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mmu_circAmbra1_2008
Basic information of circular RNA
PanCircBase ID:
mmu_circAmbra1_2008
mm39_Chr. Position ID:
chr2|91596791|91635455|+
Gene name:
Ambra1
Transcript:
ENSMUST00000099712.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
2,3,4,5,6,7,8,9
Exon/intron offsets:
0,610,1243,2468,4464,5844,6264,38577
Genomic length:
38664
Exon/intron sizes in nt:
254,59,184,173,67,147,1037,87
Flanking exon/introns:
chr2:91560724-91596791|chr2:91635455-91640374
Splice length:
2008
Other database IDs:
circAtlas: mmu-Ambra1_0010
circBase: hsa_circ_0005430, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_4458
Human Ortholog IDs:
Mature spliced Sequence:
ATTTCCATGAGGACAGCTGACAAGGACCTGAATGGCCTCATTTTAGCTATTTCTGTGTGTGGAGCTATTGCTTGCTCCTTCAGTTCTGATCCCTGGTGCGACAGTGGCTCCTGAGCACCATGAAAGTTGTCCCAGAGAAGAATGCTGTACGAATCCTCTGGGGCCGAGAACGGGGCACTCGTGCCATGGGTGCCCAGCGGCTTCTGCAGGAGCTGGTGGAGGATAAGACTCGATGGATGAAATGGGAGGGCAAGAGAGTAGAACTGCCTGATAGTCCACGCTCGACCTTCTTACTGGCCTTCAGCCCAGACAGGACTCTCTTGGCATCCACACATGTGAACCATAACATCTATATTACAGAGGTTAAGACTGGCAAGTGTGTTCACTCTCTGATCGGACACCGCCGTACTCCATGGTGTGTCACTTTTCACCCCACCATCTCAGGCCTTATTGCTTCTGGTTGCCTAGATGGGGAAGTTAGGATTTGGGATTTACATGGGGGCAGTGAAAGCTGGTTCACAGACAGCAACAATGCCATAGCCTCCTTGGCTTTCCACCCTACGGCTCAGCTTCTACTAATTGCCACTGCAAATGAGATCCATTTCTGGGATTGGAGTCGTCGGGAGCCCTTTGCTGTGGTGAAAACAGCCAGTGAGATGGAGCGTGTCCGCCTGGTGAGATTTGATCCACTTGGACACTACTTACTTACAGCTATTGTTAACCCTTCTAATCAGCAGGGTGATGACGAACCAGAAATCCCTATAGATGGAACAGAGTTATCTCATTACCGTCAACGTGCCCTCCTGCAATCACAGCCAGTTCGCCGGACACCTCTCCTCCACAATTTCCTGCACATGCTGTCCTCCCGTTCCTCTGGCATCCAGACCGAGCCCTTCCATCCCCCGGAGCAGGCTTCATCAACGCAGCAGGACCAGGGCCTCCTGAACCGGCCGTCTGCCTTCAGTACAGTCCAGAGCAGCACTGCGGGCAACACGCTCCGCAACCTCAGTCTGGGTCCTACCCGGCGCTCTTTGGGGGGCCCTTTGTCTAGCCACCCTTCTAGGTATCACAGAGAACTAGCCCCTGGGCTGACAGGTTCTGAGTGGACCCGGACAGTACTCACTCTGAACTCTCGTTCTGAGGTAGAATCTATGCCCCCACCGAGGACCAGTGCCTCCTCAGTGAGTTTGCTTTCTGTACTGAGACAGCAGGAAGGTGGCTCTCAGGCATCTGTGTATACTTCAGCCACAGAAGGGAGGGGTTTTCCATCATCAGGGTTGGCAACTGAGTCAGATGGAGGGAATGGTTCCAGCCAAAACAACTCAGGCAGCATTCGCCATGAGCTTCAATGTGACCTGAGACGCTTCTTTTTGGAGTATGACAGGCTGCAGGAGCTGGATCAGAGCCTGAGTGGGGAAACTCCCCAGACCCAACAGGCCCAGGAAATGCTCAACAATAATATTGAATCTGAGAGACCAGGTCCTTCCCACCTGCCTACCCCACACAGCAGTGAGAACAACTCCAACCTGTCTCGGGGCCACCTTAATCGATGCCGTGCTTGCCATAATCTTCTAACCTTCAACAATGATACCCTTCGTTGGGAAAGAACCACACCTAACTACTCATCTGGTGAGGCTAGCTCTTCCTGGCACGTCTCCACTACCTTTGAGGGCATGCCACCAAGTGGCAACCAGCTACCACCTCTTGAGCGGACTGAGGGCCAAATGCCTAGCTCCAGCAGGCTGGAGTTGAGCAGCTCTGCTAGTTCACAAGAGGAGAGGACTGTGGGGGTGGCCTTTAACCAGGAGACAGGCCACTGGGAACGCATTTATACCCAGTCCAGCAGATCTGGAACTGTATCACAGGAGGCCTTACATCAAGATATGCCTGAAGAAAGCTCTGAGGAAGACTCCCTCAGGAGGAGGCTGCTGGAGTCTTCCCTCATTTCATTATCCCGTTATGATGGAGCAGGATCCAGAGAGCACCCAATTTACCCAGACCCAGCGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGCAGGATCCAGAGAGCAC
59.9
GCACCAGGGATCAGAACTGA
59.38
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGCAGGATCCAGAGAGCAC
59.9
CGCACCAGGGATCAGAACTG
60.74
143
PCR template sequence:
ACTCCCTCAGGAGGAGGCTGCTGGAGTCTTCCCTCATTTCATTATCCCGTTATGATGGAGCAGGATCCAGAGAGCACCCAATTTACCCAGACCCAGCGAGATTTCCATGAGGACAGCTGACAAGGACCTGAATGGCCTCATTTTAGCTATTTCTGTGTGTGGAGCTATTGCTTGCTCCTTCAGTTCTGATCCCTGGTGCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-370-3p(3), mmu-miR-296-5p(1), mmu-miR-328-3p(1), mmu-miR-216a-5p(1), mmu-miR-7a-5p(1), mmu-miR-127-5p(1), mmu-miR-182-5p(1), mmu-miR-541-5p(1), mmu-miR-324-3p(1), mmu-miR-383-5p(1), mmu-miR-1187(1), mmu-miR-1198-5p(1), mmu-miR-3087-3p(1), mmu-miR-484(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CAGACCCAGCGAGATTTCCATGAGGA
siRNA sets
CATGGAAATCTCGCTGGGT, ATGGAAATCTCGCTGGGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAMBRA1_2008_ORF_1
0.6933
0.178129374
0.99996909
1899
ORF sequence:
ATGAAAGTTGTCCCAGAGAAGAATGCTGTACGAATCCTCTGGGGCCGAGAACGGGGCACTCGTGCCATGGGTGCCCAGCGGCTTCTGCAGGAGCTGGTGGAGGATAAGACTCGATGGATGAAATGGGAGGGCAAGAGAGTAGAACTGCCTGATAGTCCACGCTCGACCTTCTTACTGGCCTTCAGCCCAGACAGGACTCTCTTGGCATCCACACATGTGAACCATAACATCTATATTACAGAGGTTAAGACTGGCAAGTGTGTTCACTCTCTGATCGGACACCGCCGTACTCCATGGTGTGTCACTTTTCACCCCACCATCTCAGGCCTTATTGCTTCTGGTTGCCTAGATGGGGAAGTTAGGATTTGGGATTTACATGGGGGCAGTGAAAGCTGGTTCACAGACAGCAACAATGCCATAGCCTCCTTGGCTTTCCACCCTACGGCTCAGCTTCTACTAATTGCCACTGCAAATGAGATCCATTTCTGGGATTGGAGTCGTCGGGAGCCCTTTGCTGTGGTGAAAACAGCCAGTGAGATGGAGCGTGTCCGCCTGGTGAGATTTGATCCACTTGGACACTACTTACTTACAGCTATTGTTAACCCTTCTAATCAGCAGGGTGATGACGAACCAGAAATCCCTATAGATGGAACAGAGTTATCTCATTACCGTCAACGTGCCCTCCTGCAATCACAGCCAGTTCGCCGGACACCTCTCCTCCACAATTTCCTGCACATGCTGTCCTCCCGTTCCTCTGGCATCCAGACCGAGCCCTTCCATCCCCCGGAGCAGGCTTCATCAACGCAGCAGGACCAGGGCCTCCTGAACCGGCCGTCTGCCTTCAGTACAGTCCAGAGCAGCACTGCGGGCAACACGCTCCGCAACCTCAGTCTGGGTCCTACCCGGCGCTCTTTGGGGGGCCCTTTGTCTAGCCACCCTTCTAGGTATCACAGAGAACTAGCCCCTGGGCTGACAGGTTCTGAGTGGACCCGGACAGTACTCACTCTGAACTCTCGTTCTGAGGTAGAATCTATGCCCCCACCGAGGACCAGTGCCTCCTCAGTGAGTTTGCTTTCTGTACTGAGACAGCAGGAAGGTGGCTCTCAGGCATCTGTGTATACTTCAGCCACAGAAGGGAGGGGTTTTCCATCATCAGGGTTGGCAACTGAGTCAGATGGAGGGAATGGTTCCAGCCAAAACAACTCAGGCAGCATTCGCCATGAGCTTCAATGTGACCTGAGACGCTTCTTTTTGGAGTATGACAGGCTGCAGGAGCTGGATCAGAGCCTGAGTGGGGAAACTCCCCAGACCCAACAGGCCCAGGAAATGCTCAACAATAATATTGAATCTGAGAGACCAGGTCCTTCCCACCTGCCTACCCCACACAGCAGTGAGAACAACTCCAACCTGTCTCGGGGCCACCTTAATCGATGCCGTGCTTGCCATAATCTTCTAACCTTCAACAATGATACCCTTCGTTGGGAAAGAACCACACCTAACTACTCATCTGGTGAGGCTAGCTCTTCCTGGCACGTCTCCACTACCTTTGAGGGCATGCCACCAAGTGGCAACCAGCTACCACCTCTTGAGCGGACTGAGGGCCAAATGCCTAGCTCCAGCAGGCTGGAGTTGAGCAGCTCTGCTAGTTCACAAGAGGAGAGGACTGTGGGGGTGGCCTTTAACCAGGAGACAGGCCACTGGGAACGCATTTATACCCAGTCCAGCAGATCTGGAACTGTATCACAGGAGGCCTTACATCAAGATATGCCTGAAGAAAGCTCTGAGGAAGACTCCCTCAGGAGGAGGCTGCTGGAGTCTTCCCTCATTTCATTATCCCGTTATGATGGAGCAGGATCCAGAGAGCACCCAATTTACCCAGACCCAGCGAGATTTCCATGA
Peptide sequence:
MKVVPEKNAVRILWGRERGTRAMGAQRLLQELVEDKTRWMKWEGKRVELPDSPRSTFLLAFSPDRTLLASTHVNHNIYITEVKTGKCVHSLIGHRRTPWCVTFHPTISGLIASGCLDGEVRIWDLHGGSESWFTDSNNAIASLAFHPTAQLLLIATANEIHFWDWSRREPFAVVKTASEMERVRLVRFDPLGHYLLTAIVNPSNQQGDDEPEIPIDGTELSHYRQRALLQSQPVRRTPLLHNFLHMLSSRSSGIQTEPFHPPEQASSTQQDQGLLNRPSAFSTVQSSTAGNTLRNLSLGPTRRSLGGPLSSHPSRYHRELAPGLTGSEWTRTVLTLNSRSEVESMPPPRTSASSVSLLSVLRQQEGGSQASVYTSATEGRGFPSSGLATESDGGNGSSQNNSGSIRHELQCDLRRFFLEYDRLQELDQSLSGETPQTQQAQEMLNNNIESERPGPSHLPTPHSSENNSNLSRGHLNRCRACHNLLTFNNDTLRWERTTPNYSSGEASSSWHVSTTFEGMPPSGNQLPPLERTEGQMPSSSRLELSSSASSQEERTVGVAFNQETGHWERIYTQSSRSGTVSQEALHQDMPEESSEEDSLRRRLLESSLISLSRYDGAGSREHPIYPDPARFP
IRESfinder result
IRESfinder score
0.583139304
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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