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mmu_circSh3bp4_2681
Basic information of circular RNA
PanCircBase ID:
mmu_circSh3bp4_2681
mm39_Chr. Position ID:
chr1|89034979|89073628|+
Gene name:
Sh3bp4
Transcript:
ENSMUST00000066279.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,30301,36292
Genomic length:
38649
Exon/intron sizes in nt:
79,24,52,357
Flanking exon/introns:
chr1:88998319-89034979|chr1:89073628-89079921
Splice length:
2681
Other database IDs:
CIRCpedia: MMU_CIRCpedia_33344, circAtlas: mmu-Sh3bp4_0003
circBase: hsa_circ_0058787, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_40100
Human Ortholog IDs:
Mature spliced Sequence:
GGCATCCCTCTTCTCGAGGATGGAAGGTGGAGTCTTGGAGTTTTTCCTCTGACATCAAGAGGCCAACATCCCCCAGCAGGAAGAAGCACACTGCCAAGTTGACCCTGCCGTGCAGCGTGACTTTATGAGACAGCAGCTGCTGTCCCTGCTGGAACTAGGGGAGGAGACATGAGACCATAGTACCTCACCCACCCAAGAGGCTCACCATGGCAGCCCAGCGTATCCGGGCAGCCAACGCCAGTGGCCTCCCTCGGTGCAAGTCGGAGGGGACTCTGATAGACCTGAGCGAGGGCTTCTCAGAGACAAGCTTTAATGATGTCAAAGTGCCTTCCCCCAGTGCCTTGCTCGTAGACAACCCCACGCCTTTTGGAAACGCAAAGGAAGTGATTGCCATCAAAGACTATTGCCCAAACAACTTCACCACCCTGAAGTTTTCCAAGGGCGACCACCTCTACGTCTTGGACACGTCTGGTGGGGAGTGGTGGTACGCTCACAACACCACCGAGATGGGCTACATCCCTTCCTCCTACGTGCAGCCATTAAACTACCGGAATTCTACCCTGAGTGACAGTGGCATGATCGACAATCTTCCGGACAGCCCTGAAGAAGTTGCCAAGGAGTTAGATCTGCTAGGGGGTGGCTGGACCGATGACCAGAAAGAATCTGGCAGGCCCTATAGTAACAACCCTTTCTGGAATGGAGTCCGAACGAACCCCTTTCTGAATGGGAATGCACAGCCCAGTACGGATGAGCTAAACCCCAAGAGTACCGTGGATTTGCTCCTGTTTGACACGGGCACATCTTCCTTCACTGAGTCCAGCTCGGCGACCACCAACAGCACCGGCAACATCTTTGATGAGCTCCCAGCCACCAATGGACTCCAGGTGGAGCAGCCTGTCAAGCGGGACAACCCCTTTTTCAGAAGCAAGCGTTCCTACAGCCTTTCGGAACTCTCCGTCCTGCAAGCCAAATCGGATGCTCCCCCAACGTCCAGCTTCTTCACAGGCTTGAAGTCGCCTGTCCCGGAACAGTTTCAAAGCCGAGAAGACTTCCGAACCGCCTGGCTCAATCACCGGAAGCTGGCCCGTTCCTGCCATGACTTGGATCTGCTCGGCCAAAGCCCAGGCTGGGGCCAGACCCAAGCAGTGGAGACAAATATTGTGTGCAAGCTGGATAGCTCTGGGGGCTCCGTGCAGCTTCCTGACACCAACATCAGTATCCATGTGCCAGAGGGCCATGTAGCTCCTGGGGAGACACAGCAGATTTCCATGAAAGCCCTGCTGGACCCTCCGCTGGACCTTAACAGTGACAGATCCACCAGCGTAAGCCCTGTGGTGGAGGTGAAGCTGAGTAACCTAGAGGTGAGTACCTTCATCATCTTGGAGATGAAGGTCTCCGCCGAGGTGAAGGGCGACATCTTTAGCAAAAGCACGGTGGTCCTGCAGTGCCTGAGAAGTGACTCAAAGGAGGGGCCTTATGTGCCCATCCCTCTCGCCTACAGCTATGGGGACACCATACAGGTACAGCTGGACAACCTGGAACCCTGCATGTACCTAGCCATCGTTGCCCAGGGCCCCAACATCCTCTACCCTTCCACCGTGTGGGATTTCATCAATAAGAGGGTCACCGTGGGTCTCTATGGTCCCAAACACATCCATCCATCCTTCAAGACAGTAGTGACCATTTTTGGACATGATTGTGCCCCCAAGACCCTCCTGGTGAGTGAGGTGACTCGGCAGGCTCCCAGTCCTGCCCCCGTGGCCCTCCAGCTGTGGGGCAAACATCAGTTCATTCTGTCCAGGCCCCAGGATCTCAGAGTGTGTATGTTCTCCAATATGACTAACTATGAGGTCAAGGCCAACGAGCAAGCCCGAGTAGTGAGAGGGTTTCAGATGAAGCTGGGCAAGGTGAGCCGTCTGATCTTCTCCGTCATCTCCCAGAACCCCAATGAGCTGTCCGACTTCACCCTGAGGGTCCAGGTCAAGGATGATCAGGACACGATCCTCACGCAGTTTTGTGTCCAGACTCCGCAGCCGCCCCCTAAAAGCGCCATTAAACCGTCGGGACAGAGGAGGTTTCTTAAGAAGAACGAGGTCGGGAAGATCATCTTGTCCCCGTTTGTCGTTACAACCAAGTATCCAACGTTTCAGGACCGCCCCGTGTCTAGCCTCAAGTTTGGCAAGCTTCTAAAGACAGTGGTGCGGCAGAACAAGAGTCACTACCTGCTGGAGTACAAGAAAGGTGACGTCGTGGCTCTGCTCAGCGAGGAGCGCATCCGGCTCAAGGGACAGCTGTGGACCAAGGAGTGGTACATCGGCTACTACCAGGGCAAGGTGGGCCTGGTGCACACCAAGAACGTGCTGGTCGTCGGCAAGGCCCGGCCCAGCCTGTTCTCGGGGCCCGAGCTGAGCACCTCAGTGCTGCTGGAGCAGATCCTGCGGCCCTGCAAGTTCCTTACCTACATCTATGCCTCTGTGCGGACCTTACTCATGGAGAACATCAGCAGCTGGCGGGCCTTTGCTGATGCCCTGGGTTACGGCAACCTGCCGCTCACCTTCTTCTGCCGGGCAGAGCTGGACAGCGAGCCGGAACGGGTGGCTTCCGTTCTGGAAAAGCTCAAGGAAGACTGTAACAACCCTGACAACAAGGACCGGAAGTCCTTCCAGAAGGAGCTGGTGATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGACAACAAGGACCGGAA
59.89
TTGGCAGTGTGCTTCTTCCT
59.82
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACCCTGACAACAAGGACCG
60.18
TTGGCAGTGTGCTTCTTCCT
59.82
145
PCR template sequence:
CGAGCCGGAACGGGTGGCTTCCGTTCTGGAAAAGCTCAAGGAAGACTGTAACAACCCTGACAACAAGGACCGGAAGTCCTTCCAGAAGGAGCTGGTGATGGGCATCCCTCTTCTCGAGGATGGAAGGTGGAGTCTTGGAGTTTTTCCTCTGACATCAAGAGGCCAACATCCCCCAGCAGGAAGAAGCACACTGCCAAGTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
20
Interacting miRNAs (#binding sites)
mmu-miR-184-3p(2), mmu-miR-214-3p(2), mmu-miR-124-3p(1), mmu-miR-221-3p(1), mmu-miR-34a-5p(1), mmu-miR-205-5p(1), mmu-miR-15b-5p(1), mmu-miR-328-3p(1), mmu-miR-222-3p(1), mmu-miR-196a-5p(1), mmu-miR-433-5p(1), mmu-miR-382-5p(1), mmu-miR-370-3p(1), mmu-miR-362-5p(1), mmu-miR-383-5p(1), mmu-miR-27a-5p(1), mmu-miR-325-3p(1), mmu-miR-188-3p(1), mmu-miR-3470b(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAGCTGGTGATGGGCATCCCTCTTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSH3BP4_2681_ORF_1
1.2276
0.432355679
0.999999969
2577
ORF sequence:
ATGGCAGCCCAGCGTATCCGGGCAGCCAACGCCAGTGGCCTCCCTCGGTGCAAGTCGGAGGGGACTCTGATAGACCTGAGCGAGGGCTTCTCAGAGACAAGCTTTAATGATGTCAAAGTGCCTTCCCCCAGTGCCTTGCTCGTAGACAACCCCACGCCTTTTGGAAACGCAAAGGAAGTGATTGCCATCAAAGACTATTGCCCAAACAACTTCACCACCCTGAAGTTTTCCAAGGGCGACCACCTCTACGTCTTGGACACGTCTGGTGGGGAGTGGTGGTACGCTCACAACACCACCGAGATGGGCTACATCCCTTCCTCCTACGTGCAGCCATTAAACTACCGGAATTCTACCCTGAGTGACAGTGGCATGATCGACAATCTTCCGGACAGCCCTGAAGAAGTTGCCAAGGAGTTAGATCTGCTAGGGGGTGGCTGGACCGATGACCAGAAAGAATCTGGCAGGCCCTATAGTAACAACCCTTTCTGGAATGGAGTCCGAACGAACCCCTTTCTGAATGGGAATGCACAGCCCAGTACGGATGAGCTAAACCCCAAGAGTACCGTGGATTTGCTCCTGTTTGACACGGGCACATCTTCCTTCACTGAGTCCAGCTCGGCGACCACCAACAGCACCGGCAACATCTTTGATGAGCTCCCAGCCACCAATGGACTCCAGGTGGAGCAGCCTGTCAAGCGGGACAACCCCTTTTTCAGAAGCAAGCGTTCCTACAGCCTTTCGGAACTCTCCGTCCTGCAAGCCAAATCGGATGCTCCCCCAACGTCCAGCTTCTTCACAGGCTTGAAGTCGCCTGTCCCGGAACAGTTTCAAAGCCGAGAAGACTTCCGAACCGCCTGGCTCAATCACCGGAAGCTGGCCCGTTCCTGCCATGACTTGGATCTGCTCGGCCAAAGCCCAGGCTGGGGCCAGACCCAAGCAGTGGAGACAAATATTGTGTGCAAGCTGGATAGCTCTGGGGGCTCCGTGCAGCTTCCTGACACCAACATCAGTATCCATGTGCCAGAGGGCCATGTAGCTCCTGGGGAGACACAGCAGATTTCCATGAAAGCCCTGCTGGACCCTCCGCTGGACCTTAACAGTGACAGATCCACCAGCGTAAGCCCTGTGGTGGAGGTGAAGCTGAGTAACCTAGAGGTGAGTACCTTCATCATCTTGGAGATGAAGGTCTCCGCCGAGGTGAAGGGCGACATCTTTAGCAAAAGCACGGTGGTCCTGCAGTGCCTGAGAAGTGACTCAAAGGAGGGGCCTTATGTGCCCATCCCTCTCGCCTACAGCTATGGGGACACCATACAGGTACAGCTGGACAACCTGGAACCCTGCATGTACCTAGCCATCGTTGCCCAGGGCCCCAACATCCTCTACCCTTCCACCGTGTGGGATTTCATCAATAAGAGGGTCACCGTGGGTCTCTATGGTCCCAAACACATCCATCCATCCTTCAAGACAGTAGTGACCATTTTTGGACATGATTGTGCCCCCAAGACCCTCCTGGTGAGTGAGGTGACTCGGCAGGCTCCCAGTCCTGCCCCCGTGGCCCTCCAGCTGTGGGGCAAACATCAGTTCATTCTGTCCAGGCCCCAGGATCTCAGAGTGTGTATGTTCTCCAATATGACTAACTATGAGGTCAAGGCCAACGAGCAAGCCCGAGTAGTGAGAGGGTTTCAGATGAAGCTGGGCAAGGTGAGCCGTCTGATCTTCTCCGTCATCTCCCAGAACCCCAATGAGCTGTCCGACTTCACCCTGAGGGTCCAGGTCAAGGATGATCAGGACACGATCCTCACGCAGTTTTGTGTCCAGACTCCGCAGCCGCCCCCTAAAAGCGCCATTAAACCGTCGGGACAGAGGAGGTTTCTTAAGAAGAACGAGGTCGGGAAGATCATCTTGTCCCCGTTTGTCGTTACAACCAAGTATCCAACGTTTCAGGACCGCCCCGTGTCTAGCCTCAAGTTTGGCAAGCTTCTAAAGACAGTGGTGCGGCAGAACAAGAGTCACTACCTGCTGGAGTACAAGAAAGGTGACGTCGTGGCTCTGCTCAGCGAGGAGCGCATCCGGCTCAAGGGACAGCTGTGGACCAAGGAGTGGTACATCGGCTACTACCAGGGCAAGGTGGGCCTGGTGCACACCAAGAACGTGCTGGTCGTCGGCAAGGCCCGGCCCAGCCTGTTCTCGGGGCCCGAGCTGAGCACCTCAGTGCTGCTGGAGCAGATCCTGCGGCCCTGCAAGTTCCTTACCTACATCTATGCCTCTGTGCGGACCTTACTCATGGAGAACATCAGCAGCTGGCGGGCCTTTGCTGATGCCCTGGGTTACGGCAACCTGCCGCTCACCTTCTTCTGCCGGGCAGAGCTGGACAGCGAGCCGGAACGGGTGGCTTCCGTTCTGGAAAAGCTCAAGGAAGACTGTAACAACCCTGACAACAAGGACCGGAAGTCCTTCCAGAAGGAGCTGGTGATGGGCATCCCTCTTCTCGAGGATGGAAGGTGGAGTCTTGGAGTTTTTCCTCTGACATCAAGAGGCCAACATCCCCCAGCAGGAAGAAGCACACTGCCAAGTTGA
Peptide sequence:
MAAQRIRAANASGLPRCKSEGTLIDLSEGFSETSFNDVKVPSPSALLVDNPTPFGNAKEVIAIKDYCPNNFTTLKFSKGDHLYVLDTSGGEWWYAHNTTEMGYIPSSYVQPLNYRNSTLSDSGMIDNLPDSPEEVAKELDLLGGGWTDDQKESGRPYSNNPFWNGVRTNPFLNGNAQPSTDELNPKSTVDLLLFDTGTSSFTESSSATTNSTGNIFDELPATNGLQVEQPVKRDNPFFRSKRSYSLSELSVLQAKSDAPPTSSFFTGLKSPVPEQFQSREDFRTAWLNHRKLARSCHDLDLLGQSPGWGQTQAVETNIVCKLDSSGGSVQLPDTNISIHVPEGHVAPGETQQISMKALLDPPLDLNSDRSTSVSPVVEVKLSNLEVSTFIILEMKVSAEVKGDIFSKSTVVLQCLRSDSKEGPYVPIPLAYSYGDTIQVQLDNLEPCMYLAIVAQGPNILYPSTVWDFINKRVTVGLYGPKHIHPSFKTVVTIFGHDCAPKTLLVSEVTRQAPSPAPVALQLWGKHQFILSRPQDLRVCMFSNMTNYEVKANEQARVVRGFQMKLGKVSRLIFSVISQNPNELSDFTLRVQVKDDQDTILTQFCVQTPQPPPKSAIKPSGQRRFLKKNEVGKIILSPFVVTTKYPTFQDRPVSSLKFGKLLKTVVRQNKSHYLLEYKKGDVVALLSEERIRLKGQLWTKEWYIGYYQGKVGLVHTKNVLVVGKARPSLFSGPELSTSVLLEQILRPCKFLTYIYASVRTLLMENISSWRAFADALGYGNLPLTFFCRAELDSEPERVASVLEKLKEDCNNPDNKDRKSFQKELVMGIPLLEDGRWSLGVFPLTSRGQHPPAGRSTLPS
IRESfinder result
IRESfinder score
0.409892824
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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