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mmu_circAtrnl1_1239
Basic information of circular RNA
PanCircBase ID:
mmu_circAtrnl1_1239
mm39_Chr. Position ID:
chr19|57617516|57645670|+
Gene name:
Atrnl1
Transcript:
ENSMUST00000077282.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
2,3,4,5,6,7,8,9
Exon/intron offsets:
0,1141,9367,13335,21173,23838,25686,27970
Genomic length:
28154
Exon/intron sizes in nt:
84,114,129,209,175,88,256,184
Flanking exon/introns:
chr19:57600075-57617516|chr19:57645670-57661550
Splice length:
1239
Other database IDs:
circBase: mmu_circ_0007921, CIRCpedia: MMU_CIRCpedia_23878, circAtlas: mmu-Atrnl1_0008
circBase: hsa_circ_0092765, circAtlas: hsa-ATRNL1_0010, CIRCpedia: HSA_CIRCpedia_487
Human Ortholog IDs:
Mature spliced Sequence:
GTTAACAGAACCTTCTGGATATTTAACAGATGGACCAATTAACTATAAATATAAAACAAAGTGTACATGGCTAATTGAAGGCTATCCAAATGCAGTGCTAAGGTTAAGATTCAATCATTTTGCTACAGAATGCAGCTGGGATCATATGTATGTTTATGATGGAGATTCTATATACGCACCTTTAGTAGCTGTACTTAGTGGCTTGATCGTTCCTGAAGTGAGGGGTAACGAGACCGTGCCTGAGGTGGTCACGACGTCTGGCTACGCGCTGCTCCACTTTTTCAGCGATGCTGCATATAACCTAACTGGCTTCAACATTTTTTATTCGATCAATTCCTGTCCTAACAACTGCTCTGGTCATGGAAAGTGTACAACCAGTGTCTCTGTTGCAAGTCAAGTGTATTGTGAATGCGACAAATACTGGAAAGGGGAAGCATGTGACATTCCTTACTGTAAAGCCAATTGTGGGAGTCCAGATCATGGCTACTGTGACCTAACAGGAGAGAAACTCTGTGTCTGCAACGATAGTTGGCAAGGCCCAGATTGTTCTCTGAATGTCCCTTCTACTGAGTCTTACTGGATTTTGCCAAATGTTAAACCCTTCAGCCCTTCCGTAGGTCGGGCCTCACATAAAGCAGTTTTACATGGGAAATTCATGTGGGTGATTGGAGGATATACTTTTAACTACAGTTCTTTTCAAATGGTTCTGAATTACAATTTAGAAAGCAGTATATGGAATGTAGGTGCTGTATCAAGGGGCCCTCTTCAGAGATACGGACATTCTCTTGCCCTCTATCAGGAAAACATCTTTATGTACGGAGGCAGAATGGAGACCAGTGATGGCAACGTCACCGATGAATTATGGGTGTTTAACGTACGCAGTCAATCATGGAGCACGAAAACCCCCACTGTCCTTGGCCACAGTCAGCAGTACGCTGTGGAGGGACACTCGGCACACATCATGGAGCTGGACAGTAGAGACGTGGTCATGATTGTCATATTTGGATATTCTGCAATATATGGCTATACCAGCAGCATACAGGAATACCATATCTCCTCAAACACTTGGCTAGTTCCAGAAACGAAAGGAGCCATTGTGCAAGGTGGATATGGCCACACAAGTGTGTATGACGAAGTGACCAAGTCCATCTATGTTCACGGAGGCTACAAAGCATTGCCTGGCAATAAGTACGGGCTGGTGGACGACCTCTATAAGTACGAAGTCAACACCAGGACTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCAATAAGTACGGGCTGGT
60.11
AGCACTGCATTTGGATAGCCT
60.06
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCAATAAGTACGGGCTGG
60.11
AGCACTGCATTTGGATAGCCT
60.06
159
PCR template sequence:
CCAAGTCCATCTATGTTCACGGAGGCTACAAAGCATTGCCTGGCAATAAGTACGGGCTGGTGGACGACCTCTATAAGTACGAAGTCAACACCAGGACTTGGTTAACAGAACCTTCTGGATATTTAACAGATGGACCAATTAACTATAAATATAAAACAAAGTGTACATGGCTAATTGAAGGCTATCCAAATGCAGTGCTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-18a-5p(1), mmu-miR-136-5p(1), mmu-miR-382-3p(1), mmu-miR-182-5p(1), mmu-miR-499-5p(1), mmu-miR-669d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACACCAGGACTTGGTTAACAGAACCT
siRNA sets
TCTGTTAACCAAGTCCTGG, GTTCTGTTAACCAAGTCCT, TTCTGTTAACCAAGTCCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATRNL1_1239_ORF_1
0.9892
0.093809781
0.999998925
2331
ORF sequence:
ATGTATGTTTATGATGGAGATTCTATATACGCACCTTTAGTAGCTGTACTTAGTGGCTTGATCGTTCCTGAAGTGAGGGGTAACGAGACCGTGCCTGAGGTGGTCACGACGTCTGGCTACGCGCTGCTCCACTTTTTCAGCGATGCTGCATATAACCTAACTGGCTTCAACATTTTTTATTCGATCAATTCCTGTCCTAACAACTGCTCTGGTCATGGAAAGTGTACAACCAGTGTCTCTGTTGCAAGTCAAGTGTATTGTGAATGCGACAAATACTGGAAAGGGGAAGCATGTGACATTCCTTACTGTAAAGCCAATTGTGGGAGTCCAGATCATGGCTACTGTGACCTAACAGGAGAGAAACTCTGTGTCTGCAACGATAGTTGGCAAGGCCCAGATTGTTCTCTGAATGTCCCTTCTACTGAGTCTTACTGGATTTTGCCAAATGTTAAACCCTTCAGCCCTTCCGTAGGTCGGGCCTCACATAAAGCAGTTTTACATGGGAAATTCATGTGGGTGATTGGAGGATATACTTTTAACTACAGTTCTTTTCAAATGGTTCTGAATTACAATTTAGAAAGCAGTATATGGAATGTAGGTGCTGTATCAAGGGGCCCTCTTCAGAGATACGGACATTCTCTTGCCCTCTATCAGGAAAACATCTTTATGTACGGAGGCAGAATGGAGACCAGTGATGGCAACGTCACCGATGAATTATGGGTGTTTAACGTACGCAGTCAATCATGGAGCACGAAAACCCCCACTGTCCTTGGCCACAGTCAGCAGTACGCTGTGGAGGGACACTCGGCACACATCATGGAGCTGGACAGTAGAGACGTGGTCATGATTGTCATATTTGGATATTCTGCAATATATGGCTATACCAGCAGCATACAGGAATACCATATCTCCTCAAACACTTGGCTAGTTCCAGAAACGAAAGGAGCCATTGTGCAAGGTGGATATGGCCACACAAGTGTGTATGACGAAGTGACCAAGTCCATCTATGTTCACGGAGGCTACAAAGCATTGCCTGGCAATAAGTACGGGCTGGTGGACGACCTCTATAAGTACGAAGTCAACACCAGGACTTGGTTAACAGAACCTTCTGGATATTTAACAGATGGACCAATTAACTATAAATATAAAACAAAGTGTACATGGCTAATTGAAGGCTATCCAAATGCAGTGCTAAGGTTAAGATTCAATCATTTTGCTACAGAATGCAGCTGGGATCATATGTATGTTTATGATGGAGATTCTATATACGCACCTTTAGTAGCTGTACTTAGTGGCTTGATCGTTCCTGAAGTGAGGGGTAACGAGACCGTGCCTGAGGTGGTCACGACGTCTGGCTACGCGCTGCTCCACTTTTTCAGCGATGCTGCATATAACCTAACTGGCTTCAACATTTTTTATTCGATCAATTCCTGTCCTAACAACTGCTCTGGTCATGGAAAGTGTACAACCAGTGTCTCTGTTGCAAGTCAAGTGTATTGTGAATGCGACAAATACTGGAAAGGGGAAGCATGTGACATTCCTTACTGTAAAGCCAATTGTGGGAGTCCAGATCATGGCTACTGTGACCTAACAGGAGAGAAACTCTGTGTCTGCAACGATAGTTGGCAAGGCCCAGATTGTTCTCTGAATGTCCCTTCTACTGAGTCTTACTGGATTTTGCCAAATGTTAAACCCTTCAGCCCTTCCGTAGGTCGGGCCTCACATAAAGCAGTTTTACATGGGAAATTCATGTGGGTGATTGGAGGATATACTTTTAACTACAGTTCTTTTCAAATGGTTCTGAATTACAATTTAGAAAGCAGTATATGGAATGTAGGTGCTGTATCAAGGGGCCCTCTTCAGAGATACGGACATTCTCTTGCCCTCTATCAGGAAAACATCTTTATGTACGGAGGCAGAATGGAGACCAGTGATGGCAACGTCACCGATGAATTATGGGTGTTTAACGTACGCAGTCAATCATGGAGCACGAAAACCCCCACTGTCCTTGGCCACAGTCAGCAGTACGCTGTGGAGGGACACTCGGCACACATCATGGAGCTGGACAGTAGAGACGTGGTCATGATTGTCATATTTGGATATTCTGCAATATATGGCTATACCAGCAGCATACAGGAATACCATATCTCCTCAAACACTTGGCTAGTTCCAGAAACGAAAGGAGCCATTGTGCAAGGTGGATATGGCCACACAAGTGTGTATGACGAAGTGACCAAGTCCATCTATGTTCACGGAGGCTACAAAGCATTGCCTGGCAATAAGTACGGGCTGGTGGACGACCTCTATAAGTACGAAGTCAACACCAGGACT
Peptide sequence:
MYVYDGDSIYAPLVAVLSGLIVPEVRGNETVPEVVTTSGYALLHFFSDAAYNLTGFNIFYSINSCPNNCSGHGKCTTSVSVASQVYCECDKYWKGEACDIPYCKANCGSPDHGYCDLTGEKLCVCNDSWQGPDCSLNVPSTESYWILPNVKPFSPSVGRASHKAVLHGKFMWVIGGYTFNYSSFQMVLNYNLESSIWNVGAVSRGPLQRYGHSLALYQENIFMYGGRMETSDGNVTDELWVFNVRSQSWSTKTPTVLGHSQQYAVEGHSAHIMELDSRDVVMIVIFGYSAIYGYTSSIQEYHISSNTWLVPETKGAIVQGGYGHTSVYDEVTKSIYVHGGYKALPGNKYGLVDDLYKYEVNTRTWLTEPSGYLTDGPINYKYKTKCTWLIEGYPNAVLRLRFNHFATECSWDHMYVYDGDSIYAPLVAVLSGLIVPEVRGNETVPEVVTTSGYALLHFFSDAAYNLTGFNIFYSINSCPNNCSGHGKCTTSVSVASQVYCECDKYWKGEACDIPYCKANCGSPDHGYCDLTGEKLCVCNDSWQGPDCSLNVPSTESYWILPNVKPFSPSVGRASHKAVLHGKFMWVIGGYTFNYSSFQMVLNYNLESSIWNVGAVSRGPLQRYGHSLALYQENIFMYGGRMETSDGNVTDELWVFNVRSQSWSTKTPTVLGHSQQYAVEGHSAHIMELDSRDVVMIVIFGYSAIYGYTSSIQEYHISSNTWLVPETKGAIVQGGYGHTSVYDEVTKSIYVHGGYKALPGNKYGLVDDLYKYEVNTRT
IRESfinder result
IRESfinder score
0.597653365
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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