top of page
mmu_circNfxl1_2102
Basic information of circular RNA
PanCircBase ID:
mmu_circNfxl1_2102
mm39_Chr. Position ID:
chr5|72674368|72710095|-
Gene name:
Nfxl1
Transcript:
ENSMUST00000087216.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
18
Exon/intron indexes:
21,20,19,18,17,16,15,14,13,12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,1169,5122,6483,7061,7621,11133,11986,12358,16019,20340,21124,22580,23268,23466,23828,33266,35617
Genomic length:
35727
Exon/intron sizes in nt:
87,10,57,01,67,14,12,20,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr5:72673608-72674368|chr5:72710095-72713514
Splice length:
2102
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATGGAGATATACATGAATTAGAGCGAACAAAACAGTATCTGAATGAGGCTTTCCAAGCAGGGGCTATGACGTGCCTAATTTGTATTGCTTCAGTGAAGAGAAACCAGGCAGTTTGGAGCTGTTCAGGATGTTTCTGTATATTCCATATGCCCTGTATTCAGAAGTGGGCTAAAGACAGCCAGTTTCTTGTGTCTTCTGTGACAGACGATGATTTTGGAAAGAAAGATTATCCCTGGCCATGTCCAAAATGTAGATTTGAATACAAAAGATCAGAAACACCTAGTAGATATTATTGCTACTGTGGAAAAGTAGAAGATCCACCTTTAGATCCGTGGCTTGTACCTCATTCGTGTGGCCAAGTATGTGAGAGAGAATTTAAACCTTCTTGTGGTCATAAATGCTTGCTGCTCTGCCATCCAGGTCCCTGCCCTCCTTGTCCAAAGATGGTCACAACCACTTGTTACTGTAAGAAAGCCAAGCCTATCCCTCGCAGGTGCAGTGCCAAGCAGTGGTCCTGTCAGCTGCCATGTGGGCGAAAGCTGCTTTGTGGACATCATAAGTGTGAAAATCCTTGCCATGCAGGAAACTGTCAGCCTTGTCCAAGAGTTAGTAGACAAAAATGTGTATGTGGCAAAAAAGTAGCAGAAAGAAGTTGTGCAAGCCCAGTGTGGCATTGTGATCAAGTATGTGGAAAGACACTGCCATGTGGTAATCATACATGTGAGCAAGTTTGTCATGTTGGTGCTTGTGGAGAGTGTCCTCGATCTGGGAAGAGGTCCTGTCCATGTCAGAAATCAAAGTTTTCTTTGCCTTGTACAGAAGATGTACCAACTTGTGGAGACAGCTGTGACAAAATACTTGAATGTGGAATCCATAGGTGTTCACAGCGTTGCCACCGAGGTCCTTGTGAAACATGCAGACAAGAAGTGGAAAAACAGTGTCGTTGTGGAAAGCACACAAAGCGAATGCCTTGTCACAAGCCTTACCTTTGTGAAACAAAGTGTGTTAAAATGCGGGACTGTCAAAAGCATCAGTGTAGGAGAAAGTGTTGCCCTGGAAACTGTCCACCTTGTGATCAAAATTGTGGACGGACTTTAGGATGTAGAAACCATAAGTGTCCGTCTGTCTGCCATAGAGGCAGTTGCTATCCATGTCCAGAAACGGTAGATGTGAAGTGCAATTGTGGTAATGCAAAGGTGACAGTACCCTGTGGCCGAGAGCGGACCACAAGGCCACCTAAGTGCAAAGAGCTGTGCAGTCGACCACCAACATGTCATCATGCAAGTCAAGAAAAACACCGCTGTCACTTTGGCCCATGTCCACCGTGCCATCAGCCTTGCCAAAAAGTTCTGGAGAAGTGTGGGCACTTGTGTCCTGAGTCATGCCATGATCAAGCATTAGTAAAGCAGACTGGCAGGCATCAGCCATCAGGCCCTTGGGAGCAGCCAGCTGAGCCTGCATTCATCCAGACGGCCCTGCCTTGCCCTCCGTGTCAAGTTCCCATCCCTGTGGAATGTCTGGGGAAGCATGAGGTGAGCCCACTACCATGCCATGCTGTAGGACCCTATTCTTGCAAGAGACTTTGTGGAAGAATGTTGCGCTGTCAGAATCATACATGTATGAAAGAGTGCCACAAAGTTACTGAAGTTGATAGCTCTACTGGCAAAAATAAGGCTGGCCCAGAATGCTTTCACTGTGAAGAAGGGTGCTCTAAGTCACGGCCTGCGGGTTGTCCTCACCCTTGTGTTTTGCCATGTCACCCTGGAAAATGCCCTCCTTGTGTCCAGATGCTTAGAATAAAATGTCACTGCAAGATCACAAGCCTGTATGTGGAATGTAGAAAAATAACCACAGCTGATGTAAGCGAAAAGAACCTCCTCAGTTGCTGCAAAAACCAGTGCCCCAAAGAGCTTCCTTGTGGCCACAGATGCAAAGAGATGTGCCATCCTGGTGAATGCCCCTTTAATTGCAACCAGAAGGTAAAACTTAGATGCCCTTGTAAAAGAATAAAACGGGAGTTGCCTTGCAATAAAGTACGTGAAAATCAGGTTTCAGTTGAATGTGATGCAACGTGCAAGGAGATGAAGCGGAAAGCGTCTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGGGAGTTGCCTTGCAA
59.81
GGCACGTCATAGCCCCTG
60.2
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGGGAGTTGCCTTGCAA
59.81
GCACGTCATAGCCCCTGC
60.9
165
PCR template sequence:
AAGAATAAAACGGGAGTTGCCTTGCAATAAAGTACGTGAAAATCAGGTTTCAGTTGAATGTGATGCAACGTGCAAGGAGATGAAGCGGAAAGCGTCTGAGATGGAGATATACATGAATTAGAGCGAACAAAACAGTATCTGAATGAGGCTTTCCAAGCAGGGGCTATGACGTGCCTAATTTGTATTGCTTCAGTGAAGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
31
Interacting miRNAs (#binding sites)
mmu-miR-96-5p(2), mmu-miR-129-5p(2), mmu-miR-140-5p(1), mmu-miR-155-5p(1), mmu-miR-16-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-1a-3p(1), mmu-miR-32-5p(1), mmu-miR-375-3p(1), mmu-miR-206-3p(1), mmu-miR-181a-5p(1), mmu-miR-34a-5p(1), mmu-miR-92a-3p(1), mmu-miR-322-5p(1), mmu-miR-29a-3p(1), mmu-miR-23a-3p(1), mmu-miR-25-3p(1), mmu-miR-128-3p(1), mmu-miR-363-3p(1), mmu-miR-26b-5p(1), mmu-miR-382-3p(1), mmu-miR-182-5p(1), mmu-miR-218-5p(1), mmu-miR-183-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-802-5p(1), mmu-miR-673-5p(1), mmu-miR-484(1), mmu-miR-697(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAAGCGTCTGAGATGGAGATATACA
siRNA sets
TATATCTCCATCTCAGACG, ATATCTCCATCTCAGACGC, GTATATCTCCATCTCAGAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNFXL1_2102_ORF_1
0.9612
-0.115797832
0.999980083
2058
ORF sequence:
ATGACGTGCCTAATTTGTATTGCTTCAGTGAAGAGAAACCAGGCAGTTTGGAGCTGTTCAGGATGTTTCTGTATATTCCATATGCCCTGTATTCAGAAGTGGGCTAAAGACAGCCAGTTTCTTGTGTCTTCTGTGACAGACGATGATTTTGGAAAGAAAGATTATCCCTGGCCATGTCCAAAATGTAGATTTGAATACAAAAGATCAGAAACACCTAGTAGATATTATTGCTACTGTGGAAAAGTAGAAGATCCACCTTTAGATCCGTGGCTTGTACCTCATTCGTGTGGCCAAGTATGTGAGAGAGAATTTAAACCTTCTTGTGGTCATAAATGCTTGCTGCTCTGCCATCCAGGTCCCTGCCCTCCTTGTCCAAAGATGGTCACAACCACTTGTTACTGTAAGAAAGCCAAGCCTATCCCTCGCAGGTGCAGTGCCAAGCAGTGGTCCTGTCAGCTGCCATGTGGGCGAAAGCTGCTTTGTGGACATCATAAGTGTGAAAATCCTTGCCATGCAGGAAACTGTCAGCCTTGTCCAAGAGTTAGTAGACAAAAATGTGTATGTGGCAAAAAAGTAGCAGAAAGAAGTTGTGCAAGCCCAGTGTGGCATTGTGATCAAGTATGTGGAAAGACACTGCCATGTGGTAATCATACATGTGAGCAAGTTTGTCATGTTGGTGCTTGTGGAGAGTGTCCTCGATCTGGGAAGAGGTCCTGTCCATGTCAGAAATCAAAGTTTTCTTTGCCTTGTACAGAAGATGTACCAACTTGTGGAGACAGCTGTGACAAAATACTTGAATGTGGAATCCATAGGTGTTCACAGCGTTGCCACCGAGGTCCTTGTGAAACATGCAGACAAGAAGTGGAAAAACAGTGTCGTTGTGGAAAGCACACAAAGCGAATGCCTTGTCACAAGCCTTACCTTTGTGAAACAAAGTGTGTTAAAATGCGGGACTGTCAAAAGCATCAGTGTAGGAGAAAGTGTTGCCCTGGAAACTGTCCACCTTGTGATCAAAATTGTGGACGGACTTTAGGATGTAGAAACCATAAGTGTCCGTCTGTCTGCCATAGAGGCAGTTGCTATCCATGTCCAGAAACGGTAGATGTGAAGTGCAATTGTGGTAATGCAAAGGTGACAGTACCCTGTGGCCGAGAGCGGACCACAAGGCCACCTAAGTGCAAAGAGCTGTGCAGTCGACCACCAACATGTCATCATGCAAGTCAAGAAAAACACCGCTGTCACTTTGGCCCATGTCCACCGTGCCATCAGCCTTGCCAAAAAGTTCTGGAGAAGTGTGGGCACTTGTGTCCTGAGTCATGCCATGATCAAGCATTAGTAAAGCAGACTGGCAGGCATCAGCCATCAGGCCCTTGGGAGCAGCCAGCTGAGCCTGCATTCATCCAGACGGCCCTGCCTTGCCCTCCGTGTCAAGTTCCCATCCCTGTGGAATGTCTGGGGAAGCATGAGGTGAGCCCACTACCATGCCATGCTGTAGGACCCTATTCTTGCAAGAGACTTTGTGGAAGAATGTTGCGCTGTCAGAATCATACATGTATGAAAGAGTGCCACAAAGTTACTGAAGTTGATAGCTCTACTGGCAAAAATAAGGCTGGCCCAGAATGCTTTCACTGTGAAGAAGGGTGCTCTAAGTCACGGCCTGCGGGTTGTCCTCACCCTTGTGTTTTGCCATGTCACCCTGGAAAATGCCCTCCTTGTGTCCAGATGCTTAGAATAAAATGTCACTGCAAGATCACAAGCCTGTATGTGGAATGTAGAAAAATAACCACAGCTGATGTAAGCGAAAAGAACCTCCTCAGTTGCTGCAAAAACCAGTGCCCCAAAGAGCTTCCTTGTGGCCACAGATGCAAAGAGATGTGCCATCCTGGTGAATGCCCCTTTAATTGCAACCAGAAGGTAAAACTTAGATGCCCTTGTAAAAGAATAAAACGGGAGTTGCCTTGCAATAAAGTACGTGAAAATCAGGTTTCAGTTGAATGTGATGCAACGTGCAAGGAGATGAAGCGGAAAGCGTCTGAGATGGAGATATACATGAATTAG
Peptide sequence:
MTCLICIASVKRNQAVWSCSGCFCIFHMPCIQKWAKDSQFLVSSVTDDDFGKKDYPWPCPKCRFEYKRSETPSRYYCYCGKVEDPPLDPWLVPHSCGQVCEREFKPSCGHKCLLLCHPGPCPPCPKMVTTTCYCKKAKPIPRRCSAKQWSCQLPCGRKLLCGHHKCENPCHAGNCQPCPRVSRQKCVCGKKVAERSCASPVWHCDQVCGKTLPCGNHTCEQVCHVGACGECPRSGKRSCPCQKSKFSLPCTEDVPTCGDSCDKILECGIHRCSQRCHRGPCETCRQEVEKQCRCGKHTKRMPCHKPYLCETKCVKMRDCQKHQCRRKCCPGNCPPCDQNCGRTLGCRNHKCPSVCHRGSCYPCPETVDVKCNCGNAKVTVPCGRERTTRPPKCKELCSRPPTCHHASQEKHRCHFGPCPPCHQPCQKVLEKCGHLCPESCHDQALVKQTGRHQPSGPWEQPAEPAFIQTALPCPPCQVPIPVECLGKHEVSPLPCHAVGPYSCKRLCGRMLRCQNHTCMKECHKVTEVDSSTGKNKAGPECFHCEEGCSKSRPAGCPHPCVLPCHPGKCPPCVQMLRIKCHCKITSLYVECRKITTADVSEKNLLSCCKNQCPKELPCGHRCKEMCHPGECPFNCNQKVKLRCPCKRIKRELPCNKVRENQVSVECDATCKEMKRKASEMEIYMN
IRESfinder result
IRESfinder score
0.437209102
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page