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mmu_circMark1_414
Basic information of circular RNA
PanCircBase ID:
mmu_circMark1_414
mm39_Chr. Position ID:
chr1|184651506|184653805|-
Gene name:
Mark1
Transcript:
ENSMUST00000027929.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
9,8,7
Exon/intron offsets:
0,208,2242
Genomic length:
2299
Exon/intron sizes in nt:
120,237,57
Flanking exon/introns:
chr1:184648375-184651506|chr1:184653805-184658012
Splice length:
414
Other database IDs:
CIRCpedia: MMU_CIRCpedia_12507, circAtlas: mmu-Mark1_0003
circBase: hsa_circ_0112079, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_125308
Human Ortholog IDs:
Mature spliced Sequence:
ATTGTATCTGCTGTACAGTATTGCCATCAAAAATGCATTGTTCACCGTGATCTTAAGGCTGAAAACCTTCTCCTTGATGCTGATATGAATATTAAAATTGCTGACTTTGGTTTTAGCAATGAATTCACAGTGGGGAACAAATTGGACACATTCTGTGGAAGCCCGCCTTATGCTGCCCCCGAGCTTTTCCAAGGCAAGAAGTACGATGGGCCAGAAGTGGATGTGTGGAGTCTGGGCGTCATTCTCTACACGCTGGTCAGTGGCTCGCTGCCGTTTGATGGCCAGAATCTAAAGGAACTTCGGGAGCGAGTCCTTCGAGGGAAGTACCGCATCCCCTTCTACATGTCCACAGACTGTGAGAATCTCCTGAAGAAACTGTTAGTGCTGAATCCCATAAAGCGGGGCAGCCTGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAGTACCGCATCCCCTTC
60.18
TCAGCCTTAAGATCACGGTGA
58.82
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAGTACCGCATCCCCTTC
60.18
AGATCACGGTGAACAATGCA
57.82
148
PCR template sequence:
TCGAGGGAAGTACCGCATCCCCTTCTACATGTCCACAGACTGTGAGAATCTCCTGAAGAAACTGTTAGTGCTGAATCCCATAAAGCGGGGCAGCCTGGAGATTGTATCTGCTGTACAGTATTGCCATCAAAAATGCATTGTTCACCGTGATCTTAAGGCTGAAAACCTTCTCCTTGATGCTGATATGAATATTAAAATTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-103-3p(1), mmu-miR-433-5p(1), mmu-miR-107-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGGCAGCCTGGAGATTGTATCTGCTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMARK1_414_ORF_1
1.1476
0.339441202
0.974129376
744
ORF sequence:
ATGAATATTAAAATTGCTGACTTTGGTTTTAGCAATGAATTCACAGTGGGGAACAAATTGGACACATTCTGTGGAAGCCCGCCTTATGCTGCCCCCGAGCTTTTCCAAGGCAAGAAGTACGATGGGCCAGAAGTGGATGTGTGGAGTCTGGGCGTCATTCTCTACACGCTGGTCAGTGGCTCGCTGCCGTTTGATGGCCAGAATCTAAAGGAACTTCGGGAGCGAGTCCTTCGAGGGAAGTACCGCATCCCCTTCTACATGTCCACAGACTGTGAGAATCTCCTGAAGAAACTGTTAGTGCTGAATCCCATAAAGCGGGGCAGCCTGGAGATTGTATCTGCTGTACAGTATTGCCATCAAAAATGCATTGTTCACCGTGATCTTAAGGCTGAAAACCTTCTCCTTGATGCTGATATGAATATTAAAATTGCTGACTTTGGTTTTAGCAATGAATTCACAGTGGGGAACAAATTGGACACATTCTGTGGAAGCCCGCCTTATGCTGCCCCCGAGCTTTTCCAAGGCAAGAAGTACGATGGGCCAGAAGTGGATGTGTGGAGTCTGGGCGTCATTCTCTACACGCTGGTCAGTGGCTCGCTGCCGTTTGATGGCCAGAATCTAAAGGAACTTCGGGAGCGAGTCCTTCGAGGGAAGTACCGCATCCCCTTCTACATGTCCACAGACTGTGAGAATCTCCTGAAGAAACTGTTAGTGCTGAATCCCATAAAGCGGGGCAGCCTGGAG
Peptide sequence:
MNIKIADFGFSNEFTVGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKLLVLNPIKRGSLEIVSAVQYCHQKCIVHRDLKAENLLLDADMNIKIADFGFSNEFTVGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKLLVLNPIKRGSLE
IRESfinder result
IRESfinder score
0.539987548
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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