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mmu_circNdfip1_4031
Basic information of circular RNA
PanCircBase ID:
mmu_circNdfip1_4031
mm39_Chr. Position ID:
chr18|38585357|38597436|+
Gene name:
Ndfip1
Transcript:
ENSMUST00000238135.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,3750,8240
Genomic length:
12079
Exon/intron sizes in nt:
12,56,73,839
Flanking exon/introns:
chr18:38584695-38585357|None
Splice length:
4031
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TGGCATTCCTCTTCAACTGGATTGGGTTTTTCTTGTCTTTTTGCCTGACCACCTCAGCTGCGGGAAGGTATGGGGCCATCTCAGGATTTGGTCTTTCTCTAATTAAGTGGATCCTTATTGTCAGGTTTTCCACCTATTTCCCTGGATACTTTGATGGCCAGTACTGGCTCTGGTGGGTGTTCTTGGTTTTAGGCTTTCTCCTGTTTCTCAGAGGATTTATCAATTACGCAAAAGTTCGGAAGATGCCAGAAACTTTCTCAAATCTCCCCAGGACCAGAGTTCTCTTTATTTATTAAAGGTATTGGAGGAGGGGTGGGGCGCTGTGTTCCTTTGCTGTTAGGATCATGAGATGTGTTGCAGAGTTTAGAATGATACTCTAATGGGGGTACATAAATTGTAAGGAGGCCATTAAAAAAAGACCTGGCTTTCCCCCTTTTTTATTGGAGGGGTGGTGTCTGCAAAAAACTGTTGATGAGGGCAAAGGGGAAGAAGAGAAGTATTTTGCCAACATACAGGCAAGGGTCTCAGTAGTAATGGGGGCTGGAGGTAGGGCATTGATAGCATGATTGAGCCCATGGGGCCTCCTCCTTCTTCCCTAATCTCACAGAGCCCCAGAACGCCCTGAGGGAAGTCAGCAGGTACATCAGAAACAGGCTCTCTTGCTTGCACTACTGACCAGCCTACTAAAGTATCCATCTCTTAAAATTAATCCTTGGACCTTTCTTGCTGCCTGCTTTCAGGTTTATACCCAGATTTTATCACTCTGGTAGAGAGGTAGCTCAGATCCAAGGGAAGGAGAGAGACCTTTCTTGTACCTAACAGAACTAAGCCCTGAACTGATTCACACAGTTTTCCTCAGTGGCTAACTCCATCTTTTATCAGCAGCTACCTGAAGGGTAAGATAGCTTGAATACTGCAGAGTCCTGACAAGGCAGGCCATGCCTTTGCAGACTTCATTCTTTGCCCTTTGGGCTTTTGGGATTGTGTGTTTGATAAAATAAAACCTTGAGCACCCTTAAAAGCCAGTACAGTTGAAGGCCCAGAAAAGGCCTTGTGATAGCTGTGTGCAGCAGTTGTCACAAACCTTAAATGATAGTAGAACTTACCTTGCGGAAGTTGGCTATGTGTAGGAGAGCTTCAGTCTCCTGAGGTGTAGTGAGGACAGAACAGACAGCAGCTCAGCTCAGACTTCAGCCTTGCAAACAGAACTAGCCTGTAGGAATTTGATAGGAGCTTGAGATTACCCCTCTCTCGTGTATTGTCTTCATTTTTTCTTTTTTTATGTAGAAGGATATTTGACTGGCTTGGGGGTATAGCTCAGTGTACAAGGTTTGACTCCTCCTTGAAAAGGGAAGGGAGGGAAAGGGAGAAGCCGGGAAGGTTTGAGTGTACTGGGGGATTTCATACTTTGTTCATCTTCTAGTACACAACAAATAGTAGCCAAGACAGGGACTGCATAATGCTGTTTTCCAGTGTTAGGGATTTGCTGGGATTATGTTCTATAGCTTTGATTTTAAAAAAATTTTTGGAATATTTCTGAGTGGTCAACATTGAAAGTCATGAATCTGCTAGGCCACGATTTGTATCACCAGTCTTCAGGACAGTGCTGTGGGAACTGGTCAGGGACTGGTTTGAGCAGGGTTTCTGTGGTGTGCTTGAAAGGTTGTTGGAAACCTGCACACAACCTGTCTGAGGACACCAGAGCATTTATTAGCTTTCTGCCCAGCCTTGTGTGGTAGTTGGTATGAAATCACTCAGATGTGCCCAGAAAGTCTTGAGCCCAGGTGAAGGGACTAGGATTTGAAAGCAGTGTTTACAAATCTAATTGCTTCCTTATCAATTAACTCTCAGAATCCCTTAGAGGGAAATGGTAAGATTCTGTAGGCATGAGTGACCTCTGTTCATTGAAAAAACTAAATCCTCTCTATCCAGATCCACATGTAGAATATTTGCAGATATTTTGGTTAGAGGATACAGTAAAACCTCATTGTGTGAAGTATTATGGTGTTACTTCATTGAATCCGACCTTCTTATGTGGTTAATATTCTTAGTTAAAAGCAAGCTGTATGGCCGGGCGTGGTGGCGCTCGCCTTTGATCTGAGCACTTGGGAGGCAGAGGCAGGTGGATTTCTGAGTTCAAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACTCTGCCTCGAAAAAAAAAAAAACAAAACAAAAAACAACAACAACAAAAGCAAGCTGTATAGACTTACCTGCGCCAGAAAGACCATAGGTAGGGAATTTCAGAAGTAACTTCATAGAGACTATTGCACTATTGCAGCTTTCATTCTGAACTGAAATTAGTGTTTGCAGAGAGTGTTGAAATAGAGACATCTCTCACCTGGCATAGTGGTAATCAGCCAGGTCTTTGAAGCCAGACCAGTCTACATAGTTCCAGGACAGCCAGAGCTATGGAGAGATAGATTCTGTCTAAAAATACAAAACTCAAAGAGTAGAGACTTCCTTAGGCTATCCAAAATGTGGAACAAACAAGATGAACTGTGTGCAGAAGTGCAGTCATAGTGTGCTGGACAGTTTTATGTCAGCTTGACACAGCTAGACTTGGGGAAAAGGAACCTCAACTGAGAAGATGCCCCCTCCACACTGGCTTGTGGGTAACAAAAACAGCGTGGAGTGAGCCTTGTAGACTCATCTATGGGGTCTGAAGAGACTGCTCTGCAGTTAAGAGCACTTGTTGCTCTTGCAGACCCGGTTTTAGTGTCCAGCACTGGATATGGTGGATACAAGCACCCAGAACTCCAGTTCCAGGGTTCCATTGTCTGTGACTTCTAAGCTTCTTTTGGCACTACAATAAAAAGTTACTTAACACTTCCCCCCCACCCACCCCCATCCCCGTTATTTCCATGAGAATTATAAGTATGTATGATATATGTATGGGGCTGGGGATTTGGCTCAGTGGTACACATCTGCTTAGCATTCAAGGCCCTGAGTTCAGTTCTCAGCACAGGGCAGGGACACATGTAGATACAGACATCATTTAAAAAGTATACTTTTCTGTCATGATACTTTTTAAAAGGTGGTTAGGAGTTGCATATATTCTGAAAAACATGCTTCCCAGATACCTTGGTTCTTTTTGTTTGGTTGTTTTTGTTTTTGTTTTTTTCAAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAATTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCTGCCTGCCTCTGCCTCCCGAGTGCTGGTTCCCAAAAGTTTTTTAAAGATTTATGTGTATGAGTTCACTGTAGCTCTCTTCAGACACACCAGAAGAGGGCATCAGATCCCATTATAGATGGTTGTGAGCCACCATATGGTTGCTAGGAATTAAACTCAGGACCTCTGGAAGAGTAGTCAGTGCTCTTAACCACTGAGCCATCTCTCCAGTTCCCTGACTTGTTTTTTTAAGAGAGAGCATACCAAGACTGGAAAGTTAGTCAGGGGTTAAGAGCACTGGCTGCTCCTCCAGAGGATCTGGGTTCCATTTCCCAGAACCCACATGATGGTCAAAACCATCCTTAACTCCAGTTCCAGAGTATCCAACGTCCTCTTACGGTCTCTGAAGTTACTGTACATGCAGTGCACAGACATACATGCAGATAAAACACCCATAGACATAAAATAAATCTTTAGAGAGAGCATGCCAGTTATTTACAGTTGGAGAAGGGGCTTGATGTTAAGAACTGAAAATTGACTTTATTGGCTACTATGACGTCCATGTATAATAATCTTCAAATTAGGTTGAAATGCCAAATGGGTGTCTCCGAGCCTCTCTTCTATGACTGTACCTTGCTTTTAGCCAACCTAACAGGCTAACTAGAGTTTGACTGTTCAGTGTCCTTCTCTGGCAGATGTTTTCTGGCAAAGGCTTCCTGCACTGATGAAGTCCCCTGAGAAGCGAGAGCACCTGCAGGAAGTGAATCACCACCAGAATGGAGGAACAGTCACCTGCTTTAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGTCCCCTGAGAAGCGAG
59.83
CAAATCCTGAGATGGCCCCA
59.74
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGTCCCCTGAGAAGCGAG
59.83
ACCAAATCCTGAGATGGCCC
59.74
168
PCR template sequence:
CTGGCAAAGGCTTCCTGCACTGATGAAGTCCCCTGAGAAGCGAGAGCACCTGCAGGAAGTGAATCACCACCAGAATGGAGGAACAGTCACCTGCTTTAAATGGCATTCCTCTTCAACTGGATTGGGTTTTTCTTGTCTTTTTGCCTGACCACCTCAGCTGCGGGAAGGTATGGGGCCATCTCAGGATTTGGTCTTTCTCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
44
Interacting miRNAs (#binding sites)
mmu-miR-146a-5p(2), mmu-miR-709(2), mmu-miR-297a-5p(2), mmu-miR-680(2), mmu-miR-1187(2), mmu-miR-207(2), mmu-miR-20b-5p(1), mmu-miR-134-5p(1), mmu-miR-141-3p(1), mmu-miR-20a-5p(1), mmu-miR-7b-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-335-5p(1), mmu-miR-130a-3p(1), mmu-miR-152-3p(1), mmu-miR-148a-3p(1), mmu-miR-298-5p(1), mmu-miR-217-5p(1), mmu-miR-7a-5p(1), mmu-miR-222-3p(1), mmu-miR-138-5p(1), mmu-miR-139-5p(1), mmu-miR-136-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-721(1), mmu-miR-511-3p(1), mmu-miR-758-3p(1), mmu-miR-541-5p(1), mmu-miR-301a-3p(1), mmu-miR-466d-3p(1), mmu-miR-27a-5p(1), mmu-miR-384-3p(1), mmu-miR-377-3p(1), mmu-miR-1198-5p(1), mmu-miR-5101(1), mmu-miR-3087-3p(1), mmu-miR-452-3p(1), mmu-miR-188-3p(1), mmu-miR-3470b(1), mmu-miR-193b-3p(1), mmu-miR-146b-5p(1), mmu-miR-339-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CACCTGCTTTAAATGGCATTCCTCTT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNDFIP1_4031_ORF_1
0.7296
-0.149063337
0.073039662
297
ORF sequence:
ATGGCATTCCTCTTCAACTGGATTGGGTTTTTCTTGTCTTTTTGCCTGACCACCTCAGCTGCGGGAAGGTATGGGGCCATCTCAGGATTTGGTCTTTCTCTAATTAAGTGGATCCTTATTGTCAGGTTTTCCACCTATTTCCCTGGATACTTTGATGGCCAGTACTGGCTCTGGTGGGTGTTCTTGGTTTTAGGCTTTCTCCTGTTTCTCAGAGGATTTATCAATTACGCAAAAGTTCGGAAGATGCCAGAAACTTTCTCAAATCTCCCCAGGACCAGAGTTCTCTTTATTTATTAA
Peptide sequence:
MAFLFNWIGFFLSFCLTTSAAGRYGAISGFGLSLIKWILIVRFSTYFPGYFDGQYWLWWVFLVLGFLLFLRGFINYAKVRKMPETFSNLPRTRVLFIY
IRESfinder result
IRESfinder score
0.821892213
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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