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mmu_circNfxl1_1311
Basic information of circular RNA
PanCircBase ID:
mmu_circNfxl1_1311
mm39_Chr. Position ID:
chr5|72690387|72713688|-
Gene name:
Nfxl1
Transcript:
ENSMUST00000087216.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
12,11,10,9,8,7,6,5,4,3
Exon/intron offsets:
0,4321,5105,6561,7249,7447,7809,17247,19598,23127
Genomic length:
23301
Exon/intron sizes in nt:
91,12,31,25,11,51,01,10,00,00,00,00,00,000
Flanking exon/introns:
chr5:72686847-72690387|chr5:72713688-72716356
Splice length:
1311
Other database IDs:
circBase: hsa_circ_0069658, circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
AACTAATGTCTCAGAAGAAATTTGAGGAGATCAAGAAGTCCAATCAAGCTGCAGCCAGAAAGCTGTTGGAGGAGCACTGCAGCTCTTCCTCTGAAGAAGAAGGGGATGAAGACTTGGAAGGAAAACAGGGGAAAATTGTTGCTAATACATTCACAACATACACTACTCACACAGATGGAGATATACATGAATTAGAGCGAACAAAACAGTATCTGAATGAGGCTTTCCAAGCAGGGGCTATGACGTGCCTAATTTGTATTGCTTCAGTGAAGAGAAACCAGGCAGTTTGGAGCTGTTCAGGATGTTTCTGTATATTCCATATGCCCTGTATTCAGAAGTGGGCTAAAGACAGCCAGTTTCTTGTGTCTTCTGTGACAGACGATGATTTTGGAAAGAAAGATTATCCCTGGCCATGTCCAAAATGTAGATTTGAATACAAAAGATCAGAAACACCTAGTAGATATTATTGCTACTGTGGAAAAGTAGAAGATCCACCTTTAGATCCGTGGCTTGTACCTCATTCGTGTGGCCAAGTATGTGAGAGAGAATTTAAACCTTCTTGTGGTCATAAATGCTTGCTGCTCTGCCATCCAGGTCCCTGCCCTCCTTGTCCAAAGATGGTCACAACCACTTGTTACTGTAAGAAAGCCAAGCCTATCCCTCGCAGGTGCAGTGCCAAGCAGTGGTCCTGTCAGCTGCCATGTGGGCGAAAGCTGCTTTGTGGACATCATAAGTGTGAAAATCCTTGCCATGCAGGAAACTGTCAGCCTTGTCCAAGAGTTAGTAGACAAAAATGTGTATGTGGCAAAAAAGTAGCAGAAAGAAGTTGTGCAAGCCCAGTGTGGCATTGTGATCAAGTATGTGGAAAGACACTGCCATGTGGTAATCATACATGTGAGCAAGTTTGTCATGTTGGTGCTTGTGGAGAGTGTCCTCGATCTGGGAAGAGGTCCTGTCCATGTCAGAAATCAAAGTTTTCTTTGCCTTGTACAGAAGATGTACCAACTTGTGGAGACAGCTGTGACAAAATACTTGAATGTGGAATCCATAGGTGTTCACAGCGTTGCCACCGAGGTCCTTGTGAAACATGCAGACAAGAAGTGGAAAAACAGTGTCGTTGTGGAAAGCACACAAAGCGAATGCCTTGTCACAAGCCTTACCTTTGTGAAACAAAGTGTGTTAAAATGCGGGACTGTCAAAAGCATCAGTGTAGGAGAAAGTGTTGCCCTGGAAACTGTCCACCTTGTGATCAAAATTGTGGACGGACTTTAGGATGTAGAAACCATAAGTGTCCGTCTGTCTGCCATAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGAAAGTGTTGCCCTGGA
59.89
CAGTGCTCCTCCAACAGCTT
60.25
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGAAAGTGTTGCCCTGGA
59.89
TCCTCCAACAGCTTTCTGGC
60.25
172
PCR template sequence:
AGGAGAAAGTGTTGCCCTGGAAACTGTCCACCTTGTGATCAAAATTGTGGACGGACTTTAGGATGTAGAAACCATAAGTGTCCGTCTGTCTGCCATAGAGAACTAATGTCTCAGAAGAAATTTGAGGAGATCAAGAAGTCCAATCAAGCTGCAGCCAGAAAGCTGTTGGAGGAGCACTGCAGCTCTTCCTCTGAAGAAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-322-5p(2), mmu-miR-96-5p(2), mmu-miR-140-5p(1), mmu-miR-16-5p(1), mmu-miR-1a-3p(1), mmu-miR-375-3p(1), mmu-miR-206-3p(1), mmu-miR-34a-5p(1), mmu-miR-29a-3p(1), mmu-miR-26b-5p(1), mmu-miR-218-5p(1), mmu-miR-297a-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-802-5p(1), mmu-miR-1187(1), mmu-miR-673-5p(1), mmu-miR-697(1), mmu-miR-574-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCTGCCATAGAGAACTAATGTCTCA
siRNA sets
ACATTAGTTCTCTATGGCA, CATTAGTTCTCTATGGCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNFXL1_1311_ORF_1
1.0063
-0.113188497
0.999999689
2616
ORF sequence:
ATGTCTCAGAAGAAATTTGAGGAGATCAAGAAGTCCAATCAAGCTGCAGCCAGAAAGCTGTTGGAGGAGCACTGCAGCTCTTCCTCTGAAGAAGAAGGGGATGAAGACTTGGAAGGAAAACAGGGGAAAATTGTTGCTAATACATTCACAACATACACTACTCACACAGATGGAGATATACATGAATTAGAGCGAACAAAACAGTATCTGAATGAGGCTTTCCAAGCAGGGGCTATGACGTGCCTAATTTGTATTGCTTCAGTGAAGAGAAACCAGGCAGTTTGGAGCTGTTCAGGATGTTTCTGTATATTCCATATGCCCTGTATTCAGAAGTGGGCTAAAGACAGCCAGTTTCTTGTGTCTTCTGTGACAGACGATGATTTTGGAAAGAAAGATTATCCCTGGCCATGTCCAAAATGTAGATTTGAATACAAAAGATCAGAAACACCTAGTAGATATTATTGCTACTGTGGAAAAGTAGAAGATCCACCTTTAGATCCGTGGCTTGTACCTCATTCGTGTGGCCAAGTATGTGAGAGAGAATTTAAACCTTCTTGTGGTCATAAATGCTTGCTGCTCTGCCATCCAGGTCCCTGCCCTCCTTGTCCAAAGATGGTCACAACCACTTGTTACTGTAAGAAAGCCAAGCCTATCCCTCGCAGGTGCAGTGCCAAGCAGTGGTCCTGTCAGCTGCCATGTGGGCGAAAGCTGCTTTGTGGACATCATAAGTGTGAAAATCCTTGCCATGCAGGAAACTGTCAGCCTTGTCCAAGAGTTAGTAGACAAAAATGTGTATGTGGCAAAAAAGTAGCAGAAAGAAGTTGTGCAAGCCCAGTGTGGCATTGTGATCAAGTATGTGGAAAGACACTGCCATGTGGTAATCATACATGTGAGCAAGTTTGTCATGTTGGTGCTTGTGGAGAGTGTCCTCGATCTGGGAAGAGGTCCTGTCCATGTCAGAAATCAAAGTTTTCTTTGCCTTGTACAGAAGATGTACCAACTTGTGGAGACAGCTGTGACAAAATACTTGAATGTGGAATCCATAGGTGTTCACAGCGTTGCCACCGAGGTCCTTGTGAAACATGCAGACAAGAAGTGGAAAAACAGTGTCGTTGTGGAAAGCACACAAAGCGAATGCCTTGTCACAAGCCTTACCTTTGTGAAACAAAGTGTGTTAAAATGCGGGACTGTCAAAAGCATCAGTGTAGGAGAAAGTGTTGCCCTGGAAACTGTCCACCTTGTGATCAAAATTGTGGACGGACTTTAGGATGTAGAAACCATAAGTGTCCGTCTGTCTGCCATAGAGAACTAATGTCTCAGAAGAAATTTGAGGAGATCAAGAAGTCCAATCAAGCTGCAGCCAGAAAGCTGTTGGAGGAGCACTGCAGCTCTTCCTCTGAAGAAGAAGGGGATGAAGACTTGGAAGGAAAACAGGGGAAAATTGTTGCTAATACATTCACAACATACACTACTCACACAGATGGAGATATACATGAATTAGAGCGAACAAAACAGTATCTGAATGAGGCTTTCCAAGCAGGGGCTATGACGTGCCTAATTTGTATTGCTTCAGTGAAGAGAAACCAGGCAGTTTGGAGCTGTTCAGGATGTTTCTGTATATTCCATATGCCCTGTATTCAGAAGTGGGCTAAAGACAGCCAGTTTCTTGTGTCTTCTGTGACAGACGATGATTTTGGAAAGAAAGATTATCCCTGGCCATGTCCAAAATGTAGATTTGAATACAAAAGATCAGAAACACCTAGTAGATATTATTGCTACTGTGGAAAAGTAGAAGATCCACCTTTAGATCCGTGGCTTGTACCTCATTCGTGTGGCCAAGTATGTGAGAGAGAATTTAAACCTTCTTGTGGTCATAAATGCTTGCTGCTCTGCCATCCAGGTCCCTGCCCTCCTTGTCCAAAGATGGTCACAACCACTTGTTACTGTAAGAAAGCCAAGCCTATCCCTCGCAGGTGCAGTGCCAAGCAGTGGTCCTGTCAGCTGCCATGTGGGCGAAAGCTGCTTTGTGGACATCATAAGTGTGAAAATCCTTGCCATGCAGGAAACTGTCAGCCTTGTCCAAGAGTTAGTAGACAAAAATGTGTATGTGGCAAAAAAGTAGCAGAAAGAAGTTGTGCAAGCCCAGTGTGGCATTGTGATCAAGTATGTGGAAAGACACTGCCATGTGGTAATCATACATGTGAGCAAGTTTGTCATGTTGGTGCTTGTGGAGAGTGTCCTCGATCTGGGAAGAGGTCCTGTCCATGTCAGAAATCAAAGTTTTCTTTGCCTTGTACAGAAGATGTACCAACTTGTGGAGACAGCTGTGACAAAATACTTGAATGTGGAATCCATAGGTGTTCACAGCGTTGCCACCGAGGTCCTTGTGAAACATGCAGACAAGAAGTGGAAAAACAGTGTCGTTGTGGAAAGCACACAAAGCGAATGCCTTGTCACAAGCCTTACCTTTGTGAAACAAAGTGTGTTAAAATGCGGGACTGTCAAAAGCATCAGTGTAGGAGAAAGTGTTGCCCTGGAAACTGTCCACCTTGTGATCAAAATTGTGGACGGACTTTAGGATGTAGAAACCATAAGTGTCCGTCTGTCTGCCATAGA
Peptide sequence:
MSQKKFEEIKKSNQAAARKLLEEHCSSSSEEEGDEDLEGKQGKIVANTFTTYTTHTDGDIHELERTKQYLNEAFQAGAMTCLICIASVKRNQAVWSCSGCFCIFHMPCIQKWAKDSQFLVSSVTDDDFGKKDYPWPCPKCRFEYKRSETPSRYYCYCGKVEDPPLDPWLVPHSCGQVCEREFKPSCGHKCLLLCHPGPCPPCPKMVTTTCYCKKAKPIPRRCSAKQWSCQLPCGRKLLCGHHKCENPCHAGNCQPCPRVSRQKCVCGKKVAERSCASPVWHCDQVCGKTLPCGNHTCEQVCHVGACGECPRSGKRSCPCQKSKFSLPCTEDVPTCGDSCDKILECGIHRCSQRCHRGPCETCRQEVEKQCRCGKHTKRMPCHKPYLCETKCVKMRDCQKHQCRRKCCPGNCPPCDQNCGRTLGCRNHKCPSVCHRELMSQKKFEEIKKSNQAAARKLLEEHCSSSSEEEGDEDLEGKQGKIVANTFTTYTTHTDGDIHELERTKQYLNEAFQAGAMTCLICIASVKRNQAVWSCSGCFCIFHMPCIQKWAKDSQFLVSSVTDDDFGKKDYPWPCPKCRFEYKRSETPSRYYCYCGKVEDPPLDPWLVPHSCGQVCEREFKPSCGHKCLLLCHPGPCPPCPKMVTTTCYCKKAKPIPRRCSAKQWSCQLPCGRKLLCGHHKCENPCHAGNCQPCPRVSRQKCVCGKKVAERSCASPVWHCDQVCGKTLPCGNHTCEQVCHVGACGECPRSGKRSCPCQKSKFSLPCTEDVPTCGDSCDKILECGIHRCSQRCHRGPCETCRQEVEKQCRCGKHTKRMPCHKPYLCETKCVKMRDCQKHQCRRKCCPGNCPPCDQNCGRTLGCRNHKCPSVCHR
IRESfinder result
IRESfinder score
0.573896888
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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