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mmu_circKif6_1000
Basic information of circular RNA
PanCircBase ID:
mmu_circKif6_1000
mm39_Chr. Position ID:
chr17|50014537|50065665|+
Gene name:
Kif6
Transcript:
ENSMUST00000162854.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
7,8,9,10,11,12,13
Exon/intron offsets:
0,6485,7554,14731,46312,47591,50912
Genomic length:
51128
Exon/intron sizes in nt:
2,07,14,48,71,04,10,61,00,000
Flanking exon/introns:
chr17:49993548-50014537|chr17:50065665-50139168
Splice length:
1000
Other database IDs:
CIRCpedia: MMU_CIRCpedia_219596, circAtlas: mmu-Kif6_0007
circBase: hsa_circ_0131719, circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ACTCCTATGAATCAAGCTTCAACCCGGTCACACTGTATTTTCACTGTGCACTTGAGCAGCAAGGAGCCAGGTTCTGCCACCGTCCGACATGCTAAGCTCCATCTGGTTGACCTGGCAGGGTCAGAGCGTGTCTCGAAGACTGGAGTCGGGGGCCTGCTTCTGACAGAGGCCAAATACATCAACTTGTCCCTACACTACCTGGAGCAGGTCATCATTGCCCTTTCGGAAAAACACCGTACACACATCCCTTACAGGAACTCCATGATGACCAGCGTGCTCAGAGACAGTCTGGGAGGGAACTGCATGACCACCATGATTGCAACCCTGTCTTTGGAGAAGAGGAACATTGATGAGTCTATCTCCACCTGCAGATTTGCTCAGCGAGTGGCCCTAATTAAAAACGAAGCCATTCTCAACGAAGAGATTGATCCCAGGCTGATGATTGTTCGCTTGCAAAAGGAGATTGAAGACTTGAAGGCAGAGTTGGCCATGGCCACAGGAGAGCAGAGGACAGAGGCCCTCACGGAAGCAGAGCTCCTTCAGTTGGAAAAACTAATAGCATCCTATTTGGAAGACCAAGATCCAGAGAGTCGACTGGAAGTTGGCGCTGATATGCGTAAAATCCATCACTGTTTTCATCATTTTAAGAAGCTGTTGAATGACAAGAAGACCCTAGAGAATACTGTCTCCTCTGAAAGCACACGGCAAGCATGCCAAGAACCATTGAGAGATGAAGAATATACAAAGCTCCTAGGTCTTCTCAAGCAGAGGGACAACGAGATCAATATCCTGGTCAATATGTTAAAAAAGGAAAAGAAGAAAACTCAGGATGCCCTCCAGAATTCAAGCCTAGAGAAAAGCGATACCAGGCCACCTCAGAACTCGCCCTTCATCGCTGGGAGCCCAGCGGTCCCAAGGACCCCATTCTCCTCAGCCCCGAGCCACACCCAGGACCTCAGCATCTGCAGGCACAGATCCAGCTTGCTCCACAAAAAAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCCAAGGACCCCATTCTC
59.74
CTTGCTGCTCAAGTGCACAG
60.04
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAAGGACCCCATTCTCCTC
59.45
CTTGCTGCTCAAGTGCACAG
60.04
151
PCR template sequence:
AGCCCAGCGGTCCCAAGGACCCCATTCTCCTCAGCCCCGAGCCACACCCAGGACCTCAGCATCTGCAGGCACAGATCCAGCTTGCTCCACAAAAAAACAGACTCCTATGAATCAAGCTTCAACCCGGTCACACTGTATTTTCACTGTGCACTTGAGCAGCAAGGAGCCAGGTTCTGCCACCGTCCGACATGCTAAGCTCC
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-7b-5p(1), mmu-miR-135a-5p(1), mmu-miR-7a-5p(1), mmu-miR-196a-5p(1), mmu-miR-128-3p(1), mmu-miR-149-5p(1), mmu-miR-1187(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CACAAAAAAACAGACTCCTATGAATC
siRNA sets
ATAGGAGTCTGTTTTTTTG, TAGGAGTCTGTTTTTTTGT, ATTCATAGGAGTCTGTTTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKIF6_1000_ORF_1
1.0217
0.237235171
0.995673566
1089
ORF sequence:
ATGAATCAAGCTTCAACCCGGTCACACTGTATTTTCACTGTGCACTTGAGCAGCAAGGAGCCAGGTTCTGCCACCGTCCGACATGCTAAGCTCCATCTGGTTGACCTGGCAGGGTCAGAGCGTGTCTCGAAGACTGGAGTCGGGGGCCTGCTTCTGACAGAGGCCAAATACATCAACTTGTCCCTACACTACCTGGAGCAGGTCATCATTGCCCTTTCGGAAAAACACCGTACACACATCCCTTACAGGAACTCCATGATGACCAGCGTGCTCAGAGACAGTCTGGGAGGGAACTGCATGACCACCATGATTGCAACCCTGTCTTTGGAGAAGAGGAACATTGATGAGTCTATCTCCACCTGCAGATTTGCTCAGCGAGTGGCCCTAATTAAAAACGAAGCCATTCTCAACGAAGAGATTGATCCCAGGCTGATGATTGTTCGCTTGCAAAAGGAGATTGAAGACTTGAAGGCAGAGTTGGCCATGGCCACAGGAGAGCAGAGGACAGAGGCCCTCACGGAAGCAGAGCTCCTTCAGTTGGAAAAACTAATAGCATCCTATTTGGAAGACCAAGATCCAGAGAGTCGACTGGAAGTTGGCGCTGATATGCGTAAAATCCATCACTGTTTTCATCATTTTAAGAAGCTGTTGAATGACAAGAAGACCCTAGAGAATACTGTCTCCTCTGAAAGCACACGGCAAGCATGCCAAGAACCATTGAGAGATGAAGAATATACAAAGCTCCTAGGTCTTCTCAAGCAGAGGGACAACGAGATCAATATCCTGGTCAATATGTTAAAAAAGGAAAAGAAGAAAACTCAGGATGCCCTCCAGAATTCAAGCCTAGAGAAAAGCGATACCAGGCCACCTCAGAACTCGCCCTTCATCGCTGGGAGCCCAGCGGTCCCAAGGACCCCATTCTCCTCAGCCCCGAGCCACACCCAGGACCTCAGCATCTGCAGGCACAGATCCAGCTTGCTCCACAAAAAAACAGACTCCTATGAATCAAGCTTCAACCCGGTCACACTGTATTTTCACTGTGCACTTGAGCAGCAAGGAGCCAGGTTCTGCCACCGTCCGACATGCTAA
Peptide sequence:
MNQASTRSHCIFTVHLSSKEPGSATVRHAKLHLVDLAGSERVSKTGVGGLLLTEAKYINLSLHYLEQVIIALSEKHRTHIPYRNSMMTSVLRDSLGGNCMTTMIATLSLEKRNIDESISTCRFAQRVALIKNEAILNEEIDPRLMIVRLQKEIEDLKAELAMATGEQRTEALTEAELLQLEKLIASYLEDQDPESRLEVGADMRKIHHCFHHFKKLLNDKKTLENTVSSESTRQACQEPLRDEEYTKLLGLLKQRDNEINILVNMLKKEKKKTQDALQNSSLEKSDTRPPQNSPFIAGSPAVPRTPFSSAPSHTQDLSICRHRSSLLHKKTDSYESSFNPVTLYFHCALEQQGARFCHRPTC
IRESfinder result
IRESfinder score
0.514077134
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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