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mmu_circCrnkl1_1351
Basic information of circular RNA
PanCircBase ID:
mmu_circCrnkl1_1351
mm39_Chr. Position ID:
chr2|145762516|145773348|-
Gene name:
Crnkl1
Transcript:
ENSMUST00000001818.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,1175,3247,4118,4911,6179,7524,9937,10673
Genomic length:
10832
Exon/intron sizes in nt:
10,22,40,81,60,19,21,70,00,00,00,000
Flanking exon/introns:
chr2:145761908-145762516|chr2:145773348-145774165
Splice length:
1351
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGCTCGATCCATATACGAGCGTGCTTTAGATGTCGACTACCGAAATATTACCCTCTGGCTGAAATATGCAGAAATGGAGATGAAGAACCGCCAGGTCAACCATGCCCGAAACATCTGGGACCGTGCCATCACAACTCTGCCACGCGTCAACCAGTTCTGGTATAAGTACACATACATGGAGGAGATGTTGGGCAACGTTGCTGGTGCCCGCCAGGTGTTTGAGCGCTGGATGGAATGGCAGCCTGAGGAGCAGGCCTGGCATTCCTACATCAACTTCGAGCTGAGATACAAAGAGGTGGAGCGGGCCCGCACCATCTATGAACGCTTTGTGCTCGTGCACCCTGCTGTGAAAAACTGGATCAAGTACGCAAGATTTGAAGAGAAGCATGCTTACTTTGCTCATGCGCGGAAAGTCTACGAGAGAGCGGTGGAGTTTTTTGGGGATGAGCATATGGACGAACACCTCTATGTGGCCTTTGCTAAATTTGAGGAAAACCAGAAAGAATTTGAAAGGGTACGAGTTATCTACAAATATGCCCTGGATAGGATTTCAAAACAAGAGGCCCAAGAACTCTTTAAAAACTATACCATCTTTGAGAAGAAGTTTGGTGACCGGAGGGGTATAGAAGACATCATCGTGAGCAAACGGAGGTTCCAGTATGAAGAAGAAGTGAAGGCTAATCCACACAATTATGATGCATGGTTTGATTATTTACGCTTGGTGGAAAGTGATGCGGAAGCTGACACTGTGCGGGAAGTCTATGAGAGAGCCATTGCCAATGTGCCACCCATCCAGGAGAAGAGACACTGGAAGCGCTACATCTACCTTTGGGTTAACTATGCACTCTATGAAGAGCTGGAAGCCAAGGATCCCGAGAGAACAAGACAGGTATATCAAGCGTCTTTGGAACTAATTCCTCACAAAAAGTTCACATTTGCCAAAATGTGGTTATATTATGCACAGTTTGAAATAAGACAGAAAAATCTGCCATTTGCCAGAAGAGCTTTGGGAACTTCCATAGGCAAATGTCCGAAGAACAAGTTATTCAAAGGATACATAGAACTGGAACTGCAGCTTCGAGAATTTGACAGATGCAGGAAGCTTTATGAAAAGTTTTTGGAATTTGGACCTGAAAATTGTACCTCATGGATTAAGTTTGCAGAATTAGAGACAATCCTTGGTGATATTGAGAGAGCTCGGGCAATCTATGAATTAGCCATCAGCCAGCCACGCTTGGATATGCCAGAGGTACTTTGGAAATCATATATTGATTTTGAGATTGAGCAGGAAGAAACTGAAAGAACACGAAACCTTTACCGACAATTGCTTCAGCGAACACAGCATGTCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACACGAAACCTTTACCGACA
57.4
TGACCTGGCGGTTCTTCATC
60.04
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACACGAAACCTTTACCGACA
57.4
CTGGCGGTTCTTCATCTCCA
59.75
142
PCR template sequence:
ACTTTGGAAATCATATATTGATTTTGAGATTGAGCAGGAAGAAACTGAAAGAACACGAAACCTTTACCGACAATTGCTTCAGCGAACACAGCATGTCAAGGGCTCGATCCATATACGAGCGTGCTTTAGATGTCGACTACCGAAATATTACCCTCTGGCTGAAATATGCAGAAATGGAGATGAAGAACCGCCAGGTCAAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(2), mmu-miR-182-5p(2), mmu-miR-153-3p(1), mmu-miR-362-5p(1), mmu-miR-297a-5p(1), mmu-miR-666-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-410-3p(1), mmu-miR-344d-3p(1), mmu-miR-207(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACAGCATGTCAAGGGCTCGATCCATA
siRNA sets
TATGGATCGAGCCCTTGAC, ATGGATCGAGCCCTTGACA, GATCGAGCCCTTGACATGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCRNKL1_1351_ORF_1
0.8457
0.252498108
0.99955275
1443
ORF sequence:
ATGGAGATGAAGAACCGCCAGGTCAACCATGCCCGAAACATCTGGGACCGTGCCATCACAACTCTGCCACGCGTCAACCAGTTCTGGTATAAGTACACATACATGGAGGAGATGTTGGGCAACGTTGCTGGTGCCCGCCAGGTGTTTGAGCGCTGGATGGAATGGCAGCCTGAGGAGCAGGCCTGGCATTCCTACATCAACTTCGAGCTGAGATACAAAGAGGTGGAGCGGGCCCGCACCATCTATGAACGCTTTGTGCTCGTGCACCCTGCTGTGAAAAACTGGATCAAGTACGCAAGATTTGAAGAGAAGCATGCTTACTTTGCTCATGCGCGGAAAGTCTACGAGAGAGCGGTGGAGTTTTTTGGGGATGAGCATATGGACGAACACCTCTATGTGGCCTTTGCTAAATTTGAGGAAAACCAGAAAGAATTTGAAAGGGTACGAGTTATCTACAAATATGCCCTGGATAGGATTTCAAAACAAGAGGCCCAAGAACTCTTTAAAAACTATACCATCTTTGAGAAGAAGTTTGGTGACCGGAGGGGTATAGAAGACATCATCGTGAGCAAACGGAGGTTCCAGTATGAAGAAGAAGTGAAGGCTAATCCACACAATTATGATGCATGGTTTGATTATTTACGCTTGGTGGAAAGTGATGCGGAAGCTGACACTGTGCGGGAAGTCTATGAGAGAGCCATTGCCAATGTGCCACCCATCCAGGAGAAGAGACACTGGAAGCGCTACATCTACCTTTGGGTTAACTATGCACTCTATGAAGAGCTGGAAGCCAAGGATCCCGAGAGAACAAGACAGGTATATCAAGCGTCTTTGGAACTAATTCCTCACAAAAAGTTCACATTTGCCAAAATGTGGTTATATTATGCACAGTTTGAAATAAGACAGAAAAATCTGCCATTTGCCAGAAGAGCTTTGGGAACTTCCATAGGCAAATGTCCGAAGAACAAGTTATTCAAAGGATACATAGAACTGGAACTGCAGCTTCGAGAATTTGACAGATGCAGGAAGCTTTATGAAAAGTTTTTGGAATTTGGACCTGAAAATTGTACCTCATGGATTAAGTTTGCAGAATTAGAGACAATCCTTGGTGATATTGAGAGAGCTCGGGCAATCTATGAATTAGCCATCAGCCAGCCACGCTTGGATATGCCAGAGGTACTTTGGAAATCATATATTGATTTTGAGATTGAGCAGGAAGAAACTGAAAGAACACGAAACCTTTACCGACAATTGCTTCAGCGAACACAGCATGTCAAGGGCTCGATCCATATACGAGCGTGCTTTAGATGTCGACTACCGAAATATTACCCTCTGGCTGAAATATGCAGAAATGGAGATGAAGAACCGCCAGGTCAACCATGCCCGAAACATCTGGGACCGTGCCATCACAACTCTGCCACGCGTCAACCAGTTCTGGTATAA
Peptide sequence:
MEMKNRQVNHARNIWDRAITTLPRVNQFWYKYTYMEEMLGNVAGARQVFERWMEWQPEEQAWHSYINFELRYKEVERARTIYERFVLVHPAVKNWIKYARFEEKHAYFAHARKVYERAVEFFGDEHMDEHLYVAFAKFEENQKEFERVRVIYKYALDRISKQEAQELFKNYTIFEKKFGDRRGIEDIIVSKRRFQYEEEVKANPHNYDAWFDYLRLVESDAEADTVREVYERAIANVPPIQEKRHWKRYIYLWVNYALYEELEAKDPERTRQVYQASLELIPHKKFTFAKMWLYYAQFEIRQKNLPFARRALGTSIGKCPKNKLFKGYIELELQLREFDRCRKLYEKFLEFGPENCTSWIKFAELETILGDIERARAIYELAISQPRLDMPEVLWKSYIDFEIEQEETERTRNLYRQLLQRTQHVKGSIHIRACFRCRLPKYYPLAEICRNGDEEPPGQPCPKHLGPCHHNSATRQPVLV
IRESfinder result
IRESfinder score
0.463279866
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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