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mmu_circGm21970_449
Basic information of circular RNA
PanCircBase ID:
mmu_circGm21970_449
mm39_Chr. Position ID:
chr16|91204505|91211667|+
Gene name:
Gm21970
Transcript:
ENSMUST00000160764.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
3,4,5
Exon/intron offsets:
0,4265,6995
Genomic length:
7162
Exon/intron sizes in nt:
12,41,58,167
Flanking exon/introns:
chr16:91190801-91204505|chr16:91211667-91216219
Splice length:
449
Other database IDs:
CIRCpedia: MMU_CIRCpedia_223272, circAtlas: mmu-Gm21970_0001
Human Ortholog IDs:
Mature spliced Sequence:
CTCTAGGAATGATTCCACCCCCTGAGAAGGTCAGAATGAATTCAGTTAATTTCAAGAACATTCTACAGTGGGAGGTACCTGCTTTCCCCAAAACGAACCTGACTTTCACAGCTCAGTATGAAAGTTACAGGTCTTTCCAAGATCACTGCAAGCGCACTGCCTCGACTCAGTGCGACTTCTCTCATCTTTCTAAATACGGAGACTACACTGTGAGAGTCAGGGCTGAATTGGCGGATGAACATTCGGAGTGGGTCAATGTCACCTTCTGCCCCGTGGAAGACACCATCATTGGACCTCCTGAGATGCAGATAGAATCCCTTGCTGAGTCTTTACACCTGCGTTTCTCAGCCCCACAAATTGAGAATGAGCCTGAGACGTGGACCTTGAAGAACATTTATGACTCATGGGCTTACAGAGTGCAATACTGGAAAAATGGGACTAATGAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AATGAGCCTGAGACGTGGAC
59.75
GGAAAGCAGGTACCTCCCAC
60.04
174
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAATGAGCCTGAGACGTGGA
59.47
GGAAAGCAGGTACCTCCCAC
60.04
175
PCR template sequence:
CCCACAAATTGAGAATGAGCCTGAGACGTGGACCTTGAAGAACATTTATGACTCATGGGCTTACAGAGTGCAATACTGGAAAAATGGGACTAATGAGAAGCTCTAGGAATGATTCCACCCCCTGAGAAGGTCAGAATGAATTCAGTTAATTTCAAGAACATTCTACAGTGGGAGGTACCTGCTTTCCCCAAAACGAACCT
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-27a-3p(1), mmu-miR-32-5p(1), mmu-miR-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-92a-3p(1), mmu-miR-7a-5p(1), mmu-miR-25-3p(1), mmu-miR-128-3p(1), mmu-miR-541-5p(1), mmu-miR-34b-5p(1), mmu-miR-484(1), mmu-miR-3470b(1), mmu-miR-1199-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACTAATGAGAAGCTCTAGGAATGAT
siRNA sets
ATCATTCCTAGAGCTTCTC, ATTCCTAGAGCTTCTCATT, TCATTCCTAGAGCTTCTCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGM21970_449_ORF_1
0.9147
0.179376538
0.597724417
447
ORF sequence:
ATGATTCCACCCCCTGAGAAGGTCAGAATGAATTCAGTTAATTTCAAGAACATTCTACAGTGGGAGGTACCTGCTTTCCCCAAAACGAACCTGACTTTCACAGCTCAGTATGAAAGTTACAGGTCTTTCCAAGATCACTGCAAGCGCACTGCCTCGACTCAGTGCGACTTCTCTCATCTTTCTAAATACGGAGACTACACTGTGAGAGTCAGGGCTGAATTGGCGGATGAACATTCGGAGTGGGTCAATGTCACCTTCTGCCCCGTGGAAGACACCATCATTGGACCTCCTGAGATGCAGATAGAATCCCTTGCTGAGTCTTTACACCTGCGTTTCTCAGCCCCACAAATTGAGAATGAGCCTGAGACGTGGACCTTGAAGAACATTTATGACTCATGGGCTTACAGAGTGCAATACTGGAAAAATGGGACTAATGAGAAGCTCTAG
Peptide sequence:
MIPPPEKVRMNSVNFKNILQWEVPAFPKTNLTFTAQYESYRSFQDHCKRTASTQCDFSHLSKYGDYTVRVRAELADEHSEWVNVTFCPVEDTIIGPPEMQIESLAESLHLRFSAPQIENEPETWTLKNIYDSWAYRVQYWKNGTNEKL
IRESfinder result
IRESfinder score
0.669589875
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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