCTTCA
59.6
160
PCR template sequence:
TAACATATTTGAATGGAGGTTCAGAAAATGCAGATGTCCCAGTGGTTCGAGGGAAATCTACTTTGCGTACGAGAGGTGTAACTACACCAGCAATAACCAGAAATAGAAAAGTTTCAAAAGGGAGAAGGCAAGGAGGAAGAGAAGTACATTGACGTGGTGATAAACAAGAACATGAAGCTGGGACAGAAGGTGCTGATTCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-211-5p(1), mmu-miR-138-5p(1), mmu-miR-136-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-218-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CAGCAATAACCAGAAATAGAAAAGTT
siRNA sets
TTTCTATTTCTGGTTATTG, TTCTATTTCTGGTTATTGC, TTTTCTATTTCTGGTTATT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKHDRBS3_523_ORF_1
0.9474
0.203127877
0.723479281
504
ORF sequence:
ATGAAGCTGGGACAGAAGGTGCTGATTCCCGTGAAGCAGTTTCCCAAGTTCAACTTTGTGGGGAAGCTTTTGGGTCCGCGTGGCAATTCCCTGAAGCGCTTACAAGAAGAAACGTTGACAAAAATGTCCATCCTTGGCAAAGGTTCCATGAGAGACAAGGCAAAGGAGGAAGAGCTGAGGAAAAGTGGAGAAGCGAAGTACTTTCACCTCAATGACGACCTGCACGTGCTCATTGAAGTGTTCGCACCCCCAGCAGAAGCATATGCCCGGATGGGGCACGCCTTGGAAGAGATCAAGAAATTCCTGATCCCTGACTATAATGATGAAATCAGGCAAGCACAACTCCAGGAGTTAACATATTTGAATGGAGGTTCAGAAAATGCAGATGTCCCAGTGGTTCGAGGGAAATCTACTTTGCGTACGAGAGGTGTAACTACACCAGCAATAACCAGAAATAGAAAAGTTTCAAAAGGGAGAAGGCAAGGAGGAAGAGAAGTACATTGA
Peptide sequence:
MKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVLIEVFAPPAEAYARMGHALEEIKKFLIPDYNDEIRQAQLQELTYLNGGSENADVPVVRGKSTLRTRGVTTPAITRNRKVSKGRRQGGREVH
IRESfinder result
IRESfinder score
0.373115613
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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