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mmu_circUbr1_554
Basic information of circular RNA
PanCircBase ID:
mmu_circUbr1_554
mm39_Chr. Position ID:
chr2|120765696|120776422|-
Gene name:
Ubr1
Transcript:
ENSMUST00000028728.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
13,12,11,10,9
Exon/intron offsets:
0,5751,7261,9435,10618
Genomic length:
10726
Exon/intron sizes in nt:
10,01,58,99,89,108
Flanking exon/introns:
chr2:120764913-120765696|chr2:120776422-120776754
Splice length:
554
Other database IDs:
CIRCpedia: MMU_CIRCpedia_218370, circAtlas: mmu-Ubr1_0056
CIRCpedia: HSA_CIRCpedia_83021
Human Ortholog IDs:
Mature spliced Sequence:
GTGACTTTAGACAGATATTTTGCCAGGCCTGCCTCGTAGAAGAACCTGGCTCTGAAAATCCCTGTCTTATAAGCAGACTAATGCTTTGGGATGCAAAACTTTATAAAGGTGCCCGTAAGATCCTTCATGAATTGATCTTTAGTAGTTTTTTTATGGAGATGGAATACAAAAAACTCTTTGCTATGGAATTTGTGAAGTATTATAAACAGCTGCAGAAAGAGTACATCAGCGACGACCACGAGAGAAGCATCTCCATAACCGCCCTGTCCGTGCAGATGCTCACCGTCCCGACCTTGGCCCGGCATCTTATTGAAGAGCAGAATGTTATTTCTGTCATTACTGAAACGCTGCTAGAAGTTTTACCTGAATACTTGGACAGGAACAATAAATTCAACTTCCAGGGTTATAGCCAGGACAAACTGGGAAGAGTCTACGCAGTTATATGTGACCTAAAGTATATCCTGATTAGCAAGCCTGTCATATGGACAGAACGATTAAGAGCGCAGTTCCTGGAAGGTTTCCGGTCTTTTCTGAAGATTCTTACCTGTATGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGATTAGCAAGCCTGTCA
59.09
GTTCTTCTACGAGGCAGGCC
60.46
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGATTAGCAAGCCTGTCA
59.09
GGTTCTTCTACGAGGCAGGC
60.46
141
PCR template sequence:
GTATATCCTGATTAGCAAGCCTGTCATATGGACAGAACGATTAAGAGCGCAGTTCCTGGAAGGTTTCCGGTCTTTTCTGAAGATTCTTACCTGTATGCAGGTGACTTTAGACAGATATTTTGCCAGGCCTGCCTCGTAGAAGAACCTGGCTCTGAAAATCCCTGTCTTATAAGCAGACTAATGCTTTGGGATGCAAAACT
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-324-5p(1), mmu-miR-503-5p(1), mmu-miR-433-5p(1), mmu-miR-344d-3p(1), mmu-miR-350-3p(1), mmu-miR-1904(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TACCTGTATGCAGGTGACTTTAGACA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUBR1_554_ORF_1
0.9151
0.12396379
0.812176304
627
ORF sequence:
ATGGACAGAACGATTAAGAGCGCAGTTCCTGGAAGGTTTCCGGTCTTTTCTGAAGATTCTTACCTGTATGCAGGTGACTTTAGACAGATATTTTGCCAGGCCTGCCTCGTAGAAGAACCTGGCTCTGAAAATCCCTGTCTTATAAGCAGACTAATGCTTTGGGATGCAAAACTTTATAAAGGTGCCCGTAAGATCCTTCATGAATTGATCTTTAGTAGTTTTTTTATGGAGATGGAATACAAAAAACTCTTTGCTATGGAATTTGTGAAGTATTATAAACAGCTGCAGAAAGAGTACATCAGCGACGACCACGAGAGAAGCATCTCCATAACCGCCCTGTCCGTGCAGATGCTCACCGTCCCGACCTTGGCCCGGCATCTTATTGAAGAGCAGAATGTTATTTCTGTCATTACTGAAACGCTGCTAGAAGTTTTACCTGAATACTTGGACAGGAACAATAAATTCAACTTCCAGGGTTATAGCCAGGACAAACTGGGAAGAGTCTACGCAGTTATATGTGACCTAAAGTATATCCTGATTAGCAAGCCTGTCATATGGACAGAACGATTAAGAGCGCAGTTCCTGGAAGGTTTCCGGTCTTTTCTGAAGATTCTTACCTGTATGCAG
Peptide sequence:
MDRTIKSAVPGRFPVFSEDSYLYAGDFRQIFCQACLVEEPGSENPCLISRLMLWDAKLYKGARKILHELIFSSFFMEMEYKKLFAMEFVKYYKQLQKEYISDDHERSISITALSVQMLTVPTLARHLIEEQNVISVITETLLEVLPEYLDRNNKFNFQGYSQDKLGRVYAVICDLKYILISKPVIWTERLRAQFLEGFRSFLKILTCMQ
IRESfinder result
IRESfinder score
0.68881013
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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