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mmu_circNfx1_1232
Basic information of circular RNA
PanCircBase ID:
mmu_circNfx1_1232
mm39_Chr. Position ID:
chr4|40986692|41009269|+
Gene name:
Nfx1
Transcript:
ENSMUST00000091614.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
4,5,6,7,8,9,10,11,12,13,14,15
Exon/intron offsets:
0,1929,4100,5051,7066,7270,10122,12992,16325,17635,18133,22497
Genomic length:
22577
Exon/intron sizes in nt:
78,106,72,140,100,218,98,31,80,109,120,80
Flanking exon/introns:
chr4:40985051-40986692|chr4:41009269-41011526
Splice length:
1232
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATGGCCAGAGTGGTTGGAGGTGCCCTGCTTGTCAGAATGTTTCTGCACATGTTCCCAATACCTATACTTGTTTCTGTGGCAAAGTAAAGAATCCTGAATGGAGCAGAAATGAAATTCCACATAGTTGTGGTGAGGTTTGTAGAAAGAAACAGCCTGGCCAGGACTGTCCACATTCCTGTAACCTTCTCTGCCATCCTGGACCCTGCCCACCCTGCCCTGCTTTTACAACTAAAACATGTGAATGTGGACGGACCAGGCACACGGTTCGCTGTGGTCAGCCTGTCTCAGTCCACTGTTCTAATGCATGTGAGAATATCTTGAACTGTGGTCAGCACCACTGTGCTGAGCTGTGCCATGGGGGTCAATGCCAGCCTTGTCGGATCATACTGAACCAGGTGTGCTACTGTGGCAGCACCTCCCGAGATGTGTTGTGTGGAACCGATGTGGGAAAGTCTGATGGATTTGGGGACTTCAGCTGTTTAAAGATATGTGGCAAGGACTTGAAGTGTGGGAGCCATACCTGTTCTCAGGTTTGCCACCCTCAGCCGTGTCAGCCTTGCCCACGGCTCCCCCATTTGGTGCGATACTGCCCTTGCGGCCAAACACCTCTCAGCCAGTTGCTGGAACATGGAAGTAATGCTCGGAAAACATGCATGGATCCTGTCCCTTCCTGTGGAAAAGTGTGTGGCAAACCCTTGGCCTGTGGTTCCTCAGATTTCATCCACACCTGTGAAAAGCTTTGCCATGAAGGAGACTGTGGGCCGTGCTCTCGCACATCAGTCATTTCCTGCAGATGCTCCTTCAGAACAAAGGAACTTCCGTGTACCAGTCTTAAAAGTGAAGATGCTACATTTATGTGCGACAAACGGTGTAACAAGAAACGATTGTGCGGACGGCATAAATGTAACGAGATCTGCTGTGTGGACAAGGAGCACAAGTGTCCTTTGATTTGTGGGAGGAAACTCCGCTGTGGCCTTCATCGGTGTGAAGAACCTTGTCATCGAGGGAACTGTCAGACCTGCTGGCAAGCCAGCTTTGATGAATTAACCTGCCACTGTGGCGCCTCTGTGATCTACCCACCAGTTCCCTGTGGGACTAGGCCTCCTGAGTGTACCCAAACCTGTGCCAGGATCCATGAATGTGACCATCCAGTATATCATTCTTGTCATAGCGAGGAGAAGTGTCCCCCTTGTACTTTCCTAACTCAGAAGTGGTGCATGGGCAAGCATGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCATGAATGTGACCATCCAGT
57.99
ACATTCTGACAAGCAGGGCA
59.89
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCATGAATGTGACCATCCAG
56.17
ACATTCTGACAAGCAGGGCA
59.89
140
PCR template sequence:
CCATGAATGTGACCATCCAGTATATCATTCTTGTCATAGCGAGGAGAAGTGTCCCCCTTGTACTTTCCTAACTCAGAAGTGGTGCATGGGCAAGCATGAGATGGCCAGAGTGGTTGGAGGTGCCCTGCTTGTCAGAATGTTTCTGCACATGTTCCCAATACCTATACTTGTTTCTGTGGCAAAGTAAAGAATCCTGAATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-181a-5p(1), mmu-miR-320-3p(1), mmu-miR-23a-3p(1), mmu-miR-181b-5p(1), mmu-miR-214-3p(1), mmu-miR-128-3p(1), mmu-miR-212-3p(1), mmu-miR-499-5p(1), mmu-miR-207(1), mmu-miR-335-3p(1), mmu-miR-452-3p(1), mmu-miR-188-3p(1), mmu-miR-1904(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGGCAAGCATGAGATGGCCAGAGTGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNFX1_1232_ORF_1
0.703
-0.006673662
0.686844089
666
ORF sequence:
ATGGATCCTGTCCCTTCCTGTGGAAAAGTGTGTGGCAAACCCTTGGCCTGTGGTTCCTCAGATTTCATCCACACCTGTGAAAAGCTTTGCCATGAAGGAGACTGTGGGCCGTGCTCTCGCACATCAGTCATTTCCTGCAGATGCTCCTTCAGAACAAAGGAACTTCCGTGTACCAGTCTTAAAAGTGAAGATGCTACATTTATGTGCGACAAACGGTGTAACAAGAAACGATTGTGCGGACGGCATAAATGTAACGAGATCTGCTGTGTGGACAAGGAGCACAAGTGTCCTTTGATTTGTGGGAGGAAACTCCGCTGTGGCCTTCATCGGTGTGAAGAACCTTGTCATCGAGGGAACTGTCAGACCTGCTGGCAAGCCAGCTTTGATGAATTAACCTGCCACTGTGGCGCCTCTGTGATCTACCCACCAGTTCCCTGTGGGACTAGGCCTCCTGAGTGTACCCAAACCTGTGCCAGGATCCATGAATGTGACCATCCAGTATATCATTCTTGTCATAGCGAGGAGAAGTGTCCCCCTTGTACTTTCCTAACTCAGAAGTGGTGCATGGGCAAGCATGAGATGGCCAGAGTGGTTGGAGGTGCCCTGCTTGTCAGAATGTTTCTGCACATGTTCCCAATACCTATACTTGTTTCTGTGGCAAAGTAA
Peptide sequence:
MDPVPSCGKVCGKPLACGSSDFIHTCEKLCHEGDCGPCSRTSVISCRCSFRTKELPCTSLKSEDATFMCDKRCNKKRLCGRHKCNEICCVDKEHKCPLICGRKLRCGLHRCEEPCHRGNCQTCWQASFDELTCHCGASVIYPPVPCGTRPPECTQTCARIHECDHPVYHSCHSEEKCPPCTFLTQKWCMGKHEMARVVGGALLVRMFLHMFPIPILVSVAK
IRESfinder result
IRESfinder score
0.599556535
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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