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mmu_circMark1_1147
Basic information of circular RNA
PanCircBase ID:
mmu_circMark1_1147
mm39_Chr. Position ID:
chr1|184640525|184658083|-
Gene name:
Mark1
Transcript:
ENSMUST00000027929.10
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:
0,3667,4153,6188,7750,10981,11189,13223,17487
Genomic length:
17558
Exon/intron sizes in nt:
101,194,154,113,100,120,237,57,71
Flanking exon/introns:
chr1:184639444-184640525|chr1:184658083-184660230
Splice length:
1147
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAAGTCTTTGATTACTTAGTTGCCCACGGAAGAATGAAAGAGAAAGAGGCCCGTGCCAAATTCAGGCAGATTGTATCTGCTGTACAGTATTGCCATCAAAAATGCATTGTTCACCGTGATCTTAAGGCTGAAAACCTTCTCCTTGATGCTGATATGAATATTAAAATTGCTGACTTTGGTTTTAGCAATGAATTCACAGTGGGGAACAAATTGGACACATTCTGTGGAAGCCCGCCTTATGCTGCCCCCGAGCTTTTCCAAGGCAAGAAGTACGATGGGCCAGAAGTGGATGTGTGGAGTCTGGGCGTCATTCTCTACACGCTGGTCAGTGGCTCGCTGCCGTTTGATGGCCAGAATCTAAAGGAACTTCGGGAGCGAGTCCTTCGAGGGAAGTACCGCATCCCCTTCTACATGTCCACAGACTGTGAGAATCTCCTGAAGAAACTGTTAGTGCTGAATCCCATAAAGCGGGGCAGCCTGGAGCAAATAATGAAAGACCGATGGATGAATGTTGGTCATGAGGAAGAAGAGCTAAAGCCGTACTCTGAGCCTGAGCTTGATCTCAGCGATGCAAAAAGAATAGACATTATGGTCACCATGGGTTTTGCACGAGATGAAATCAATGATGCCTTAGTAAGTCAGAAATATGATGAAGTTATGGCTACTTACATCCTTCTAGGTAGAAAACCACCCGAGTTCGAAGGTGGTGAGTCACTGTCCAGTGGGAGCTTGTGCCAGCGGTCGCGGCCGAGCAGCGACCTGAACAACAGCACCCTTCAGTCGCCTGCTCACCTGAAGGTCCAGCGGAGCATCTCGGCCAACCAGAAGCAGAGGCGCTTCAGCGACCACGCCGGCCCCTCCATCCCCCCTGCCGTCTCATACACCAAGAGGCCTCAGGCCAACAGCGTGGAGAGTGAACAGAAGGAGGAGTGGGGCAAAGACACAGCCCGCAGACTTGGCAGCACCACAGTGGGATCAAAGAGCGAAGTCACAGCCAGCCCCTTGGTGGGGCCAGACAGGAAAAAGTCCACAGCGAGCCCAAGTAACAACGTATATTCTGGCGGTAGCATGGCGAGGAGGAATACGTATGTGTGTGAGAGGAGCACAGACCGGTACGCAGCCTTGCAGAATGGAAGAGACAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTAGCATGGCGAGGAGGAAT
59.61
GCACGGGCCTCTTTCTCTTT
60.61
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTAGCATGGCGAGGAGGAAT
59.61
GCACGGGCCTCTTTCTCTT
60
140
PCR template sequence:
ACAACGTATATTCTGGCGGTAGCATGGCGAGGAGGAATACGTATGTGTGTGAGAGGAGCACAGACCGGTACGCAGCCTTGCAGAATGGAAGAGACAGCAGGTGAAGTCTTTGATTACTTAGTTGCCCACGGAAGAATGAAAGAGAAAGAGGCCCGTGCCAAATTCAGGCAGATTGTATCTGCTGTACAGTATTGCCATCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-181a-5p(1), mmu-miR-103-3p(1), mmu-miR-19b-3p(1), mmu-miR-19a-3p(1), mmu-miR-181b-5p(1), mmu-miR-433-5p(1), mmu-miR-96-5p(1), mmu-miR-107-3p(1), mmu-miR-342-3p(1), mmu-miR-129-5p(1), mmu-miR-335-3p(1), mmu-miR-484(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAGAGACAGCAGGTGAAGTCTTTGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMARK1_1147_ORF_1
1.0253
0.302658783
0.998541152
1203
ORF sequence:
ATGTGTGTGAGAGGAGCACAGACCGGTACGCAGCCTTGCAGAATGGAAGAGACAGCAGGTGAAGTCTTTGATTACTTAGTTGCCCACGGAAGAATGAAAGAGAAAGAGGCCCGTGCCAAATTCAGGCAGATTGTATCTGCTGTACAGTATTGCCATCAAAAATGCATTGTTCACCGTGATCTTAAGGCTGAAAACCTTCTCCTTGATGCTGATATGAATATTAAAATTGCTGACTTTGGTTTTAGCAATGAATTCACAGTGGGGAACAAATTGGACACATTCTGTGGAAGCCCGCCTTATGCTGCCCCCGAGCTTTTCCAAGGCAAGAAGTACGATGGGCCAGAAGTGGATGTGTGGAGTCTGGGCGTCATTCTCTACACGCTGGTCAGTGGCTCGCTGCCGTTTGATGGCCAGAATCTAAAGGAACTTCGGGAGCGAGTCCTTCGAGGGAAGTACCGCATCCCCTTCTACATGTCCACAGACTGTGAGAATCTCCTGAAGAAACTGTTAGTGCTGAATCCCATAAAGCGGGGCAGCCTGGAGCAAATAATGAAAGACCGATGGATGAATGTTGGTCATGAGGAAGAAGAGCTAAAGCCGTACTCTGAGCCTGAGCTTGATCTCAGCGATGCAAAAAGAATAGACATTATGGTCACCATGGGTTTTGCACGAGATGAAATCAATGATGCCTTAGTAAGTCAGAAATATGATGAAGTTATGGCTACTTACATCCTTCTAGGTAGAAAACCACCCGAGTTCGAAGGTGGTGAGTCACTGTCCAGTGGGAGCTTGTGCCAGCGGTCGCGGCCGAGCAGCGACCTGAACAACAGCACCCTTCAGTCGCCTGCTCACCTGAAGGTCCAGCGGAGCATCTCGGCCAACCAGAAGCAGAGGCGCTTCAGCGACCACGCCGGCCCCTCCATCCCCCCTGCCGTCTCATACACCAAGAGGCCTCAGGCCAACAGCGTGGAGAGTGAACAGAAGGAGGAGTGGGGCAAAGACACAGCCCGCAGACTTGGCAGCACCACAGTGGGATCAAAGAGCGAAGTCACAGCCAGCCCCTTGGTGGGGCCAGACAGGAAAAAGTCCACAGCGAGCCCAAGTAACAACGTATATTCTGGCGGTAGCATGGCGAGGAGGAATACGTATGTGTGTGAGAGGAGCACAGACCGGTACGCAGCCTTGCAGAATGGAAGAGACAGC
Peptide sequence:
MCVRGAQTGTQPCRMEETAGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKCIVHRDLKAENLLLDADMNIKIADFGFSNEFTVGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKLLVLNPIKRGSLEQIMKDRWMNVGHEEEELKPYSEPELDLSDAKRIDIMVTMGFARDEINDALVSQKYDEVMATYILLGRKPPEFEGGESLSSGSLCQRSRPSSDLNNSTLQSPAHLKVQRSISANQKQRRFSDHAGPSIPPAVSYTKRPQANSVESEQKEEWGKDTARRLGSTTVGSKSEVTASPLVGPDRKKSTASPSNNVYSGGSMARRNTYVCERSTDRYAALQNGRDS
IRESfinder result
IRESfinder score
0.387078351
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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