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mmu_circNphp1_982
Basic information of circular RNA
PanCircBase ID:
mmu_circNphp1_982
mm39_Chr. Position ID:
chr2|127601495|127616019|-
Gene name:
Nphp1
Transcript:
ENSMUST00000028857.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
13,12,11,10,9,8,7,6,5
Exon/intron offsets:
0,1586,4203,6448,8595,10039,10683,12525,14322
Genomic length:
14524
Exon/intron sizes in nt:
11,17,51,29,98,88,43,10,00,00,000
Flanking exon/introns:
chr2:127599681-127601495|chr2:127616019-127619188
Splice length:
982
Other database IDs:
CIRCpedia: HSA_CIRCpedia_92569
Human Ortholog IDs:
Mature spliced Sequence:
AGTTGAGGCACACAGTGACAAGGAGGAAGATGACACGACTGAAGATGATGAAGAAGAAACTGGTGGAGAGGAAGAAGAGTCAGAAGGGGATGGAGAAGGAAAGCAAGAGCAAGCCTCCCCGAAACAAGCAGAAACAGAAACTGTCACATACATCGCTCTTGGGGACTTCGCTGCTCAGCAGACTGGGGACTTGACCTTTAAGAAAGGGGACGTTCTCCATATAATTGAAAAGAAGCCTGATGGTTGGTGGCTGGCTAAGGATGCTGAAGGAGTTGAGGGTCTCATTCCCAGGACCTACTTGGAGCCCTATAATAAAGAAGACAAGCTGGAGTCAAGCGAAGGCAGCGAGGAGGGCGGTGAGGAGGACGGTGAGGAGGACGGTGAGGAGGACGTGGAGGTGGTGGATGAAACTGCAGATGGAGCCCAGGTGAAGCAGAGAACTGATTCCCACTGGAGTGCTGTACGAAAAGCTATCTCAGAGCAGATAAATACCGTTGATGTGTTAGCCACAATGGGAGCCATTCCTGCAGGATTCCGGCCTTCCACGCTCTCCCAGCTGCTGGATGAAGCAGGGAACCAGTTTCGAGCAAGTTACTTCTTGCAGCCAGAGCTCACGACATCGCAGCTGGCCTTCAGAGATCTAACATGGGATGCTAAGGCAGGCACGATCATGTCGAGACCAAGTCGTGTTTCATTGATTCTGACCCTATGGAGCTGTAAAATGATCCCTCTCCCAGGAACAAGCATACAGGTTCTCAGCAGACACATCCGCCTCTGCCTGTTTGACGGCAGCAAGGTCCTGAGTAATATCCATACAGTTCGAGCCGTGTGGCAGCCTAAGAAGCCAAAAACATGGACCTTCTCTCCTCAGGTCACTGGCATCTTGCCATGCTTGCTCGATGGTGACTGTTTTATCAGGTCCAATTCTTCAACTCCAGACCTTGGGATATTATTTGAACTTGGAATTTCTTACATTCGCAAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTGCCATGCTTGCTCGATG
60.25
TCAGTCGTGTCATCTTCCTCC
59.18
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTTGCCATGCTTGCTCGATG
60.25
CAGTCGTGTCATCTTCCTCCT
59.18
141
PCR template sequence:
CTTGCCATGCTTGCTCGATGGTGACTGTTTTATCAGGTCCAATTCTTCAACTCCAGACCTTGGGATATTATTTGAACTTGGAATTTCTTACATTCGCAATAGTTGAGGCACACAGTGACAAGGAGGAAGATGACACGACTGAAGATGATGAAGAAGAAACTGGTGGAGAGGAAGAAGAGTCAGAAGGGGATGGAGAAGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-31-5p(1), mmu-miR-298-5p(1), mmu-miR-185-5p(1), mmu-miR-212-3p(1), mmu-miR-207(1), mmu-miR-540-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TTACATTCGCAATAGTTGAGGCACAC
siRNA sets
GTGTGCCTCAACTATTGCG, TGTGCCTCAACTATTGCGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNPHP1_982_ORF_1
0.9642
0.250935109
0.994597105
1065
ORF sequence:
ATGGTGACTGTTTTATCAGGTCCAATTCTTCAACTCCAGACCTTGGGATATTATTTGAACTTGGAATTTCTTACATTCGCAATAGTTGAGGCACACAGTGACAAGGAGGAAGATGACACGACTGAAGATGATGAAGAAGAAACTGGTGGAGAGGAAGAAGAGTCAGAAGGGGATGGAGAAGGAAAGCAAGAGCAAGCCTCCCCGAAACAAGCAGAAACAGAAACTGTCACATACATCGCTCTTGGGGACTTCGCTGCTCAGCAGACTGGGGACTTGACCTTTAAGAAAGGGGACGTTCTCCATATAATTGAAAAGAAGCCTGATGGTTGGTGGCTGGCTAAGGATGCTGAAGGAGTTGAGGGTCTCATTCCCAGGACCTACTTGGAGCCCTATAATAAAGAAGACAAGCTGGAGTCAAGCGAAGGCAGCGAGGAGGGCGGTGAGGAGGACGGTGAGGAGGACGGTGAGGAGGACGTGGAGGTGGTGGATGAAACTGCAGATGGAGCCCAGGTGAAGCAGAGAACTGATTCCCACTGGAGTGCTGTACGAAAAGCTATCTCAGAGCAGATAAATACCGTTGATGTGTTAGCCACAATGGGAGCCATTCCTGCAGGATTCCGGCCTTCCACGCTCTCCCAGCTGCTGGATGAAGCAGGGAACCAGTTTCGAGCAAGTTACTTCTTGCAGCCAGAGCTCACGACATCGCAGCTGGCCTTCAGAGATCTAACATGGGATGCTAAGGCAGGCACGATCATGTCGAGACCAAGTCGTGTTTCATTGATTCTGACCCTATGGAGCTGTAAAATGATCCCTCTCCCAGGAACAAGCATACAGGTTCTCAGCAGACACATCCGCCTCTGCCTGTTTGACGGCAGCAAGGTCCTGAGTAATATCCATACAGTTCGAGCCGTGTGGCAGCCTAAGAAGCCAAAAACATGGACCTTCTCTCCTCAGGTCACTGGCATCTTGCCATGCTTGCTCGATGGTGACTGTTTTATCAGGTCCAATTCTTCAACTCCAGACCTTGGGATATTATTTGAACTTGGAATTTCTTACATTCGCAAT
Peptide sequence:
MVTVLSGPILQLQTLGYYLNLEFLTFAIVEAHSDKEEDDTTEDDEEETGGEEEESEGDGEGKQEQASPKQAETETVTYIALGDFAAQQTGDLTFKKGDVLHIIEKKPDGWWLAKDAEGVEGLIPRTYLEPYNKEDKLESSEGSEEGGEEDGEEDGEEDVEVVDETADGAQVKQRTDSHWSAVRKAISEQINTVDVLATMGAIPAGFRPSTLSQLLDEAGNQFRASYFLQPELTTSQLAFRDLTWDAKAGTIMSRPSRVSLILTLWSCKMIPLPGTSIQVLSRHIRLCLFDGSKVLSNIHTVRAVWQPKKPKTWTFSPQVTGILPCLLDGDCFIRSNSSTPDLGILFELGISYIRN
IRESfinder result
IRESfinder score
0.412263486
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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