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mmu_circAmbra1_2370
Basic information of circular RNA
PanCircBase ID:
mmu_circAmbra1_2370
mm39_Chr. Position ID:
chr2|91596791|91655697|+
Gene name:
Ambra1
Transcript:
ENSMUST00000099712.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
2,3,4,5,6,7,8,9,10,11,12
Exon/intron offsets:
0,610,1243,2468,4464,5844,6264,38577,43583,58013,58805
Genomic length:
58906
Exon/intron sizes in nt:
2,54,59,18,41,73,67,14,00,00,00,00,00,00,000
Flanking exon/introns:
chr2:91560724-91596791|chr2:91655697-91706060
Splice length:
2370
Other database IDs:
circBase: mmu_circ_0010254, CIRCpedia: MMU_CIRCpedia_34195, circAtlas: mmu-Ambra1_0006
circBase: hsa_circ_0008415, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_4452
Human Ortholog IDs:
Mature spliced Sequence:
ATTTCCATGAGGACAGCTGACAAGGACCTGAATGGCCTCATTTTAGCTATTTCTGTGTGTGGAGCTATTGCTTGCTCCTTCAGTTCTGATCCCTGGTGCGACAGTGGCTCCTGAGCACCATGAAAGTTGTCCCAGAGAAGAATGCTGTACGAATCCTCTGGGGCCGAGAACGGGGCACTCGTGCCATGGGTGCCCAGCGGCTTCTGCAGGAGCTGGTGGAGGATAAGACTCGATGGATGAAATGGGAGGGCAAGAGAGTAGAACTGCCTGATAGTCCACGCTCGACCTTCTTACTGGCCTTCAGCCCAGACAGGACTCTCTTGGCATCCACACATGTGAACCATAACATCTATATTACAGAGGTTAAGACTGGCAAGTGTGTTCACTCTCTGATCGGACACCGCCGTACTCCATGGTGTGTCACTTTTCACCCCACCATCTCAGGCCTTATTGCTTCTGGTTGCCTAGATGGGGAAGTTAGGATTTGGGATTTACATGGGGGCAGTGAAAGCTGGTTCACAGACAGCAACAATGCCATAGCCTCCTTGGCTTTCCACCCTACGGCTCAGCTTCTACTAATTGCCACTGCAAATGAGATCCATTTCTGGGATTGGAGTCGTCGGGAGCCCTTTGCTGTGGTGAAAACAGCCAGTGAGATGGAGCGTGTCCGCCTGGTGAGATTTGATCCACTTGGACACTACTTACTTACAGCTATTGTTAACCCTTCTAATCAGCAGGGTGATGACGAACCAGAAATCCCTATAGATGGAACAGAGTTATCTCATTACCGTCAACGTGCCCTCCTGCAATCACAGCCAGTTCGCCGGACACCTCTCCTCCACAATTTCCTGCACATGCTGTCCTCCCGTTCCTCTGGCATCCAGACCGAGCCCTTCCATCCCCCGGAGCAGGCTTCATCAACGCAGCAGGACCAGGGCCTCCTGAACCGGCCGTCTGCCTTCAGTACAGTCCAGAGCAGCACTGCGGGCAACACGCTCCGCAACCTCAGTCTGGGTCCTACCCGGCGCTCTTTGGGGGGCCCTTTGTCTAGCCACCCTTCTAGGTATCACAGAGAACTAGCCCCTGGGCTGACAGGTTCTGAGTGGACCCGGACAGTACTCACTCTGAACTCTCGTTCTGAGGTAGAATCTATGCCCCCACCGAGGACCAGTGCCTCCTCAGTGAGTTTGCTTTCTGTACTGAGACAGCAGGAAGGTGGCTCTCAGGCATCTGTGTATACTTCAGCCACAGAAGGGAGGGGTTTTCCATCATCAGGGTTGGCAACTGAGTCAGATGGAGGGAATGGTTCCAGCCAAAACAACTCAGGCAGCATTCGCCATGAGCTTCAATGTGACCTGAGACGCTTCTTTTTGGAGTATGACAGGCTGCAGGAGCTGGATCAGAGCCTGAGTGGGGAAACTCCCCAGACCCAACAGGCCCAGGAAATGCTCAACAATAATATTGAATCTGAGAGACCAGGTCCTTCCCACCTGCCTACCCCACACAGCAGTGAGAACAACTCCAACCTGTCTCGGGGCCACCTTAATCGATGCCGTGCTTGCCATAATCTTCTAACCTTCAACAATGATACCCTTCGTTGGGAAAGAACCACACCTAACTACTCATCTGGTGAGGCTAGCTCTTCCTGGCACGTCTCCACTACCTTTGAGGGCATGCCACCAAGTGGCAACCAGCTACCACCTCTTGAGCGGACTGAGGGCCAAATGCCTAGCTCCAGCAGGCTGGAGTTGAGCAGCTCTGCTAGTTCACAAGAGGAGAGGACTGTGGGGGTGGCCTTTAACCAGGAGACAGGCCACTGGGAACGCATTTATACCCAGTCCAGCAGATCTGGAACTGTATCACAGGAGGCCTTACATCAAGATATGCCTGAAGAAAGCTCTGAGGAAGACTCCCTCAGGAGGAGGCTGCTGGAGTCTTCCCTCATTTCATTATCCCGTTATGATGGAGCAGGATCCAGAGAGCACCCAATTTACCCAGACCCAGCGAGATTATCTCCTGCTGCATACTACGCCCAGAGGATGATCCAGTATCTCTCAAGGAGAGACAGTATTCGCCAGCGCTCCATGCGCTACCAACAGAATCGGCTTCGTTCTTCCACCTCCTCTTCTTCCTCAGACAACCAGGGTCCATCAGTAGAGGGAACCGACTTGGAATTTGAGGACTTTGAGGACAATGGTGACAGATCTAGGCACCGAGCTCCCCGAAATGCCCGAATGTCTGCACCTTCACTTGGACGATTTGTTCCAAGGCGTTTTTTGCTGCCTGAGTACTTGCCTTATGCTGGGATTTTTCATGAACGTGGACAGCCTGGCTTGGCTACTCATTCTTCTGTTAACAGGGTCCTGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCATGAACGTGGACAGCCTG
60.32
GCACCAGGGATCAGAACTGA
59.38
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCATGAACGTGGACAGCCT
59.6
GCACCAGGGATCAGAACTGA
59.38
159
PCR template sequence:
CGTTTTTTGCTGCCTGAGTACTTGCCTTATGCTGGGATTTTTCATGAACGTGGACAGCCTGGCTTGGCTACTCATTCTTCTGTTAACAGGGTCCTGGCAGATTTCCATGAGGACAGCTGACAAGGACCTGAATGGCCTCATTTTAGCTATTTCTGTGTGTGGAGCTATTGCTTGCTCCTTCAGTTCTGATCCCTGGTGCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
20
Interacting miRNAs (#binding sites)
mmu-miR-370-3p(3), mmu-miR-296-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-328-3p(1), mmu-miR-216a-5p(1), mmu-miR-7a-5p(1), mmu-miR-10b-5p(1), mmu-miR-10a-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), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGGGTCCTGGCAGATTTCCATGAGGA
siRNA sets
ATGGAAATCTGCCAGGACC, CATGGAAATCTGCCAGGAC, TGGAAATCTGCCAGGACCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAMBRA1_2370_ORF_1
0.7334
0.185023109
0.999998064
2271
ORF sequence:
ATGAAAGTTGTCCCAGAGAAGAATGCTGTACGAATCCTCTGGGGCCGAGAACGGGGCACTCGTGCCATGGGTGCCCAGCGGCTTCTGCAGGAGCTGGTGGAGGATAAGACTCGATGGATGAAATGGGAGGGCAAGAGAGTAGAACTGCCTGATAGTCCACGCTCGACCTTCTTACTGGCCTTCAGCCCAGACAGGACTCTCTTGGCATCCACACATGTGAACCATAACATCTATATTACAGAGGTTAAGACTGGCAAGTGTGTTCACTCTCTGATCGGACACCGCCGTACTCCATGGTGTGTCACTTTTCACCCCACCATCTCAGGCCTTATTGCTTCTGGTTGCCTAGATGGGGAAGTTAGGATTTGGGATTTACATGGGGGCAGTGAAAGCTGGTTCACAGACAGCAACAATGCCATAGCCTCCTTGGCTTTCCACCCTACGGCTCAGCTTCTACTAATTGCCACTGCAAATGAGATCCATTTCTGGGATTGGAGTCGTCGGGAGCCCTTTGCTGTGGTGAAAACAGCCAGTGAGATGGAGCGTGTCCGCCTGGTGAGATTTGATCCACTTGGACACTACTTACTTACAGCTATTGTTAACCCTTCTAATCAGCAGGGTGATGACGAACCAGAAATCCCTATAGATGGAACAGAGTTATCTCATTACCGTCAACGTGCCCTCCTGCAATCACAGCCAGTTCGCCGGACACCTCTCCTCCACAATTTCCTGCACATGCTGTCCTCCCGTTCCTCTGGCATCCAGACCGAGCCCTTCCATCCCCCGGAGCAGGCTTCATCAACGCAGCAGGACCAGGGCCTCCTGAACCGGCCGTCTGCCTTCAGTACAGTCCAGAGCAGCACTGCGGGCAACACGCTCCGCAACCTCAGTCTGGGTCCTACCCGGCGCTCTTTGGGGGGCCCTTTGTCTAGCCACCCTTCTAGGTATCACAGAGAACTAGCCCCTGGGCTGACAGGTTCTGAGTGGACCCGGACAGTACTCACTCTGAACTCTCGTTCTGAGGTAGAATCTATGCCCCCACCGAGGACCAGTGCCTCCTCAGTGAGTTTGCTTTCTGTACTGAGACAGCAGGAAGGTGGCTCTCAGGCATCTGTGTATACTTCAGCCACAGAAGGGAGGGGTTTTCCATCATCAGGGTTGGCAACTGAGTCAGATGGAGGGAATGGTTCCAGCCAAAACAACTCAGGCAGCATTCGCCATGAGCTTCAATGTGACCTGAGACGCTTCTTTTTGGAGTATGACAGGCTGCAGGAGCTGGATCAGAGCCTGAGTGGGGAAACTCCCCAGACCCAACAGGCCCAGGAAATGCTCAACAATAATATTGAATCTGAGAGACCAGGTCCTTCCCACCTGCCTACCCCACACAGCAGTGAGAACAACTCCAACCTGTCTCGGGGCCACCTTAATCGATGCCGTGCTTGCCATAATCTTCTAACCTTCAACAATGATACCCTTCGTTGGGAAAGAACCACACCTAACTACTCATCTGGTGAGGCTAGCTCTTCCTGGCACGTCTCCACTACCTTTGAGGGCATGCCACCAAGTGGCAACCAGCTACCACCTCTTGAGCGGACTGAGGGCCAAATGCCTAGCTCCAGCAGGCTGGAGTTGAGCAGCTCTGCTAGTTCACAAGAGGAGAGGACTGTGGGGGTGGCCTTTAACCAGGAGACAGGCCACTGGGAACGCATTTATACCCAGTCCAGCAGATCTGGAACTGTATCACAGGAGGCCTTACATCAAGATATGCCTGAAGAAAGCTCTGAGGAAGACTCCCTCAGGAGGAGGCTGCTGGAGTCTTCCCTCATTTCATTATCCCGTTATGATGGAGCAGGATCCAGAGAGCACCCAATTTACCCAGACCCAGCGAGATTATCTCCTGCTGCATACTACGCCCAGAGGATGATCCAGTATCTCTCAAGGAGAGACAGTATTCGCCAGCGCTCCATGCGCTACCAACAGAATCGGCTTCGTTCTTCCACCTCCTCTTCTTCCTCAGACAACCAGGGTCCATCAGTAGAGGGAACCGACTTGGAATTTGAGGACTTTGAGGACAATGGTGACAGATCTAGGCACCGAGCTCCCCGAAATGCCCGAATGTCTGCACCTTCACTTGGACGATTTGTTCCAAGGCGTTTTTTGCTGCCTGAGTACTTGCCTTATGCTGGGATTTTTCATGAACGTGGACAGCCTGGCTTGGCTACTCATTCTTCTGTTAACAGGGTCCTGGCAGATTTCCATGAGGACAGCTGA
Peptide sequence:
MKVVPEKNAVRILWGRERGTRAMGAQRLLQELVEDKTRWMKWEGKRVELPDSPRSTFLLAFSPDRTLLASTHVNHNIYITEVKTGKCVHSLIGHRRTPWCVTFHPTISGLIASGCLDGEVRIWDLHGGSESWFTDSNNAIASLAFHPTAQLLLIATANEIHFWDWSRREPFAVVKTASEMERVRLVRFDPLGHYLLTAIVNPSNQQGDDEPEIPIDGTELSHYRQRALLQSQPVRRTPLLHNFLHMLSSRSSGIQTEPFHPPEQASSTQQDQGLLNRPSAFSTVQSSTAGNTLRNLSLGPTRRSLGGPLSSHPSRYHRELAPGLTGSEWTRTVLTLNSRSEVESMPPPRTSASSVSLLSVLRQQEGGSQASVYTSATEGRGFPSSGLATESDGGNGSSQNNSGSIRHELQCDLRRFFLEYDRLQELDQSLSGETPQTQQAQEMLNNNIESERPGPSHLPTPHSSENNSNLSRGHLNRCRACHNLLTFNNDTLRWERTTPNYSSGEASSSWHVSTTFEGMPPSGNQLPPLERTEGQMPSSSRLELSSSASSQEERTVGVAFNQETGHWERIYTQSSRSGTVSQEALHQDMPEESSEEDSLRRRLLESSLISLSRYDGAGSREHPIYPDPARLSPAAYYAQRMIQYLSRRDSIRQRSMRYQQNRLRSSTSSSSSDNQGPSVEGTDLEFEDFEDNGDRSRHRAPRNARMSAPSLGRFVPRRFLLPEYLPYAGIFHERGQPGLATHSSVNRVLADFHEDS
IRESfinder result
IRESfinder score
0.593896187
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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