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mmu_circNfxl1_1684
Basic information of circular RNA
PanCircBase ID:
mmu_circNfxl1_1684
mm39_Chr. Position ID:
chr5|72685501|72713688|-
Gene name:
Nfxl1
Transcript:
ENSMUST00000087216.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
13
Exon/intron indexes:
15,14,13,12,11,10,9,8,7,6,5,4,3
Exon/intron offsets:
0,853,1225,4886,9207,9991,11447,12135,12333,12695,22133,24484,28013
Genomic length:
28187
Exon/intron sizes in nt:
92,16,01,21,91,12,31,20,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr5:72682011-72685501|chr5:72713688-72716356
Splice length:
1684
Other database IDs:
circBase: hsa_circ_0069654, circAtlas: hsa-NFXL1_0016, CIRCpedia: HSA_CIRCpedia_117728
Human Ortholog IDs:
Mature spliced Sequence:
AACTAATGTCTCAGAAGAAATTTGAGGAGATCAAGAAGTCCAATCAAGCTGCAGCCAGAAAGCTGTTGGAGGAGCACTGCAGCTCTTCCTCTGAAGAAGAAGGGGATGAAGACTTGGAAGGAAAACAGGGGAAAATTGTTGCTAATACATTCACAACATACACTACTCACACAGATGGAGATATACATGAATTAGAGCGAACAAAACAGTATCTGAATGAGGCTTTCCAAGCAGGGGCTATGACGTGCCTAATTTGTATTGCTTCAGTGAAGAGAAACCAGGCAGTTTGGAGCTGTTCAGGATGTTTCTGTATATTCCATATGCCCTGTATTCAGAAGTGGGCTAAAGACAGCCAGTTTCTTGTGTCTTCTGTGACAGACGATGATTTTGGAAAGAAAGATTATCCCTGGCCATGTCCAAAATGTAGATTTGAATACAAAAGATCAGAAACACCTAGTAGATATTATTGCTACTGTGGAAAAGTAGAAGATCCACCTTTAGATCCGTGGCTTGTACCTCATTCGTGTGGCCAAGTATGTGAGAGAGAATTTAAACCTTCTTGTGGTCATAAATGCTTGCTGCTCTGCCATCCAGGTCCCTGCCCTCCTTGTCCAAAGATGGTCACAACCACTTGTTACTGTAAGAAAGCCAAGCCTATCCCTCGCAGGTGCAGTGCCAAGCAGTGGTCCTGTCAGCTGCCATGTGGGCGAAAGCTGCTTTGTGGACATCATAAGTGTGAAAATCCTTGCCATGCAGGAAACTGTCAGCCTTGTCCAAGAGTTAGTAGACAAAAATGTGTATGTGGCAAAAAAGTAGCAGAAAGAAGTTGTGCAAGCCCAGTGTGGCATTGTGATCAAGTATGTGGAAAGACACTGCCATGTGGTAATCATACATGTGAGCAAGTTTGTCATGTTGGTGCTTGTGGAGAGTGTCCTCGATCTGGGAAGAGGTCCTGTCCATGTCAGAAATCAAAGTTTTCTTTGCCTTGTACAGAAGATGTACCAACTTGTGGAGACAGCTGTGACAAAATACTTGAATGTGGAATCCATAGGTGTTCACAGCGTTGCCACCGAGGTCCTTGTGAAACATGCAGACAAGAAGTGGAAAAACAGTGTCGTTGTGGAAAGCACACAAAGCGAATGCCTTGTCACAAGCCTTACCTTTGTGAAACAAAGTGTGTTAAAATGCGGGACTGTCAAAAGCATCAGTGTAGGAGAAAGTGTTGCCCTGGAAACTGTCCACCTTGTGATCAAAATTGTGGACGGACTTTAGGATGTAGAAACCATAAGTGTCCGTCTGTCTGCCATAGAGGCAGTTGCTATCCATGTCCAGAAACGGTAGATGTGAAGTGCAATTGTGGTAATGCAAAGGTGACAGTACCCTGTGGCCGAGAGCGGACCACAAGGCCACCTAAGTGCAAAGAGCTGTGCAGTCGACCACCAACATGTCATCATGCAAGTCAAGAAAAACACCGCTGTCACTTTGGCCCATGTCCACCGTGCCATCAGCCTTGCCAAAAAGTTCTGGAGAAGTGTGGGCACTTGTGTCCTGAGTCATGCCATGATCAAGCATTAGTAAAGCAGACTGGCAGGCATCAGCCATCAGGCCCTTGGGAGCAGCCAGCTGAGCCTGCATTCATCCAGACGGCCCTGCCTTGCCCTCCGTGTCAAGTTCCCATCCCTGT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTGAGCCTGCATTCATCC
60.47
CAGTGCTCCTCCAACAGCTT
60.25
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCTGAGCCTGCATTCATC
59.34
CAGTGCTCCTCCAACAGCTT
60.25
143
PCR template sequence:
CTGGCAGGCATCAGCCATCAGGCCCTTGGGAGCAGCCAGCTGAGCCTGCATTCATCCAGACGGCCCTGCCTTGCCCTCCGTGTCAAGTTCCCATCCCTGTAACTAATGTCTCAGAAGAAATTTGAGGAGATCAAGAAGTCCAATCAAGCTGCAGCCAGAAAGCTGTTGGAGGAGCACTGCAGCTCTTCCTCTGAAGAAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
27
Interacting miRNAs (#binding sites)
mmu-miR-322-5p(2), mmu-miR-96-5p(2), mmu-miR-140-5p(1), mmu-miR-155-5p(1), mmu-miR-16-5p(1), mmu-miR-1a-3p(1), mmu-miR-32-5p(1), mmu-miR-375-3p(1), mmu-miR-206-3p(1), mmu-miR-34a-5p(1), mmu-miR-92a-3p(1), mmu-miR-29a-3p(1), mmu-miR-25-3p(1), mmu-miR-363-3p(1), mmu-miR-26b-5p(1), mmu-miR-182-5p(1), mmu-miR-218-5p(1), mmu-miR-183-5p(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-484(1), mmu-miR-697(1), mmu-miR-574-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCCCATCCCTGTAACTAATGTCTCA
siRNA sets
ATTAGTTACAGGGATGGGA,GAGACATTAGTTACAGGGA,CATTAGTTACAGGGATGGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNFXL1_1684_ORF_1
1.0327
-0.085276952
0.999805837
1704
ORF sequence:
ATGTCTCAGAAGAAATTTGAGGAGATCAAGAAGTCCAATCAAGCTGCAGCCAGAAAGCTGTTGGAGGAGCACTGCAGCTCTTCCTCTGAAGAAGAAGGGGATGAAGACTTGGAAGGAAAACAGGGGAAAATTGTTGCTAATACATTCACAACATACACTACTCACACAGATGGAGATATACATGAATTAGAGCGAACAAAACAGTATCTGAATGAGGCTTTCCAAGCAGGGGCTATGACGTGCCTAATTTGTATTGCTTCAGTGAAGAGAAACCAGGCAGTTTGGAGCTGTTCAGGATGTTTCTGTATATTCCATATGCCCTGTATTCAGAAGTGGGCTAAAGACAGCCAGTTTCTTGTGTCTTCTGTGACAGACGATGATTTTGGAAAGAAAGATTATCCCTGGCCATGTCCAAAATGTAGATTTGAATACAAAAGATCAGAAACACCTAGTAGATATTATTGCTACTGTGGAAAAGTAGAAGATCCACCTTTAGATCCGTGGCTTGTACCTCATTCGTGTGGCCAAGTATGTGAGAGAGAATTTAAACCTTCTTGTGGTCATAAATGCTTGCTGCTCTGCCATCCAGGTCCCTGCCCTCCTTGTCCAAAGATGGTCACAACCACTTGTTACTGTAAGAAAGCCAAGCCTATCCCTCGCAGGTGCAGTGCCAAGCAGTGGTCCTGTCAGCTGCCATGTGGGCGAAAGCTGCTTTGTGGACATCATAAGTGTGAAAATCCTTGCCATGCAGGAAACTGTCAGCCTTGTCCAAGAGTTAGTAGACAAAAATGTGTATGTGGCAAAAAAGTAGCAGAAAGAAGTTGTGCAAGCCCAGTGTGGCATTGTGATCAAGTATGTGGAAAGACACTGCCATGTGGTAATCATACATGTGAGCAAGTTTGTCATGTTGGTGCTTGTGGAGAGTGTCCTCGATCTGGGAAGAGGTCCTGTCCATGTCAGAAATCAAAGTTTTCTTTGCCTTGTACAGAAGATGTACCAACTTGTGGAGACAGCTGTGACAAAATACTTGAATGTGGAATCCATAGGTGTTCACAGCGTTGCCACCGAGGTCCTTGTGAAACATGCAGACAAGAAGTGGAAAAACAGTGTCGTTGTGGAAAGCACACAAAGCGAATGCCTTGTCACAAGCCTTACCTTTGTGAAACAAAGTGTGTTAAAATGCGGGACTGTCAAAAGCATCAGTGTAGGAGAAAGTGTTGCCCTGGAAACTGTCCACCTTGTGATCAAAATTGTGGACGGACTTTAGGATGTAGAAACCATAAGTGTCCGTCTGTCTGCCATAGAGGCAGTTGCTATCCATGTCCAGAAACGGTAGATGTGAAGTGCAATTGTGGTAATGCAAAGGTGACAGTACCCTGTGGCCGAGAGCGGACCACAAGGCCACCTAAGTGCAAAGAGCTGTGCAGTCGACCACCAACATGTCATCATGCAAGTCAAGAAAAACACCGCTGTCACTTTGGCCCATGTCCACCGTGCCATCAGCCTTGCCAAAAAGTTCTGGAGAAGTGTGGGCACTTGTGTCCTGAGTCATGCCATGATCAAGCATTAGTAAAGCAGACTGGCAGGCATCAGCCATCAGGCCCTTGGGAGCAGCCAGCTGAGCCTGCATTCATCCAGACGGCCCTGCCTTGCCCTCCGTGTCAAGTTCCCATCCCTGTAACTAATGTCTCAGAAGAAATTTGA
Peptide sequence:
MSQKKFEEIKKSNQAAARKLLEEHCSSSSEEEGDEDLEGKQGKIVANTFTTYTTHTDGDIHELERTKQYLNEAFQAGAMTCLICIASVKRNQAVWSCSGCFCIFHMPCIQKWAKDSQFLVSSVTDDDFGKKDYPWPCPKCRFEYKRSETPSRYYCYCGKVEDPPLDPWLVPHSCGQVCEREFKPSCGHKCLLLCHPGPCPPCPKMVTTTCYCKKAKPIPRRCSAKQWSCQLPCGRKLLCGHHKCENPCHAGNCQPCPRVSRQKCVCGKKVAERSCASPVWHCDQVCGKTLPCGNHTCEQVCHVGACGECPRSGKRSCPCQKSKFSLPCTEDVPTCGDSCDKILECGIHRCSQRCHRGPCETCRQEVEKQCRCGKHTKRMPCHKPYLCETKCVKMRDCQKHQCRRKCCPGNCPPCDQNCGRTLGCRNHKCPSVCHRGSCYPCPETVDVKCNCGNAKVTVPCGRERTTRPPKCKELCSRPPTCHHASQEKHRCHFGPCPPCHQPCQKVLEKCGHLCPESCHDQALVKQTGRHQPSGPWEQPAEPAFIQTALPCPPCQVPIPVTNVSEEI
IRESfinder result
IRESfinder score
0.495196633
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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