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mmu_circNedd4l_1301
Basic information of circular RNA
PanCircBase ID:
mmu_circNedd4l_1301
mm39_Chr. Position ID:
chr18|65305345|65337020|+
Gene name:
Nedd4l
Transcript:
ENSMUST00000235343.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
14,15,16,17,18,19,20,21,22,23,24,25
Exon/intron offsets:
0,641,1770,6644,9053,14051,19162,20801,22785,23640,26356,31601
Genomic length:
31675
Exon/intron sizes in nt:
132,120,198,78,55,59,66,230,122,71,96,74
Flanking exon/introns:
chr18:65300644-65305345|chr18:65337020-65338703
Splice length:
1301
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_132257
Human Ortholog IDs:
Mature spliced Sequence:
CCATCAGTGGCCTATGTACATACCACGCCGGGCCTGCCTTCAGGCTGGGAAGAAAGAAAGGATGCAAAGGGACGCACATACTATGTCAATCATAACAATCGAACCACAACTTGGACTCGGCCAATCATGCAGCTTGCAGAAGACGGTGCCTCCGGATCAGCCACAAACAGTAACAACCACCTAGTCGAACCCCAGATCCGCCGGCCCCGTAGCCTCAGCTCGCCAACAGTAACTTTATCTGCCCCACTGGAGGGTGCCAAGGATTCACCCATCCGCCGTGCCGTGAAAGATACCCTTTCCAATCCACAGTCCCCTCAGCCATCACCTTACAACTCCCCCAAACCACAACACAAAGTCACACAGAGCTTCCTGCCACCAGGCTGGGAGATGAGGATAGCCCCCAACGGCCGACCCTTCTTCATTGACCATAACACAAAGACTACAACCTGGGAAGATCCACGGTTGAAATTTCCAGTACACATGCGGTCAAAAGCATCTTTAAACCCCAATGACCTGGGCCCTCTTCCTCCTGGCTGGGAAGAGAGGATCCACTTGGATGGCCGCACGTTTTACATTGACCATAATAGTAAAATTACCCAGTGGGAAGATCCAAGACTACAGAACCCAGCCATCACTGGTCCGGCTGTTCCGTACTCCAGAGAGTTTAAGCAGAAATACGACTACTTTAGGAAGAAATTAAAGAAGCCTGCTGATATTCCAAACAGGTTTGAAATGAAACTTCACAGAAACAACATATTTGAAGAGTCCTATCGGAGGATCATGTCTGTAAAGAGACCTGACGTCCTAAAGGCTAGGCTGTGGATTGAGTTTGAATCAGAGAAAGGCCTGGACTATGGGGGCGTGGCCAGAGAATGGTTCTTCTTACTGTCCAAAGAGATGTTTAACCCCTACTATGGCCTCTTCGAGTACTCTGCCACGGACAACTACACACTTCAGATCAATCCCAACTCAGGCCTCTGTAATGAAGACCATTTGTCCTATTTCACCTTCATTGGAAGAGTTGCTGGCCTAGCGGTGTTTCATGGGAAACTCTTAGATGGATTCTTCATTCGACCATTCTACAAGATGATGCTGGGGAAGCAGATAACGCTGAACGACATGGAGTCCGTGGACAGCGAGTACTACAACTCTTTGAAGTGGATCTTAGAAAACGACCCCACGGAACTTGACCTCATGTTCTGCATAGACGAAGAGAACTTTGGGCAGACATACCAAGTGGATCTGAAGCCCAACGGGTCAGAAATAATGGTAACCAATGAGAACAAACGAGAATACATTGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGGATCTGAAGCCCAACG
60.04
AGTATGTGCGTCCCTTTGCA
59.96
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGGATCTGAAGCCCAACG
60.04
GCGTCCCTTTGCATCCTTTC
59.83
141
PCR template sequence:
GCATAGACGAAGAGAACTTTGGGCAGACATACCAAGTGGATCTGAAGCCCAACGGGTCAGAAATAATGGTAACCAATGAGAACAAACGAGAATACATTGACCATCAGTGGCCTATGTACATACCACGCCGGGCCTGCCTTCAGGCTGGGAAGAAAGAAAGGATGCAAAGGGACGCACATACTATGTCAATCATAACAATC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-382-5p(1), mmu-miR-362-5p(1), mmu-miR-673-5p(1), mmu-miR-1904(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGAATACATTGACCATCAGTGGCCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNEDD4L_1301_ORF_1
0.8702
0.246213472
0.999198303
1359
ORF sequence:
ATGCAGCTTGCAGAAGACGGTGCCTCCGGATCAGCCACAAACAGTAACAACCACCTAGTCGAACCCCAGATCCGCCGGCCCCGTAGCCTCAGCTCGCCAACAGTAACTTTATCTGCCCCACTGGAGGGTGCCAAGGATTCACCCATCCGCCGTGCCGTGAAAGATACCCTTTCCAATCCACAGTCCCCTCAGCCATCACCTTACAACTCCCCCAAACCACAACACAAAGTCACACAGAGCTTCCTGCCACCAGGCTGGGAGATGAGGATAGCCCCCAACGGCCGACCCTTCTTCATTGACCATAACACAAAGACTACAACCTGGGAAGATCCACGGTTGAAATTTCCAGTACACATGCGGTCAAAAGCATCTTTAAACCCCAATGACCTGGGCCCTCTTCCTCCTGGCTGGGAAGAGAGGATCCACTTGGATGGCCGCACGTTTTACATTGACCATAATAGTAAAATTACCCAGTGGGAAGATCCAAGACTACAGAACCCAGCCATCACTGGTCCGGCTGTTCCGTACTCCAGAGAGTTTAAGCAGAAATACGACTACTTTAGGAAGAAATTAAAGAAGCCTGCTGATATTCCAAACAGGTTTGAAATGAAACTTCACAGAAACAACATATTTGAAGAGTCCTATCGGAGGATCATGTCTGTAAAGAGACCTGACGTCCTAAAGGCTAGGCTGTGGATTGAGTTTGAATCAGAGAAAGGCCTGGACTATGGGGGCGTGGCCAGAGAATGGTTCTTCTTACTGTCCAAAGAGATGTTTAACCCCTACTATGGCCTCTTCGAGTACTCTGCCACGGACAACTACACACTTCAGATCAATCCCAACTCAGGCCTCTGTAATGAAGACCATTTGTCCTATTTCACCTTCATTGGAAGAGTTGCTGGCCTAGCGGTGTTTCATGGGAAACTCTTAGATGGATTCTTCATTCGACCATTCTACAAGATGATGCTGGGGAAGCAGATAACGCTGAACGACATGGAGTCCGTGGACAGCGAGTACTACAACTCTTTGAAGTGGATCTTAGAAAACGACCCCACGGAACTTGACCTCATGTTCTGCATAGACGAAGAGAACTTTGGGCAGACATACCAAGTGGATCTGAAGCCCAACGGGTCAGAAATAATGGTAACCAATGAGAACAAACGAGAATACATTGACCATCAGTGGCCTATGTACATACCACGCCGGGCCTGCCTTCAGGCTGGGAAGAAAGAAAGGATGCAAAGGGACGCACATACTATGTCAATCATAACAATCGAACCACAACTTGGACTCGGCCAATCATGCAGCTTGCAGAAGACGGTGCCTCCGGATCAGCCACAAACAGTAACAACCACCTAG
Peptide sequence:
MQLAEDGASGSATNSNNHLVEPQIRRPRSLSSPTVTLSAPLEGAKDSPIRRAVKDTLSNPQSPQPSPYNSPKPQHKVTQSFLPPGWEMRIAPNGRPFFIDHNTKTTTWEDPRLKFPVHMRSKASLNPNDLGPLPPGWEERIHLDGRTFYIDHNSKITQWEDPRLQNPAITGPAVPYSREFKQKYDYFRKKLKKPADIPNRFEMKLHRNNIFEESYRRIMSVKRPDVLKARLWIEFESEKGLDYGGVAREWFFLLSKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYFTFIGRVAGLAVFHGKLLDGFFIRPFYKMMLGKQITLNDMESVDSEYYNSLKWILENDPTELDLMFCIDEENFGQTYQVDLKPNGSEIMVTNENKREYIDHQWPMYIPRRACLQAGKKERMQRDAHTMSIITIEPQLGLGQSCSLQKTVPPDQPQTVTTT
IRESfinder result
IRESfinder score
0.554035202
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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