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mmu_circR3hdm1_1129
Basic information of circular RNA
PanCircBase ID:
mmu_circR3hdm1_1129
mm39_Chr. Position ID:
chr1|128102685|128114646|+
Gene name:
R3hdm1
Transcript:
ENSMUST00000036288.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
8,9,10,11,12,13,14,15,16
Exon/intron offsets:
0,143,3934,4138,6768,6889,7037,9451,11809
Genomic length:
11961
Exon/intron sizes in nt:
60,14,11,09,96,38,51,20,00,00,000
Flanking exon/introns:
chr1:128096794-128102685|chr1:128114646-128118374
Splice length:
1129
Other database IDs:
CIRCpedia: MMU_CIRCpedia_225259, circAtlas: mmu-R3hdm1_0005
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_117086
Human Ortholog IDs:
Mature spliced Sequence:
GGACAGAATGATGCTGCTGAAATTGGAACAAGAAATTTTAGATTTCATTGGTAATAATGAGTCCCCACGTAAGAAGTTTCCCCCGATGACATCTTACCACAGGATGCTGTTACACAGAGTGGCTGCCTACTTTGGATTAGACCACAATGTTGATCAGAGTGGGAAGTCTGTCATAGTGAACAAAACTAGCAACACAAGAATACCTGATCAGAAATTTAATGAACATATAAAGGATGATAGAGGTGAAGACTTTCAGAAACGATACATCCTTAAGAGAGATAACTCTAGCTTTGACAAAGATGATAGCCAGATGAGAATACGTTTGAAAGATGACAGAAGAAGCAAATCTATAGAAGAAAGAGAAGAAGAATACCAGAGAGCTAGAGACCGAATATTTTCCCAAGATTCCCTGTGTTCCCAAGAAAACTACATTATTGACAAAAGAATCCAAGATGAGGACACTATTGGTACCCAGCAGAGGCGCCAGATATTTAGAGTTAATAAAGATGCTTCAGGCCGATCGACAAACAGCCATCAGAGCAGCACTGAAAATGAGTTGAAATACTCAGAGCCACGACCCTGGAGCAGCACCGATTCAGACAGCTCCCTCAGAAACCTGAAACCCGCTGTCACCAAAGCCAGCAGCTTTAGCGGAATCTCAGTCCTGACAAGAGGTGATAGCTCTGGAAGCAGCAAAAGCATAGGCAGGCTTTCAAAAACAGGATCTGAGTCTTCAGGTAGTGTAGGGTCCTCTACAGGCTCTCTTTCTCACACCCAGCAGCCTCTCCCAGGTTCAGCTCTTAGCCAGTCTTCTCATGGCGCACCTGTCATCTACCCGGCAGCCAGCAATCACAGTTCTCTTTCCTTTGATGGTGGCCTCAGTGGTCAAGGTGCATCTCCTAGCACTAGCTTCCTTTTGCTTCCCTTGGAAGCAACTGGCATACCACCTGGCAGTATTCTGATCAACCCACAAACAGGTCAGCCCTTCTTAAACCCAGATGGAAGTCCAGTTGTGTACAATCCTCCTATGACTCAACAGCCAGTTCGAACCCAAGTGCCTGGTCCTCCACAGCCACCTCTGCCACCCCCACCACCTCAGCAGCCAGCAGCCAGTCACATGTTCTCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACAGCCAGTTCGAACCCAA
60.11
GGGAAACTTCTTACGTGGGGA
59.65
177
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTCGAACCCAAGTGCCTG
60.54
TCGGGGGAAACTTCTTACGTG
60
174
PCR template sequence:
GACTCAACAGCCAGTTCGAACCCAAGTGCCTGGTCCTCCACAGCCACCTCTGCCACCCCCACCACCTCAGCAGCCAGCAGCCAGTCACATGTTCTCACAGGGACAGAATGATGCTGCTGAAATTGGAACAAGAAATTTTAGATTTCATTGGTAATAATGAGTCCCCACGTAAGAAGTTTCCCCCGATGACATCTTACCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-15a-5p(1), mmu-miR-7b-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-103-3p(1), mmu-miR-200c-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-146a-5p(1), mmu-miR-298-5p(1), mmu-miR-7a-5p(1), mmu-miR-194-5p(1), mmu-miR-107-3p(1), mmu-miR-383-5p(1), mmu-miR-669d-5p(1), mmu-miR-3470b(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATGTTCTCACAGGGACAGAATGATG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCR3HDM1_1129_ORF_1
0.8226
0.091922658
0.993916567
1176
ORF sequence:
ATGATGCTGCTGAAATTGGAACAAGAAATTTTAGATTTCATTGGTAATAATGAGTCCCCACGTAAGAAGTTTCCCCCGATGACATCTTACCACAGGATGCTGTTACACAGAGTGGCTGCCTACTTTGGATTAGACCACAATGTTGATCAGAGTGGGAAGTCTGTCATAGTGAACAAAACTAGCAACACAAGAATACCTGATCAGAAATTTAATGAACATATAAAGGATGATAGAGGTGAAGACTTTCAGAAACGATACATCCTTAAGAGAGATAACTCTAGCTTTGACAAAGATGATAGCCAGATGAGAATACGTTTGAAAGATGACAGAAGAAGCAAATCTATAGAAGAAAGAGAAGAAGAATACCAGAGAGCTAGAGACCGAATATTTTCCCAAGATTCCCTGTGTTCCCAAGAAAACTACATTATTGACAAAAGAATCCAAGATGAGGACACTATTGGTACCCAGCAGAGGCGCCAGATATTTAGAGTTAATAAAGATGCTTCAGGCCGATCGACAAACAGCCATCAGAGCAGCACTGAAAATGAGTTGAAATACTCAGAGCCACGACCCTGGAGCAGCACCGATTCAGACAGCTCCCTCAGAAACCTGAAACCCGCTGTCACCAAAGCCAGCAGCTTTAGCGGAATCTCAGTCCTGACAAGAGGTGATAGCTCTGGAAGCAGCAAAAGCATAGGCAGGCTTTCAAAAACAGGATCTGAGTCTTCAGGTAGTGTAGGGTCCTCTACAGGCTCTCTTTCTCACACCCAGCAGCCTCTCCCAGGTTCAGCTCTTAGCCAGTCTTCTCATGGCGCACCTGTCATCTACCCGGCAGCCAGCAATCACAGTTCTCTTTCCTTTGATGGTGGCCTCAGTGGTCAAGGTGCATCTCCTAGCACTAGCTTCCTTTTGCTTCCCTTGGAAGCAACTGGCATACCACCTGGCAGTATTCTGATCAACCCACAAACAGGTCAGCCCTTCTTAAACCCAGATGGAAGTCCAGTTGTGTACAATCCTCCTATGACTCAACAGCCAGTTCGAACCCAAGTGCCTGGTCCTCCACAGCCACCTCTGCCACCCCCACCACCTCAGCAGCCAGCAGCCAGTCACATGTTCTCACAGGGACAGAATGATGCTGCTGAAATTGGAACAAGAAATTTTAGATTTCATTGGTAA
Peptide sequence:
MMLLKLEQEILDFIGNNESPRKKFPPMTSYHRMLLHRVAAYFGLDHNVDQSGKSVIVNKTSNTRIPDQKFNEHIKDDRGEDFQKRYILKRDNSSFDKDDSQMRIRLKDDRRSKSIEEREEEYQRARDRIFSQDSLCSQENYIIDKRIQDEDTIGTQQRRQIFRVNKDASGRSTNSHQSSTENELKYSEPRPWSSTDSDSSLRNLKPAVTKASSFSGISVLTRGDSSGSSKSIGRLSKTGSESSGSVGSSTGSLSHTQQPLPGSALSQSSHGAPVIYPAASNHSSLSFDGGLSGQGASPSTSFLLLPLEATGIPPGSILINPQTGQPFLNPDGSPVVYNPPMTQQPVRTQVPGPPQPPLPPPPPQQPAASHMFSQGQNDAAEIGTRNFRFHW
IRESfinder result
IRESfinder score
0.65844518
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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