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mmu_circAmbra1_904
Basic information of circular RNA
PanCircBase ID:
mmu_circAmbra1_904
mm39_Chr. Position ID:
chr2|91635368|91717323|+
Gene name:
Ambra1
Transcript:
ENSMUST00000099712.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
9,10,11,12,13,14,15
Exon/intron offsets:
0,5006,19436,20228,70692,80577,81800
Genomic length:
81955
Exon/intron sizes in nt:
87,18,08,11,01,11,11,80,000
Flanking exon/introns:
chr2:91604092-91635368|chr2:91717323-91730842
Splice length:
904
Other database IDs:
circBase: hsa_circ_0021845, circAtlas: hsa-AMBRA1_0043, CIRCpedia: HSA_CIRCpedia_372795
Human Ortholog IDs:
Mature spliced Sequence:
GAGGCTGCTGGAGTCTTCCCTCATTTCATTATCCCGTTATGATGGAGCAGGATCCAGAGAGCACCCAATTTACCCAGACCCAGCGAGATTATCTCCTGCTGCATACTACGCCCAGAGGATGATCCAGTATCTCTCAAGGAGAGACAGTATTCGCCAGCGCTCCATGCGCTACCAACAGAATCGGCTTCGTTCTTCCACCTCCTCTTCTTCCTCAGACAACCAGGGTCCATCAGTAGAGGGAACCGACTTGGAATTTGAGGACTTTGAGGACAATGGTGACAGATCTAGGCACCGAGCTCCCCGAAATGCCCGAATGTCTGCACCTTCACTTGGACGATTTGTTCCAAGGCGTTTTTTGCTGCCTGAGTACTTGCCTTATGCTGGGATTTTTCATGAACGTGGACAGCCTGGCTTGGCTACTCATTCTTCTGTTAACAGGGTCCTGGCAGGGGCAGTAATTGGAGATGGACAGTCTGCTGTGGCCAGTAACATTGCCAATACTACCTACAGGCTCCAGTGGTGGGACTTCACTAAGTTTGACCTTCCAGAAATCAGTAATGCCTCTGTGAATGTCCTGGTACAGAATTGCAAGATCTACAATGATGCCAGCTGTGACATTTCTGCAGATGGTCAGCTCCTGGCAGCCTTCATCCCGAGCAGCCAGAGGGGCTTTCCTGATGAAGGCATCCTGGCAGTGTATTCCCTGGCCCCCCATAACTTGGGGGAAATGCTCTACACCAAGCGATTTGGTCCCAATGCCATTTCTGTAAGCCTGTCCCCGATGGGCCGATACGTTATGGTGGGCTTGGCCTCACGAAGGATCCTACTGCACCCCTCCACAGAGCACATGGTAGCCCAGGTCTTCAGGCTGCAACAGGCCCATGGTGGTGAGACTTCCATGAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGATCCTACTGCACCCCT
59.96
GTGCTCTCTGGATCCTGCTC
59.9
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGAAGGATCCTACTGCACCC
59.89
GTGCTCTCTGGATCCTGCTC
59.9
154
PCR template sequence:
CTTGGCCTCACGAAGGATCCTACTGCACCCCTCCACAGAGCACATGGTAGCCCAGGTCTTCAGGCTGCAACAGGCCCATGGTGGTGAGACTTCCATGAGGGAGGCTGCTGGAGTCTTCCCTCATTTCATTATCCCGTTATGATGGAGCAGGATCCAGAGAGCACCCAATTTACCCAGACCCAGCGAGATTATCTCCTGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-196a-5p(1), mmu-miR-10b-5p(1), mmu-miR-10a-5p(1), mmu-miR-382-3p(1), mmu-miR-182-5p(1), mmu-miR-673-5p(1), mmu-miR-532-5p(1), mmu-miR-1904(1), mmu-miR-193b-3p(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACTTCCATGAGGGAGGCTGCTGGAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAMBRA1_904_ORF_1
0.8493
0.237297674
0.962288061
828
ORF sequence:
ATGATCCAGTATCTCTCAAGGAGAGACAGTATTCGCCAGCGCTCCATGCGCTACCAACAGAATCGGCTTCGTTCTTCCACCTCCTCTTCTTCCTCAGACAACCAGGGTCCATCAGTAGAGGGAACCGACTTGGAATTTGAGGACTTTGAGGACAATGGTGACAGATCTAGGCACCGAGCTCCCCGAAATGCCCGAATGTCTGCACCTTCACTTGGACGATTTGTTCCAAGGCGTTTTTTGCTGCCTGAGTACTTGCCTTATGCTGGGATTTTTCATGAACGTGGACAGCCTGGCTTGGCTACTCATTCTTCTGTTAACAGGGTCCTGGCAGGGGCAGTAATTGGAGATGGACAGTCTGCTGTGGCCAGTAACATTGCCAATACTACCTACAGGCTCCAGTGGTGGGACTTCACTAAGTTTGACCTTCCAGAAATCAGTAATGCCTCTGTGAATGTCCTGGTACAGAATTGCAAGATCTACAATGATGCCAGCTGTGACATTTCTGCAGATGGTCAGCTCCTGGCAGCCTTCATCCCGAGCAGCCAGAGGGGCTTTCCTGATGAAGGCATCCTGGCAGTGTATTCCCTGGCCCCCCATAACTTGGGGGAAATGCTCTACACCAAGCGATTTGGTCCCAATGCCATTTCTGTAAGCCTGTCCCCGATGGGCCGATACGTTATGGTGGGCTTGGCCTCACGAAGGATCCTACTGCACCCCTCCACAGAGCACATGGTAGCCCAGGTCTTCAGGCTGCAACAGGCCCATGGTGGTGAGACTTCCATGAGGGAGGCTGCTGGAGTCTTCCCTCATTTCATTATCCCGTTATGA
Peptide sequence:
MIQYLSRRDSIRQRSMRYQQNRLRSSTSSSSSDNQGPSVEGTDLEFEDFEDNGDRSRHRAPRNARMSAPSLGRFVPRRFLLPEYLPYAGIFHERGQPGLATHSSVNRVLAGAVIGDGQSAVASNIANTTYRLQWWDFTKFDLPEISNASVNVLVQNCKIYNDASCDISADGQLLAAFIPSSQRGFPDEGILAVYSLAPHNLGEMLYTKRFGPNAISVSLSPMGRYVMVGLASRRILLHPSTEHMVAQVFRLQQAHGGETSMREAAGVFPHFIIPL
IRESfinder result
IRESfinder score
0.556511622
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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