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mmu_circNup98_2273
Basic information of circular RNA
PanCircBase ID:
mmu_circNup98_2273
mm39_Chr. Position ID:
chr7|101796406|101841249|-
Gene name:
Nup98
Transcript:
ENSMUST00000210682.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
15
Exon/intron indexes:
19,18,17,16,15,14,13,12,11,10,9,8,7,6,5
Exon/intron offsets:
0,5118,5936,6595,9852,13341,16489,22163,29113,33177,36263,37606,38661,39432,44703
Genomic length:
44843
Exon/intron sizes in nt:
1,78,13,91,14,29,91,17,00,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr7:101794928-101796406|chr7:101841249-101843867
Splice length:
2273
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_173278
Human Ortholog IDs:
Mature spliced Sequence:
ATTTTGGAACCAGTACTAGCAGTGGAGGACTCTTTGGAACTACAAATACCACCTCTAATCCTTTTGGTAGCACATCTGGCTCCCTTTTTGGGCCAAGTAGTTTTACAGCAGCACCTACAGGAACTACCATCAAATTTAATCCTCCCACTGGTACAGATACTATGGTCAAAGCTGGAGTTAGCACTAACATCAGTACAAAGCATCAGTGTATTACTGCTATGAAAGAATATGAAAGCAAGTCATTAGAGGAACTACGTTTGGAGGATTATCAGGCTAACCGGAAAGGCCCACAGAACCAAGTGGGAGGAGGCACCACGGCTGGCTTATTTGGGTCTTCTCCAGCAACTTCCAGTGCAACAGGGCTCTTCAGCTCCTCCACCACTAATTCAGCCTTTTCATATGGTCAGAACAAAACTGCCTTTGGAACTAGCACAACTGGATTTGGAACAAATCCAGGTGGTCTCTTTGGCCAACAGAATCAACAGACTACCAGTCTCTTCAGCAAACCATTTGGCCAGGCTACAACCACCCCGAATACTGGCTTTTCCTTTGGTAATACCAGCACCCTTGGACAGCCAAGCACCAATACTATGGGCCTATTTGGAGTAACCCAAGCCTCACAACCAGGAGGTCTTTTTGGGACAGCTACAAACACCAGCACTGGGACAGCATTTGGGACAGGAACAGGTCTCTTTGGGCAGCCCAATACTGGATTTGGTGCAGTTGGTTCGACCCTGTTTGGCAATAACAAGCTTACAACTTTTGGAACCAGCACAACCAGTGCTCCTTCATTTGGTACAACCAGTGGCGGGCTCTTCGGTAACAAACCAACCCTGACTTTAGGAACCAATACAAACACTTCCAATTTTGGGTTTGGCACAAATAACAGTGGGAGCAGTATTTTTGGAAGTAAGCCAGCAGCTGGAACTTTGGGAACTGGACTTGGTACAGGATTTGGAACAGCTCTTGGTGCTGGACAGGCATCTTTGTTTGGAAACAACCAACCTAAGATTGGAGGGCCTCTTGGTACAGGAGCCTTTGGGGCCCCTGGATTTAATACTTCGACAGCCATTTTGGGCTTTGGCGCCCCCCAGGCCCCAGTAGCTTTGACAGATCCAAATGCTTCTGCTGCCCAGCAGGCTGTTCTCCAGCAGCACCTCAATAGCCTAACATACTCACCCTTTGGAGACTCCCCCCTCTTCCGGAATCCTATGTCAGATCCTAAGAAGAAAGAAGAGAGACTGAAACCAACCAATCCAGCTGCTCAGAAAGCTCTTACAACACCTACTCATTATAAACTTACACCTCGCCCTGCTACCAGAGTCAGGCCAAAGGCTTTGCAAACAACAGGCACAGCCAAATCACATCTCTTTGATGGGCTGGATGACGATGAACCATCTCTAGCCAACGGAGCATTCATGCCTAAAAAGAGCATCAAGAAGTTGGTTTTGAAAAATCTCAACAATAGCAATCTCTTTTCTCCTGTTAATCATGATTCAGAAGATCTAGCTTCACCCTCTGAGTATCCAGAAAATGGAGAAAGATTTAGCTTCCTGAGCAAACCTGTTGATGAGAACAATCAGCAGGATGGAGAAGATGACTCTCTTGTATCACGATTTTACACTAATCCTATTGCCAAACCCATTCCACAAACTCCAGAGAGTGTTGGAAACAAAAATAACAGTAGCAGCAATGTGGAAGATACCATTGTTGCCTTGAACATGCGTGCTGCTTTGCGCAATGGATTGGAAGGAAGCAGTGAAGAGACGTCATTCCATGATGAGTCATTGCAAGATGACCGAGAAGAGATAGAAAATAATGCTTACCACATACACCCAGCAGGCATTGTTCTCACAAAAGTTGGTTATTACACTATCCCATCTATGGATGACCTTGCTAAAATTACCAACGAGAAGGGAGAATGCATTGTTTCTGACTTCACCATTGGTCGTAAAGGATATGGCTCAATCTATTTTGAAGGAGATGTGAATTTGACAAATCTAAATTTGGATGATATTGTGCATATCCGAAGGAAAGAAGTTATTGTCTATGTAGATGATAACCAAAAGCCACCTGTGGGTGAAGGGCTAAATAGGAAGGCTGAAGTTACTTTGGATGGAGTTTGGCCAACAGATAAAACATCCCGGTGTTTAATAAAGAGTCCAGATCGACTTGCTGATATCAACTATGAGGGGAGATTAGAAGCAGTCTCAAGAAAGCAAGGGGCCCAATTCAAGGAGTATCGGCCTGAAACTGGTTCTTGGGTATTTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAAAGCAAGGGGCCCAATT
60.18
GGAGCCAGATGTGCTACCAA
59.75
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGAAAGCAAGGGGCCCAAT
60.18
GGAGCCAGATGTGCTACCAA
59.75
144
PCR template sequence:
TGCTGATATCAACTATGAGGGGAGATTAGAAGCAGTCTCAAGAAAGCAAGGGGCCCAATTCAAGGAGTATCGGCCTGAAACTGGTTCTTGGGTATTTAAGATTTTGGAACCAGTACTAGCAGTGGAGGACTCTTTGGAACTACAAATACCACCTCTAATCCTTTTGGTAGCACATCTGGCTCCCTTTTTGGGCCAAGTAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-370-3p(2), mmu-miR-9-5p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-200b-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-138-5p(1), mmu-miR-381-3p(1), mmu-miR-136-5p(1), mmu-miR-182-5p(1), mmu-miR-297a-5p(1), mmu-miR-544-5p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTGGGTATTTAAGATTTTGGAACCAG
siRNA sets
TTCCAAAATCTTAAATACC, TCCAAAATCTTAAATACCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNUP98_2273_ORF_1
1.0276
0.084146733
0.999998931
2334
ORF sequence:
ATGGTCAAAGCTGGAGTTAGCACTAACATCAGTACAAAGCATCAGTGTATTACTGCTATGAAAGAATATGAAAGCAAGTCATTAGAGGAACTACGTTTGGAGGATTATCAGGCTAACCGGAAAGGCCCACAGAACCAAGTGGGAGGAGGCACCACGGCTGGCTTATTTGGGTCTTCTCCAGCAACTTCCAGTGCAACAGGGCTCTTCAGCTCCTCCACCACTAATTCAGCCTTTTCATATGGTCAGAACAAAACTGCCTTTGGAACTAGCACAACTGGATTTGGAACAAATCCAGGTGGTCTCTTTGGCCAACAGAATCAACAGACTACCAGTCTCTTCAGCAAACCATTTGGCCAGGCTACAACCACCCCGAATACTGGCTTTTCCTTTGGTAATACCAGCACCCTTGGACAGCCAAGCACCAATACTATGGGCCTATTTGGAGTAACCCAAGCCTCACAACCAGGAGGTCTTTTTGGGACAGCTACAAACACCAGCACTGGGACAGCATTTGGGACAGGAACAGGTCTCTTTGGGCAGCCCAATACTGGATTTGGTGCAGTTGGTTCGACCCTGTTTGGCAATAACAAGCTTACAACTTTTGGAACCAGCACAACCAGTGCTCCTTCATTTGGTACAACCAGTGGCGGGCTCTTCGGTAACAAACCAACCCTGACTTTAGGAACCAATACAAACACTTCCAATTTTGGGTTTGGCACAAATAACAGTGGGAGCAGTATTTTTGGAAGTAAGCCAGCAGCTGGAACTTTGGGAACTGGACTTGGTACAGGATTTGGAACAGCTCTTGGTGCTGGACAGGCATCTTTGTTTGGAAACAACCAACCTAAGATTGGAGGGCCTCTTGGTACAGGAGCCTTTGGGGCCCCTGGATTTAATACTTCGACAGCCATTTTGGGCTTTGGCGCCCCCCAGGCCCCAGTAGCTTTGACAGATCCAAATGCTTCTGCTGCCCAGCAGGCTGTTCTCCAGCAGCACCTCAATAGCCTAACATACTCACCCTTTGGAGACTCCCCCCTCTTCCGGAATCCTATGTCAGATCCTAAGAAGAAAGAAGAGAGACTGAAACCAACCAATCCAGCTGCTCAGAAAGCTCTTACAACACCTACTCATTATAAACTTACACCTCGCCCTGCTACCAGAGTCAGGCCAAAGGCTTTGCAAACAACAGGCACAGCCAAATCACATCTCTTTGATGGGCTGGATGACGATGAACCATCTCTAGCCAACGGAGCATTCATGCCTAAAAAGAGCATCAAGAAGTTGGTTTTGAAAAATCTCAACAATAGCAATCTCTTTTCTCCTGTTAATCATGATTCAGAAGATCTAGCTTCACCCTCTGAGTATCCAGAAAATGGAGAAAGATTTAGCTTCCTGAGCAAACCTGTTGATGAGAACAATCAGCAGGATGGAGAAGATGACTCTCTTGTATCACGATTTTACACTAATCCTATTGCCAAACCCATTCCACAAACTCCAGAGAGTGTTGGAAACAAAAATAACAGTAGCAGCAATGTGGAAGATACCATTGTTGCCTTGAACATGCGTGCTGCTTTGCGCAATGGATTGGAAGGAAGCAGTGAAGAGACGTCATTCCATGATGAGTCATTGCAAGATGACCGAGAAGAGATAGAAAATAATGCTTACCACATACACCCAGCAGGCATTGTTCTCACAAAAGTTGGTTATTACACTATCCCATCTATGGATGACCTTGCTAAAATTACCAACGAGAAGGGAGAATGCATTGTTTCTGACTTCACCATTGGTCGTAAAGGATATGGCTCAATCTATTTTGAAGGAGATGTGAATTTGACAAATCTAAATTTGGATGATATTGTGCATATCCGAAGGAAAGAAGTTATTGTCTATGTAGATGATAACCAAAAGCCACCTGTGGGTGAAGGGCTAAATAGGAAGGCTGAAGTTACTTTGGATGGAGTTTGGCCAACAGATAAAACATCCCGGTGTTTAATAAAGAGTCCAGATCGACTTGCTGATATCAACTATGAGGGGAGATTAGAAGCAGTCTCAAGAAAGCAAGGGGCCCAATTCAAGGAGTATCGGCCTGAAACTGGTTCTTGGGTATTTAAGATTTTGGAACCAGTACTAGCAGTGGAGGACTCTTTGGAACTACAAATACCACCTCTAATCCTTTTGGTAGCACATCTGGCTCCCTTTTTGGGCCAAGTAGTTTTACAGCAGCACCTACAGGAACTACCATCAAATTTAATCCTCCCACTGGTACAGATACTATGGTCAAAGCTGGAGTTAGCACTAACATCAGTACAAAGCATCAGTGTATTACTGCTATGA
Peptide sequence:
MVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRKGPQNQVGGGTTAGLFGSSPATSSATGLFSSSTTNSAFSYGQNKTAFGTSTTGFGTNPGGLFGQQNQQTTSLFSKPFGQATTTPNTGFSFGNTSTLGQPSTNTMGLFGVTQASQPGGLFGTATNTSTGTAFGTGTGLFGQPNTGFGAVGSTLFGNNKLTTFGTSTTSAPSFGTTSGGLFGNKPTLTLGTNTNTSNFGFGTNNSGSSIFGSKPAAGTLGTGLGTGFGTALGAGQASLFGNNQPKIGGPLGTGAFGAPGFNTSTAILGFGAPQAPVALTDPNASAAQQAVLQQHLNSLTYSPFGDSPLFRNPMSDPKKKEERLKPTNPAAQKALTTPTHYKLTPRPATRVRPKALQTTGTAKSHLFDGLDDDEPSLANGAFMPKKSIKKLVLKNLNNSNLFSPVNHDSEDLASPSEYPENGERFSFLSKPVDENNQQDGEDDSLVSRFYTNPIAKPIPQTPESVGNKNNSSSNVEDTIVALNMRAALRNGLEGSSEETSFHDESLQDDREEIENNAYHIHPAGIVLTKVGYYTIPSMDDLAKITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNLDDIVHIRRKEVIVYVDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRLEAVSRKQGAQFKEYRPETGSWVFKILEPVLAVEDSLELQIPPLILLVAHLAPFLGQVVLQQHLQELPSNLILPLVQILWSKLELALTSVQSISVLLL
IRESfinder result
IRESfinder score
0.683529701
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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