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mmu_circSnx29_1173
Basic information of circular RNA
PanCircBase ID:
mmu_circSnx29_1173
mm39_Chr. Position ID:
chr16|11217628|11265372|+
Gene name:
Snx29
Transcript:
ENSMUST00000180792.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
6,7,8,9,10,11,12,13
Exon/intron offsets:
0,1036,3695,13461,19058,20939,45400,47615
Genomic length:
47744
Exon/intron sizes in nt:
7,12,49,37,31,31,76,80,00,000
Flanking exon/introns:
chr16:11213263-11217628|chr16:11265372-11328823
Splice length:
1173
Other database IDs:
circAtlas: mmu-Snx29_0020
Human Ortholog IDs:
Mature spliced Sequence:
CACATTCTATGAAGATTGGTCTTTTGTGATGGATGAAGAAAGGTCCAGCATGCTCCCTACCATGGCAGCTGGTCTGAACTCCATACTCTTTGCAATTAACATTGACAATAAGGATTTGAATGGGCAGAGCAAATTTGCTCCCACTGTCTCTGACCTCTTAAAGGAGTCAACGCAGAATGTGACATCTTTGCTGAAGGAGTCCACACAGGGCATGAGCAGCCTTCTCAGGGAGATCACAGCATCCTCTGCTGTCTCCATTCTCATCAAGCCAGAGCAGGAGACTGACCCTCTGCCTGTCATATCCAAGAACGTTCATGTTGATACCCGATGTAAAAGGGAGCGGAGAAGGAGGAAGAAGGTGACCAACATTGTCTCTTTTGATGATGATGAGGAGGAGCAGGGTACTGGGGACACTTTAAAAAAGATGCCTGGGACTGCAGAAAGCTCGGAGGAGAACTCTGACCGATCCTCCGTCAACATCATGGCAGCCTTTGAAGGCACCTTTGGGCCAAATTCCAACGGGAGCCAGAGCAGCAGCTCATGGAAGATTGATTCTGCGTCTTTGAATGGGGAGCTGGGCTACCAGAAGCTTGATGTGAAGAGCATTGATGACGACGTGGATGAGAACGAGGAGGATGCGTACAGGAGCCCGCTAGGAAGGGGGCACACTGGCCACGCGGAGTCGCCAGACAGGACACTGGATGGGAACGCCTGCCTGGCCCAGGTCCATGGCTGGGCTCCACTGCAGGTGCTTCATGGAGATGCGGATGCTGACACTGATGTACTCTTCCCTGTCAGTGGAGTGGGCTCCTATGGTGCAGCAGATGCCCCTGTGGGAAGTCTGGAGAATGGAACAGGAACAGAAAACCATATAATCCCAGAGCCTGGCCTTCGGTACAGGGAAGCCAGTTCTCCAGGCCAAGGAAGTCCTCTGAGCAGCTTGCTACCTTCTGCCTCAGTGCCTGAGTCCATGACAGTCCATGAACTGCGCCAAGCCATCGTGGCCATGATGAACAGAAAGGATGAATTGGAAGAAGAGAATGGGTCACTGCGGAATCTCCTTGACGGTGAGATGGAGCACTCAGCAGCGCTCCGGCAAGAGGTGGATGCCCTGAGGCGGAAGGTGACAGAACAGCAGGAGCGCCATGCCACAAAGGTCCAGGCACTGGCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAAGAGGTGGATGCCCTGAG
60.11
GAGTTCAGACCAGCTGCCAT
60.04
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAAGAGGTGGATGCCCTGAG
60.11
ATGGAGTTCAGACCAGCTGC
60.04
161
PCR template sequence:
TGGAGCACTCAGCAGCGCTCCGGCAAGAGGTGGATGCCCTGAGGCGGAAGGTGACAGAACAGCAGGAGCGCCATGCCACAAAGGTCCAGGCACTGGCCAGCACATTCTATGAAGATTGGTCTTTTGTGATGGATGAAGAAAGGTCCAGCATGCTCCCTACCATGGCAGCTGGTCTGAACTCCATACTCTTTGCAATTAAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
21
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(2), mmu-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-146a-5p(1), mmu-miR-18a-5p(1), mmu-miR-298-5p(1), mmu-miR-709(1), mmu-let-7d-5p(1), mmu-miR-351-5p(1), mmu-miR-22-3p(1), mmu-miR-370-3p(1), mmu-miR-98-5p(1), mmu-miR-680(1), mmu-miR-129-5p(1), mmu-miR-207(1), mmu-miR-540-3p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGGCACTGGCCAGCACATTCTATGAA
siRNA sets
TTCATAGAATGTGCTGGCC, TAGAATGTGCTGGCCAGTG, CATAGAATGTGCTGGCCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSNX29_1173_ORF_1
1.209
0.370640452
0.999999744
2316
ORF sequence:
ATGGATGAAGAAAGGTCCAGCATGCTCCCTACCATGGCAGCTGGTCTGAACTCCATACTCTTTGCAATTAACATTGACAATAAGGATTTGAATGGGCAGAGCAAATTTGCTCCCACTGTCTCTGACCTCTTAAAGGAGTCAACGCAGAATGTGACATCTTTGCTGAAGGAGTCCACACAGGGCATGAGCAGCCTTCTCAGGGAGATCACAGCATCCTCTGCTGTCTCCATTCTCATCAAGCCAGAGCAGGAGACTGACCCTCTGCCTGTCATATCCAAGAACGTTCATGTTGATACCCGATGTAAAAGGGAGCGGAGAAGGAGGAAGAAGGTGACCAACATTGTCTCTTTTGATGATGATGAGGAGGAGCAGGGTACTGGGGACACTTTAAAAAAGATGCCTGGGACTGCAGAAAGCTCGGAGGAGAACTCTGACCGATCCTCCGTCAACATCATGGCAGCCTTTGAAGGCACCTTTGGGCCAAATTCCAACGGGAGCCAGAGCAGCAGCTCATGGAAGATTGATTCTGCGTCTTTGAATGGGGAGCTGGGCTACCAGAAGCTTGATGTGAAGAGCATTGATGACGACGTGGATGAGAACGAGGAGGATGCGTACAGGAGCCCGCTAGGAAGGGGGCACACTGGCCACGCGGAGTCGCCAGACAGGACACTGGATGGGAACGCCTGCCTGGCCCAGGTCCATGGCTGGGCTCCACTGCAGGTGCTTCATGGAGATGCGGATGCTGACACTGATGTACTCTTCCCTGTCAGTGGAGTGGGCTCCTATGGTGCAGCAGATGCCCCTGTGGGAAGTCTGGAGAATGGAACAGGAACAGAAAACCATATAATCCCAGAGCCTGGCCTTCGGTACAGGGAAGCCAGTTCTCCAGGCCAAGGAAGTCCTCTGAGCAGCTTGCTACCTTCTGCCTCAGTGCCTGAGTCCATGACAGTCCATGAACTGCGCCAAGCCATCGTGGCCATGATGAACAGAAAGGATGAATTGGAAGAAGAGAATGGGTCACTGCGGAATCTCCTTGACGGTGAGATGGAGCACTCAGCAGCGCTCCGGCAAGAGGTGGATGCCCTGAGGCGGAAGGTGACAGAACAGCAGGAGCGCCATGCCACAAAGGTCCAGGCACTGGCCAGCACATTCTATGAAGATTGGTCTTTTGTGATGGATGAAGAAAGGTCCAGCATGCTCCCTACCATGGCAGCTGGTCTGAACTCCATACTCTTTGCAATTAACATTGACAATAAGGATTTGAATGGGCAGAGCAAATTTGCTCCCACTGTCTCTGACCTCTTAAAGGAGTCAACGCAGAATGTGACATCTTTGCTGAAGGAGTCCACACAGGGCATGAGCAGCCTTCTCAGGGAGATCACAGCATCCTCTGCTGTCTCCATTCTCATCAAGCCAGAGCAGGAGACTGACCCTCTGCCTGTCATATCCAAGAACGTTCATGTTGATACCCGATGTAAAAGGGAGCGGAGAAGGAGGAAGAAGGTGACCAACATTGTCTCTTTTGATGATGATGAGGAGGAGCAGGGTACTGGGGACACTTTAAAAAAGATGCCTGGGACTGCAGAAAGCTCGGAGGAGAACTCTGACCGATCCTCCGTCAACATCATGGCAGCCTTTGAAGGCACCTTTGGGCCAAATTCCAACGGGAGCCAGAGCAGCAGCTCATGGAAGATTGATTCTGCGTCTTTGAATGGGGAGCTGGGCTACCAGAAGCTTGATGTGAAGAGCATTGATGACGACGTGGATGAGAACGAGGAGGATGCGTACAGGAGCCCGCTAGGAAGGGGGCACACTGGCCACGCGGAGTCGCCAGACAGGACACTGGATGGGAACGCCTGCCTGGCCCAGGTCCATGGCTGGGCTCCACTGCAGGTGCTTCATGGAGATGCGGATGCTGACACTGATGTACTCTTCCCTGTCAGTGGAGTGGGCTCCTATGGTGCAGCAGATGCCCCTGTGGGAAGTCTGGAGAATGGAACAGGAACAGAAAACCATATAATCCCAGAGCCTGGCCTTCGGTACAGGGAAGCCAGTTCTCCAGGCCAAGGAAGTCCTCTGAGCAGCTTGCTACCTTCTGCCTCAGTGCCTGAGTCCATGACAGTCCATGAACTGCGCCAAGCCATCGTGGCCATGATGAACAGAAAGGATGAATTGGAAGAAGAGAATGGGTCACTGCGGAATCTCCTTGACGGTGAGATGGAGCACTCAGCAGCGCTCCGGCAAGAGGTGGATGCCCTGAGGCGGAAGGTGACAGAACAGCAGGAGCGCCATGCCACAAAGGTCCAGGCACTGGCC
Peptide sequence:
MDEERSSMLPTMAAGLNSILFAINIDNKDLNGQSKFAPTVSDLLKESTQNVTSLLKESTQGMSSLLREITASSAVSILIKPEQETDPLPVISKNVHVDTRCKRERRRRKKVTNIVSFDDDEEEQGTGDTLKKMPGTAESSEENSDRSSVNIMAAFEGTFGPNSNGSQSSSSWKIDSASLNGELGYQKLDVKSIDDDVDENEEDAYRSPLGRGHTGHAESPDRTLDGNACLAQVHGWAPLQVLHGDADADTDVLFPVSGVGSYGAADAPVGSLENGTGTENHIIPEPGLRYREASSPGQGSPLSSLLPSASVPESMTVHELRQAIVAMMNRKDELEEENGSLRNLLDGEMEHSAALRQEVDALRRKVTEQQERHATKVQALASTFYEDWSFVMDEERSSMLPTMAAGLNSILFAINIDNKDLNGQSKFAPTVSDLLKESTQNVTSLLKESTQGMSSLLREITASSAVSILIKPEQETDPLPVISKNVHVDTRCKRERRRRKKVTNIVSFDDDEEEQGTGDTLKKMPGTAESSEENSDRSSVNIMAAFEGTFGPNSNGSQSSSSWKIDSASLNGELGYQKLDVKSIDDDVDENEEDAYRSPLGRGHTGHAESPDRTLDGNACLAQVHGWAPLQVLHGDADADTDVLFPVSGVGSYGAADAPVGSLENGTGTENHIIPEPGLRYREASSPGQGSPLSSLLPSASVPESMTVHELRQAIVAMMNRKDELEEENGSLRNLLDGEMEHSAALRQEVDALRRKVTEQQERHATKVQALA
IRESfinder result
IRESfinder score
0.280963241
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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