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mmu_circNek9_1101_2
Basic information of circular RNA
PanCircBase ID:
mmu_circNek9_1101_2
mm39_Chr. Position ID:
chr12|85359719|85376749|-
Gene name:
Nek9
Transcript:
ENSMUST00000040992.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
14,13,12,11,10,9,8,7,6
Exon/intron offsets:
0,1236,1456,2634,7768,9083,12362,14443,16898
Genomic length:
17030
Exon/intron sizes in nt:
1,56,47,20,11,45,19,35,00,00,00,000
Flanking exon/introns:
chr12:85358220-85359719|chr12:85376749-85379274
Splice length:
1101
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CTTGTGGGCACTCCATATTACATGTCTCCAGAGCTCTGCCAAGGAGTAAAATACAATTTCAAGTCTGATATATGGGCAGTTGGCTGTGTCATTTTTGAACTGCTTACTCTGAAAAGAACATTTGATGCTACAAACCCACTCAACCTATGTGTGAAGATCGTGCAGGGAATCCGGGCCATGGAAGTTGACTCGAGTCAGTATTCTTTGGAACTGATCCAGTTGGTACACGCATGCCTCGACCAGGATCCTGAGCAGAGGCCCGCTGCAGATGCACTCCTGGATCTCCCCCTTCTCAGGACCCGCAGGAGAGAGATGGAGGAAAAAGTCACTCTGCTCAATGCACCTACAAAGAGACCAAGGTCAAGCACTGTGACGGAAGCACCCATTGCTGTGGTAACATCACGAACCAGTGAAGTCTATGTTTGGGGTGGTGGAAAATCCACACCTCAGAAATTGGACGTCATCAAGAGTGGCTGTAGTGCTCGACAGGTGTGTGCGGGGAACACCCACTTTGCTGTGGTCACCGTGGAGAAGGAACTATATACCTGGGTGAACATGCAAGGGGGCACTAAACTTCACGGTCAGCTAGGACATGGAGACAAAGCTTCCTACCGACAGCCAAAGCATGTAGAAAAGTTACAAGGGAAGGCTATCCACCAGGTGTCGTGTGGGGATGATTTCACTGTCTGTGTCACAGATGAGGGTCAGCTCTACGCCTTTGGATCAGATTATTATGGCTGCATGGGAGTGGACAAGGTTTCTGGCCCTGAAGTGCTAGAACCCATGCAGCTGAACTTCTTCCTCAGCAATCCTGTGGAGCAGGTCTCCTGTGGGGATAATCATGTGGTAGTTCTGACACGAAACAAAGAAGTCTACTCTTGGGGCTGTGGTGAATATGGACGGCTGGGTTTGGATTCAGAAGAGGATTACTATACACCACAGAGGGTGGATGTTCCAAAGGCCTTAATCATTGTTGCAGTTCAATGTGGCTGTGATGGGACCTTTCTGCTCACTCAGTCAGGCAAAGTGCTGGCCTGTGGACTCAATGAGTTCAACAAGCTGGGGCTGAATCAGTGCATGTCTGGAATCATCAACCATGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTGCTCACTCAGTCAGGC
59.68
CTTGGCAGAGCTCTGGAGAC
60.11
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGCTCACTCAGTCAGGCA
60.83
CTTGGCAGAGCTCTGGAGAC
60.11
140
PCR template sequence:
CTTTCTGCTCACTCAGTCAGGCAAAGTGCTGGCCTGTGGACTCAATGAGTTCAACAAGCTGGGGCTGAATCAGTGCATGTCTGGAATCATCAACCATGAACTTGTGGGCACTCCATATTACATGTCTCCAGAGCTCTGCCAAGGAGTAAAATACAATTTCAAGTCTGATATATGGGCAGTTGGCTGTGTCATTTTTGAAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-200c-3p(1), mmu-miR-128-3p(1), mmu-miR-425-5p(1), mmu-miR-377-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CATCAACCATGAACTTGTGGGCACTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNEK9_1101_2_ORF_1
1.0575
0.235981872
0.999998448
2181
ORF sequence:
ATGTCTCCAGAGCTCTGCCAAGGAGTAAAATACAATTTCAAGTCTGATATATGGGCAGTTGGCTGTGTCATTTTTGAACTGCTTACTCTGAAAAGAACATTTGATGCTACAAACCCACTCAACCTATGTGTGAAGATCGTGCAGGGAATCCGGGCCATGGAAGTTGACTCGAGTCAGTATTCTTTGGAACTGATCCAGTTGGTACACGCATGCCTCGACCAGGATCCTGAGCAGAGGCCCGCTGCAGATGCACTCCTGGATCTCCCCCTTCTCAGGACCCGCAGGAGAGAGATGGAGGAAAAAGTCACTCTGCTCAATGCACCTACAAAGAGACCAAGGTCAAGCACTGTGACGGAAGCACCCATTGCTGTGGTAACATCACGAACCAGTGAAGTCTATGTTTGGGGTGGTGGAAAATCCACACCTCAGAAATTGGACGTCATCAAGAGTGGCTGTAGTGCTCGACAGGTGTGTGCGGGGAACACCCACTTTGCTGTGGTCACCGTGGAGAAGGAACTATATACCTGGGTGAACATGCAAGGGGGCACTAAACTTCACGGTCAGCTAGGACATGGAGACAAAGCTTCCTACCGACAGCCAAAGCATGTAGAAAAGTTACAAGGGAAGGCTATCCACCAGGTGTCGTGTGGGGATGATTTCACTGTCTGTGTCACAGATGAGGGTCAGCTCTACGCCTTTGGATCAGATTATTATGGCTGCATGGGAGTGGACAAGGTTTCTGGCCCTGAAGTGCTAGAACCCATGCAGCTGAACTTCTTCCTCAGCAATCCTGTGGAGCAGGTCTCCTGTGGGGATAATCATGTGGTAGTTCTGACACGAAACAAAGAAGTCTACTCTTGGGGCTGTGGTGAATATGGACGGCTGGGTTTGGATTCAGAAGAGGATTACTATACACCACAGAGGGTGGATGTTCCAAAGGCCTTAATCATTGTTGCAGTTCAATGTGGCTGTGATGGGACCTTTCTGCTCACTCAGTCAGGCAAAGTGCTGGCCTGTGGACTCAATGAGTTCAACAAGCTGGGGCTGAATCAGTGCATGTCTGGAATCATCAACCATGAACTTGTGGGCACTCCATATTACATGTCTCCAGAGCTCTGCCAAGGAGTAAAATACAATTTCAAGTCTGATATATGGGCAGTTGGCTGTGTCATTTTTGAACTGCTTACTCTGAAAAGAACATTTGATGCTACAAACCCACTCAACCTATGTGTGAAGATCGTGCAGGGAATCCGGGCCATGGAAGTTGACTCGAGTCAGTATTCTTTGGAACTGATCCAGTTGGTACACGCATGCCTCGACCAGGATCCTGAGCAGAGGCCCGCTGCAGATGCACTCCTGGATCTCCCCCTTCTCAGGACCCGCAGGAGAGAGATGGAGGAAAAAGTCACTCTGCTCAATGCACCTACAAAGAGACCAAGGTCAAGCACTGTGACGGAAGCACCCATTGCTGTGGTAACATCACGAACCAGTGAAGTCTATGTTTGGGGTGGTGGAAAATCCACACCTCAGAAATTGGACGTCATCAAGAGTGGCTGTAGTGCTCGACAGGTGTGTGCGGGGAACACCCACTTTGCTGTGGTCACCGTGGAGAAGGAACTATATACCTGGGTGAACATGCAAGGGGGCACTAAACTTCACGGTCAGCTAGGACATGGAGACAAAGCTTCCTACCGACAGCCAAAGCATGTAGAAAAGTTACAAGGGAAGGCTATCCACCAGGTGTCGTGTGGGGATGATTTCACTGTCTGTGTCACAGATGAGGGTCAGCTCTACGCCTTTGGATCAGATTATTATGGCTGCATGGGAGTGGACAAGGTTTCTGGCCCTGAAGTGCTAGAACCCATGCAGCTGAACTTCTTCCTCAGCAATCCTGTGGAGCAGGTCTCCTGTGGGGATAATCATGTGGTAGTTCTGACACGAAACAAAGAAGTCTACTCTTGGGGCTGTGGTGAATATGGACGGCTGGGTTTGGATTCAGAAGAGGATTACTATACACCACAGAGGGTGGATGTTCCAAAGGCCTTAATCATTGTTGCAGTTCAATGTGGCTGTGATGGGACCTTTCTGCTCACTCAGTCAGGCAAAGTGCTGGCCTGTGGACTCAATGAGTTCAACAAGCTGGGGCTGAATCAGTGCATGTCTGGAATCATCAACCATGAA
Peptide sequence:
MSPELCQGVKYNFKSDIWAVGCVIFELLTLKRTFDATNPLNLCVKIVQGIRAMEVDSSQYSLELIQLVHACLDQDPEQRPAADALLDLPLLRTRRREMEEKVTLLNAPTKRPRSSTVTEAPIAVVTSRTSEVYVWGGGKSTPQKLDVIKSGCSARQVCAGNTHFAVVTVEKELYTWVNMQGGTKLHGQLGHGDKASYRQPKHVEKLQGKAIHQVSCGDDFTVCVTDEGQLYAFGSDYYGCMGVDKVSGPEVLEPMQLNFFLSNPVEQVSCGDNHVVVLTRNKEVYSWGCGEYGRLGLDSEEDYYTPQRVDVPKALIIVAVQCGCDGTFLLTQSGKVLACGLNEFNKLGLNQCMSGIINHELVGTPYYMSPELCQGVKYNFKSDIWAVGCVIFELLTLKRTFDATNPLNLCVKIVQGIRAMEVDSSQYSLELIQLVHACLDQDPEQRPAADALLDLPLLRTRRREMEEKVTLLNAPTKRPRSSTVTEAPIAVVTSRTSEVYVWGGGKSTPQKLDVIKSGCSARQVCAGNTHFAVVTVEKELYTWVNMQGGTKLHGQLGHGDKASYRQPKHVEKLQGKAIHQVSCGDDFTVCVTDEGQLYAFGSDYYGCMGVDKVSGPEVLEPMQLNFFLSNPVEQVSCGDNHVVVLTRNKEVYSWGCGEYGRLGLDSEEDYYTPQRVDVPKALIIVAVQCGCDGTFLLTQSGKVLACGLNEFNKLGLNQCMSGIINHE
IRESfinder result
IRESfinder score
0.488234118
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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