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mmu_circSynrg_1689
Basic information of circular RNA
PanCircBase ID:
mmu_circSynrg_1689
mm39_Chr. Position ID:
chr11|83880505|83900376|+
Gene name:
Synrg
Transcript:
ENSMUST00000049714.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
9,10,11,12,13,14
Exon/intron offsets:
0,1015,4649,12178,12493,18938
Genomic length:
19871
Exon/intron sizes in nt:
19,72,49,13,41,13,63,900
Flanking exon/introns:
chr11:83878816-83880505|chr11:83900376-83910185
Splice length:
1689
Other database IDs:
circAtlas: mmu-Synrg_0013
circBase: hsa_circ_0043295, circAtlas: hsa-SYNRG_0013, CIRCpedia: HSA_CIRCpedia_20398
Human Ortholog IDs:
Mature spliced Sequence:
ATGCCTATAAGAAAATTTTAGAAACCACAATGACTCCAACTGGAATAGATACTGCTAAACTTTATCCCATTCTGATGTCATCTGGACTTCCCAGGGAAACTCTCGGACAGATATGGGCCTTAGCTAATCGAACCACACCTGGCAGGCTCACTAAGGAGGAGCTTTACACGGTTCTCGCCATGGTAGCAGTAACACAGAGGGGTGTTCCTGCCATGAGCCCTGATGCTTTGAGCCAGTTCCCTGCGGCTCCCATCCCTACCTTAAGCGGCTTTCCTATGACTCTGCCTACCCCAGTGAGCCAGCCAACGGCGATGCCCTCTGGCCCTACAGGCTCCATGCCCCTCACCCTTGGACAACCCATCATGGGTATCAACCTTGTTGGACCAGTGGGTGGAGCTGCAGCACCAACTTCCAGTGGCTTCATGCCAGCCTACCCATCAAACCAGGTGGGAAAGACAGAAGAAGATGACTTCCAGGATTTTCAAGATGCTTCGAAATCAGGATCCATCGATGATTCCTTCACTGACTTCCAAGAGATGCCTGCTTCCTCAAAAACCAGTAATTCCCAGCATGGAAACAGTGCTCCATCACTCTTGATCCCATTTCCTGGAACTAAAGCCTCCACAGACAAATACGCAGTGTTCAAAGGGATTTCCACTGACAAGCCCTCTGAAAACCCTGCTTCGTTTGGAGAGTCTGGTGATAAATACAGTGCTTTCAGGGAACTCGAGCAAACGACAGACAGTAAACCTTTAGGAGAGAGCTTTGCCGAGTTCAGATCCACAGGAACCGATGATGGCTTCACTGACTTCAAGACCGCCGATAGTGTGTCACCCCTAGAGCCACCCACAAAAGACACTTTCCCATCAGCTTTTGCCTCAGGAGCTGCACAGCAGACACAGACACAGGTGAAAACCCCTCTGAACTTAGAAGATCTAGATATGTTCTCCTCAGTGGATTGCAGTGGCGAGAAACAGGTGCCCTTTTCAGCTACATTTAGCACAGCAAAGTCCGTTTCCACTCGACCTCAGCCAGCGGGCTCTGCAGCAGCGTCAGCAGCACTGGCATCCACTAAAACTTCTAGTTTGGCAGATGATTTTGGAGAGTTCAACCTCTTTGGGGAGTATTCAAACCCTGCATCTGCTGGGGAGCAGGACGACTTTGCAGATTTTATGGCTTTCGGTAACAGCTCCATTTCATCTGAGCCAAAAGCAAGTGACAAGTATGAAGCCCTCAGGGAGGAAGTGAGTCCCAGCCCCTTGTCCAGCAGCACTGTGGAAGGGGCACAGCACCCACCTGCTGCGGCAACCAAGTATGATGTCTTCAAACAGCTGTCCCTAGAGGGCGCTGGGCTGGCCATGGAGGAGTTCAAAGAGAACACTTCCTCCACCAAGAGTGAAGATGACTTTGCCGACTTCCACTCCAGTAAATTCTCATCCACGAGCTCAGACAAATCCCTGGGAGAGAAAGCCGTGGCTTTCAGACATGCCAAAGAAGACTCCTCCTCGGTGAAGTCTTTAGACCTCCCCTCCATCGGTGGCAGCAGTGTTGGCAAGGAGGACTCTGAAGATGCACTTTCTGTTCAATTTGACATGAAATTGGCTGATGTGGGAGGAGATCTTAAGCATGTCATGTCTGATAGCTCTTTGGATTTACCAACAGTTAGTGGCCAGCATCCTCCTGCCGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCTGATGTGGGAGGAGAT
60.33
GTCCAGATGACATCAGAATGGGA
59.86
177
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTGATGTGGGAGGAGATC
59.6
GTCCAGATGACATCAGAATGGGA
59.86
176
PCR template sequence:
GACATGAAATTGGCTGATGTGGGAGGAGATCTTAAGCATGTCATGTCTGATAGCTCTTTGGATTTACCAACAGTTAGTGGCCAGCATCCTCCTGCCGCAGATGCCTATAAGAAAATTTTAGAAACCACAATGACTCCAACTGGAATAGATACTGCTAAACTTTATCCCATTCTGATGTCATCTGGACTTCCCAGGGAAAC
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-670-5p(2), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-135a-5p(1), mmu-miR-320-3p(1), mmu-miR-125b-5p(1), mmu-miR-24-3p(1), mmu-miR-125a-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-541-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-188-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CCTCCTGCCGCAGATGCCTATAAGAA
siRNA sets
TATAGGCATCTGCGGCAGG,TTCTTATAGGCATCTGCGG,TTATAGGCATCTGCGGCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSYNRG_1689_ORF_1
1.0127
0.221159405
1
3348
ORF sequence:
ATGACTCCAACTGGAATAGATACTGCTAAACTTTATCCCATTCTGATGTCATCTGGACTTCCCAGGGAAACTCTCGGACAGATATGGGCCTTAGCTAATCGAACCACACCTGGCAGGCTCACTAAGGAGGAGCTTTACACGGTTCTCGCCATGGTAGCAGTAACACAGAGGGGTGTTCCTGCCATGAGCCCTGATGCTTTGAGCCAGTTCCCTGCGGCTCCCATCCCTACCTTAAGCGGCTTTCCTATGACTCTGCCTACCCCAGTGAGCCAGCCAACGGCGATGCCCTCTGGCCCTACAGGCTCCATGCCCCTCACCCTTGGACAACCCATCATGGGTATCAACCTTGTTGGACCAGTGGGTGGAGCTGCAGCACCAACTTCCAGTGGCTTCATGCCAGCCTACCCATCAAACCAGGTGGGAAAGACAGAAGAAGATGACTTCCAGGATTTTCAAGATGCTTCGAAATCAGGATCCATCGATGATTCCTTCACTGACTTCCAAGAGATGCCTGCTTCCTCAAAAACCAGTAATTCCCAGCATGGAAACAGTGCTCCATCACTCTTGATCCCATTTCCTGGAACTAAAGCCTCCACAGACAAATACGCAGTGTTCAAAGGGATTTCCACTGACAAGCCCTCTGAAAACCCTGCTTCGTTTGGAGAGTCTGGTGATAAATACAGTGCTTTCAGGGAACTCGAGCAAACGACAGACAGTAAACCTTTAGGAGAGAGCTTTGCCGAGTTCAGATCCACAGGAACCGATGATGGCTTCACTGACTTCAAGACCGCCGATAGTGTGTCACCCCTAGAGCCACCCACAAAAGACACTTTCCCATCAGCTTTTGCCTCAGGAGCTGCACAGCAGACACAGACACAGGTGAAAACCCCTCTGAACTTAGAAGATCTAGATATGTTCTCCTCAGTGGATTGCAGTGGCGAGAAACAGGTGCCCTTTTCAGCTACATTTAGCACAGCAAAGTCCGTTTCCACTCGACCTCAGCCAGCGGGCTCTGCAGCAGCGTCAGCAGCACTGGCATCCACTAAAACTTCTAGTTTGGCAGATGATTTTGGAGAGTTCAACCTCTTTGGGGAGTATTCAAACCCTGCATCTGCTGGGGAGCAGGACGACTTTGCAGATTTTATGGCTTTCGGTAACAGCTCCATTTCATCTGAGCCAAAAGCAAGTGACAAGTATGAAGCCCTCAGGGAGGAAGTGAGTCCCAGCCCCTTGTCCAGCAGCACTGTGGAAGGGGCACAGCACCCACCTGCTGCGGCAACCAAGTATGATGTCTTCAAACAGCTGTCCCTAGAGGGCGCTGGGCTGGCCATGGAGGAGTTCAAAGAGAACACTTCCTCCACCAAGAGTGAAGATGACTTTGCCGACTTCCACTCCAGTAAATTCTCATCCACGAGCTCAGACAAATCCCTGGGAGAGAAAGCCGTGGCTTTCAGACATGCCAAAGAAGACTCCTCCTCGGTGAAGTCTTTAGACCTCCCCTCCATCGGTGGCAGCAGTGTTGGCAAGGAGGACTCTGAAGATGCACTTTCTGTTCAATTTGACATGAAATTGGCTGATGTGGGAGGAGATCTTAAGCATGTCATGTCTGATAGCTCTTTGGATTTACCAACAGTTAGTGGCCAGCATCCTCCTGCCGCAGATGCCTATAAGAAAATTTTAGAAACCACAATGACTCCAACTGGAATAGATACTGCTAAACTTTATCCCATTCTGATGTCATCTGGACTTCCCAGGGAAACTCTCGGACAGATATGGGCCTTAGCTAATCGAACCACACCTGGCAGGCTCACTAAGGAGGAGCTTTACACGGTTCTCGCCATGGTAGCAGTAACACAGAGGGGTGTTCCTGCCATGAGCCCTGATGCTTTGAGCCAGTTCCCTGCGGCTCCCATCCCTACCTTAAGCGGCTTTCCTATGACTCTGCCTACCCCAGTGAGCCAGCCAACGGCGATGCCCTCTGGCCCTACAGGCTCCATGCCCCTCACCCTTGGACAACCCATCATGGGTATCAACCTTGTTGGACCAGTGGGTGGAGCTGCAGCACCAACTTCCAGTGGCTTCATGCCAGCCTACCCATCAAACCAGGTGGGAAAGACAGAAGAAGATGACTTCCAGGATTTTCAAGATGCTTCGAAATCAGGATCCATCGATGATTCCTTCACTGACTTCCAAGAGATGCCTGCTTCCTCAAAAACCAGTAATTCCCAGCATGGAAACAGTGCTCCATCACTCTTGATCCCATTTCCTGGAACTAAAGCCTCCACAGACAAATACGCAGTGTTCAAAGGGATTTCCACTGACAAGCCCTCTGAAAACCCTGCTTCGTTTGGAGAGTCTGGTGATAAATACAGTGCTTTCAGGGAACTCGAGCAAACGACAGACAGTAAACCTTTAGGAGAGAGCTTTGCCGAGTTCAGATCCACAGGAACCGATGATGGCTTCACTGACTTCAAGACCGCCGATAGTGTGTCACCCCTAGAGCCACCCACAAAAGACACTTTCCCATCAGCTTTTGCCTCAGGAGCTGCACAGCAGACACAGACACAGGTGAAAACCCCTCTGAACTTAGAAGATCTAGATATGTTCTCCTCAGTGGATTGCAGTGGCGAGAAACAGGTGCCCTTTTCAGCTACATTTAGCACAGCAAAGTCCGTTTCCACTCGACCTCAGCCAGCGGGCTCTGCAGCAGCGTCAGCAGCACTGGCATCCACTAAAACTTCTAGTTTGGCAGATGATTTTGGAGAGTTCAACCTCTTTGGGGAGTATTCAAACCCTGCATCTGCTGGGGAGCAGGACGACTTTGCAGATTTTATGGCTTTCGGTAACAGCTCCATTTCATCTGAGCCAAAAGCAAGTGACAAGTATGAAGCCCTCAGGGAGGAAGTGAGTCCCAGCCCCTTGTCCAGCAGCACTGTGGAAGGGGCACAGCACCCACCTGCTGCGGCAACCAAGTATGATGTCTTCAAACAGCTGTCCCTAGAGGGCGCTGGGCTGGCCATGGAGGAGTTCAAAGAGAACACTTCCTCCACCAAGAGTGAAGATGACTTTGCCGACTTCCACTCCAGTAAATTCTCATCCACGAGCTCAGACAAATCCCTGGGAGAGAAAGCCGTGGCTTTCAGACATGCCAAAGAAGACTCCTCCTCGGTGAAGTCTTTAGACCTCCCCTCCATCGGTGGCAGCAGTGTTGGCAAGGAGGACTCTGAAGATGCACTTTCTGTTCAATTTGACATGAAATTGGCTGATGTGGGAGGAGATCTTAAGCATGTCATGTCTGATAGCTCTTTGGATTTACCAACAGTTAGTGGCCAGCATCCTCCTGCCGCA
Peptide sequence:
MTPTGIDTAKLYPILMSSGLPRETLGQIWALANRTTPGRLTKEELYTVLAMVAVTQRGVPAMSPDALSQFPAAPIPTLSGFPMTLPTPVSQPTAMPSGPTGSMPLTLGQPIMGINLVGPVGGAAAPTSSGFMPAYPSNQVGKTEEDDFQDFQDASKSGSIDDSFTDFQEMPASSKTSNSQHGNSAPSLLIPFPGTKASTDKYAVFKGISTDKPSENPASFGESGDKYSAFRELEQTTDSKPLGESFAEFRSTGTDDGFTDFKTADSVSPLEPPTKDTFPSAFASGAAQQTQTQVKTPLNLEDLDMFSSVDCSGEKQVPFSATFSTAKSVSTRPQPAGSAAASAALASTKTSSLADDFGEFNLFGEYSNPASAGEQDDFADFMAFGNSSISSEPKASDKYEALREEVSPSPLSSSTVEGAQHPPAAATKYDVFKQLSLEGAGLAMEEFKENTSSTKSEDDFADFHSSKFSSTSSDKSLGEKAVAFRHAKEDSSSVKSLDLPSIGGSSVGKEDSEDALSVQFDMKLADVGGDLKHVMSDSSLDLPTVSGQHPPAADAYKKILETTMTPTGIDTAKLYPILMSSGLPRETLGQIWALANRTTPGRLTKEELYTVLAMVAVTQRGVPAMSPDALSQFPAAPIPTLSGFPMTLPTPVSQPTAMPSGPTGSMPLTLGQPIMGINLVGPVGGAAAPTSSGFMPAYPSNQVGKTEEDDFQDFQDASKSGSIDDSFTDFQEMPASSKTSNSQHGNSAPSLLIPFPGTKASTDKYAVFKGISTDKPSENPASFGESGDKYSAFRELEQTTDSKPLGESFAEFRSTGTDDGFTDFKTADSVSPLEPPTKDTFPSAFASGAAQQTQTQVKTPLNLEDLDMFSSVDCSGEKQVPFSATFSTAKSVSTRPQPAGSAAASAALASTKTSSLADDFGEFNLFGEYSNPASAGEQDDFADFMAFGNSSISSEPKASDKYEALREEVSPSPLSSSTVEGAQHPPAAATKYDVFKQLSLEGAGLAMEEFKENTSSTKSEDDFADFHSSKFSSTSSDKSLGEKAVAFRHAKEDSSSVKSLDLPSIGGSSVGKEDSEDALSVQFDMKLADVGGDLKHVMSDSSLDLPTVSGQHPPAA
IRESfinder result
IRESfinder score
0.51484599
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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