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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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