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mmu_circMark1_1161
Basic information of circular RNA
PanCircBase ID:
mmu_circMark1_1161
mm39_Chr. Position ID:
chr1|184644192|184661567|-
Gene name:
Mark1
Transcript:
ENSMUST00000027929.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
13,12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,486,2521,4083,7314,7522,9556,13820,16038,17326
Genomic length:
17375
Exon/intron sizes in nt:
194,154,113,100,120,237,57,71,66,49
Flanking exon/introns:
chr1:184640626-184644192|chr1:184661567-184675402
Splice length:
1161
Other database IDs:
circAtlas: mmu-Mark1_0016
circBase: hsa_circ_0112074, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_160091
Human Ortholog IDs:
Mature spliced Sequence:
TTGTTCCGAGAAGTACGAATAATGAAGATACTGAACCATCCTAACATAGTGAAACTGTTTGAAGTTATTGAAACAGAGAAGACACTCTATTTGGTCATGGAATACGCAAGTGGGGGTGAAGTCTTTGATTACTTAGTTGCCCACGGAAGAATGAAAGAGAAAGAGGCCCGTGCCAAATTCAGGCAGATTGTATCTGCTGTACAGTATTGCCATCAAAAATGCATTGTTCACCGTGATCTTAAGGCTGAAAACCTTCTCCTTGATGCTGATATGAATATTAAAATTGCTGACTTTGGTTTTAGCAATGAATTCACAGTGGGGAACAAATTGGACACATTCTGTGGAAGCCCGCCTTATGCTGCCCCCGAGCTTTTCCAAGGCAAGAAGTACGATGGGCCAGAAGTGGATGTGTGGAGTCTGGGCGTCATTCTCTACACGCTGGTCAGTGGCTCGCTGCCGTTTGATGGCCAGAATCTAAAGGAACTTCGGGAGCGAGTCCTTCGAGGGAAGTACCGCATCCCCTTCTACATGTCCACAGACTGTGAGAATCTCCTGAAGAAACTGTTAGTGCTGAATCCCATAAAGCGGGGCAGCCTGGAGCAAATAATGAAAGACCGATGGATGAATGTTGGTCATGAGGAAGAAGAGCTAAAGCCGTACTCTGAGCCTGAGCTTGATCTCAGCGATGCAAAAAGAATAGACATTATGGTCACCATGGGTTTTGCACGAGATGAAATCAATGATGCCTTAGTAAGTCAGAAATATGATGAAGTTATGGCTACTTACATCCTTCTAGGTAGAAAACCACCCGAGTTCGAAGGTGGTGAGTCACTGTCCAGTGGGAGCTTGTGCCAGCGGTCGCGGCCGAGCAGCGACCTGAACAACAGCACCCTTCAGTCGCCTGCTCACCTGAAGGTCCAGCGGAGCATCTCGGCCAACCAGAAGCAGAGGCGCTTCAGCGACCACGCCGGCCCCTCCATCCCCCCTGCCGTCTCATACACCAAGAGGCCTCAGGCCAACAGCGTGGAGAGTGAACAGAAGGAGGAGTGGGGCAAAGACACAGCCCGCAGACTTGGCAGCACCACAGTGGGATCAAAGAGCGAAGTCACAGCCAGCCCCTTGGTGGGGCCAGACAGGAAAAAGTCCACAGCGAGCCCAAGT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAGAGCGAAGTCACAGCCA
59.89
TGACCAAATAGAGTGTCTTCTCTGT
59.46
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAGAGCGAAGTCACAGCCA
59.89
CCATGACCAAATAGAGTGTCTTCT
58.26
167
PCR template sequence:
AGCCCGCAGACTTGGCAGCACCACAGTGGGATCAAAGAGCGAAGTCACAGCCAGCCCCTTGGTGGGGCCAGACAGGAAAAAGTCCACAGCGAGCCCAAGTTTGTTCCGAGAAGTACGAATAATGAAGATACTGAACCATCCTAACATAGTGAAACTGTTTGAAGTTATTGAAACAGAGAAGACACTCTATTTGGTCATGG
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-335-3p(2), 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-129-5p(1), mmu-miR-484(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCGAGCCCAAGTTTGTTCCGAGAAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMARK1_1161_ORF_1
1.1848
0.31548059
0.999999627
2301
ORF sequence:
ATGAAGATACTGAACCATCCTAACATAGTGAAACTGTTTGAAGTTATTGAAACAGAGAAGACACTCTATTTGGTCATGGAATACGCAAGTGGGGGTGAAGTCTTTGATTACTTAGTTGCCCACGGAAGAATGAAAGAGAAAGAGGCCCGTGCCAAATTCAGGCAGATTGTATCTGCTGTACAGTATTGCCATCAAAAATGCATTGTTCACCGTGATCTTAAGGCTGAAAACCTTCTCCTTGATGCTGATATGAATATTAAAATTGCTGACTTTGGTTTTAGCAATGAATTCACAGTGGGGAACAAATTGGACACATTCTGTGGAAGCCCGCCTTATGCTGCCCCCGAGCTTTTCCAAGGCAAGAAGTACGATGGGCCAGAAGTGGATGTGTGGAGTCTGGGCGTCATTCTCTACACGCTGGTCAGTGGCTCGCTGCCGTTTGATGGCCAGAATCTAAAGGAACTTCGGGAGCGAGTCCTTCGAGGGAAGTACCGCATCCCCTTCTACATGTCCACAGACTGTGAGAATCTCCTGAAGAAACTGTTAGTGCTGAATCCCATAAAGCGGGGCAGCCTGGAGCAAATAATGAAAGACCGATGGATGAATGTTGGTCATGAGGAAGAAGAGCTAAAGCCGTACTCTGAGCCTGAGCTTGATCTCAGCGATGCAAAAAGAATAGACATTATGGTCACCATGGGTTTTGCACGAGATGAAATCAATGATGCCTTAGTAAGTCAGAAATATGATGAAGTTATGGCTACTTACATCCTTCTAGGTAGAAAACCACCCGAGTTCGAAGGTGGTGAGTCACTGTCCAGTGGGAGCTTGTGCCAGCGGTCGCGGCCGAGCAGCGACCTGAACAACAGCACCCTTCAGTCGCCTGCTCACCTGAAGGTCCAGCGGAGCATCTCGGCCAACCAGAAGCAGAGGCGCTTCAGCGACCACGCCGGCCCCTCCATCCCCCCTGCCGTCTCATACACCAAGAGGCCTCAGGCCAACAGCGTGGAGAGTGAACAGAAGGAGGAGTGGGGCAAAGACACAGCCCGCAGACTTGGCAGCACCACAGTGGGATCAAAGAGCGAAGTCACAGCCAGCCCCTTGGTGGGGCCAGACAGGAAAAAGTCCACAGCGAGCCCAAGTTTGTTCCGAGAAGTACGAATAATGAAGATACTGAACCATCCTAACATAGTGAAACTGTTTGAAGTTATTGAAACAGAGAAGACACTCTATTTGGTCATGGAATACGCAAGTGGGGGTGAAGTCTTTGATTACTTAGTTGCCCACGGAAGAATGAAAGAGAAAGAGGCCCGTGCCAAATTCAGGCAGATTGTATCTGCTGTACAGTATTGCCATCAAAAATGCATTGTTCACCGTGATCTTAAGGCTGAAAACCTTCTCCTTGATGCTGATATGAATATTAAAATTGCTGACTTTGGTTTTAGCAATGAATTCACAGTGGGGAACAAATTGGACACATTCTGTGGAAGCCCGCCTTATGCTGCCCCCGAGCTTTTCCAAGGCAAGAAGTACGATGGGCCAGAAGTGGATGTGTGGAGTCTGGGCGTCATTCTCTACACGCTGGTCAGTGGCTCGCTGCCGTTTGATGGCCAGAATCTAAAGGAACTTCGGGAGCGAGTCCTTCGAGGGAAGTACCGCATCCCCTTCTACATGTCCACAGACTGTGAGAATCTCCTGAAGAAACTGTTAGTGCTGAATCCCATAAAGCGGGGCAGCCTGGAGCAAATAATGAAAGACCGATGGATGAATGTTGGTCATGAGGAAGAAGAGCTAAAGCCGTACTCTGAGCCTGAGCTTGATCTCAGCGATGCAAAAAGAATAGACATTATGGTCACCATGGGTTTTGCACGAGATGAAATCAATGATGCCTTAGTAAGTCAGAAATATGATGAAGTTATGGCTACTTACATCCTTCTAGGTAGAAAACCACCCGAGTTCGAAGGTGGTGAGTCACTGTCCAGTGGGAGCTTGTGCCAGCGGTCGCGGCCGAGCAGCGACCTGAACAACAGCACCCTTCAGTCGCCTGCTCACCTGAAGGTCCAGCGGAGCATCTCGGCCAACCAGAAGCAGAGGCGCTTCAGCGACCACGCCGGCCCCTCCATCCCCCCTGCCGTCTCATACACCAAGAGGCCTCAGGCCAACAGCGTGGAGAGTGAACAGAAGGAGGAGTGGGGCAAAGACACAGCCCGCAGACTTGGCAGCACCACAGTGGGATCAAAGAGCGAAGTCACAGCCAGCCCCTTGGTGGGGCCAGACAGGAAAAAGTCCACAGCGAGCCCAAGT
Peptide sequence:
MKILNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKCIVHRDLKAENLLLDADMNIKIADFGFSNEFTVGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKLLVLNPIKRGSLEQIMKDRWMNVGHEEEELKPYSEPELDLSDAKRIDIMVTMGFARDEINDALVSQKYDEVMATYILLGRKPPEFEGGESLSSGSLCQRSRPSSDLNNSTLQSPAHLKVQRSISANQKQRRFSDHAGPSIPPAVSYTKRPQANSVESEQKEEWGKDTARRLGSTTVGSKSEVTASPLVGPDRKKSTASPSLFREVRIMKILNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKCIVHRDLKAENLLLDADMNIKIADFGFSNEFTVGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKLLVLNPIKRGSLEQIMKDRWMNVGHEEEELKPYSEPELDLSDAKRIDIMVTMGFARDEINDALVSQKYDEVMATYILLGRKPPEFEGGESLSSGSLCQRSRPSSDLNNSTLQSPAHLKVQRSISANQKQRRFSDHAGPSIPPAVSYTKRPQANSVESEQKEEWGKDTARRLGSTTVGSKSEVTASPLVGPDRKKSTASPS
IRESfinder result
IRESfinder score
0.443664964
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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