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mmu_circStam2_639
Basic information of circular RNA
PanCircBase ID:
mmu_circStam2_639
mm39_Chr. Position ID:
chr2|52590016|52599702|-
Gene name:
Stam2
Transcript:
ENSMUST00000102759.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
13,12,11,10,9,8
Exon/intron offsets:
0,3097,6394,7913,8138,9591
Genomic length:
9686
Exon/intron sizes in nt:
167,151,55,88,83,95
Flanking exon/introns:
chr2:52584949-52590016|chr2:52599702-52604829
Splice length:
639
Other database IDs:
circBase: hsa_circ_0117643, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_122657
Human Ortholog IDs:
Mature spliced Sequence:
TGACGCCAACTGGTGGCAAGGAGAAAATCACAGAGGAACAGGACTCTTCCCCTCCAACTTTGTAACGACTGACTTAAGCACAGAGGTTGAGACAGCAACGGTGGACAAATTGAATGTAATTGATGATGATGTGGAGGAAATTAAGAAATCAGAACCTGAGCCTGTTTATATAGATGAGGGTAAAATGGATAGAGCCCTGCAGATTCTCCAGAGCATAGATCCAAAAGAGTCAAAACCCGACTCCCAAGACCTCTTGGACTTGGAAGATGTTTGCCAACAGATGGGTCCGATGATAGATGAAAAACTTGAAGAGATTGATAGGAAGCATTCAGAACTGTCTGAGTTGAACGTAAAGGTGCTGGAAGCCCTGGACCTGTACAATAAGTTGGTGAATGAAGCGCCTGTGTACTCGGTCTATTCAAAGCTGCATCCCGCACATTACCCACCCGCAGCAGCTGGGGTTCCAGTGCAGACATATCCAGTCCAGTCGCATGGTGGAAACTACCTGGGCCACGGCATTCACCAAGTATCTGTTGCCCAGAACTATAACCTAGGACCTGATCCTATGGGCTCGCTGAGATCTCTGCCTCCAAATATGAACTCGGTAACAGCACACACCGTCCAACCTCCATACTTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGATCCTATGGGCTCGCTG
60.04
GCTGTCTCAACCTCTGTGCT
59.97
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTATGGGCTCGCTGAGAT
60.18
GCTGTCTCAACCTCTGTGCT
59.97
174
PCR template sequence:
AGAACTATAACCTAGGACCTGATCCTATGGGCTCGCTGAGATCTCTGCCTCCAAATATGAACTCGGTAACAGCACACACCGTCCAACCTCCATACTTAAGTGACGCCAACTGGTGGCAAGGAGAAAATCACAGAGGAACAGGACTCTTCCCCTCCAACTTTGTAACGACTGACTTAAGCACAGAGGTTGAGACAGCAACG
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-181a-5p(1), mmu-miR-196a-5p(1), mmu-miR-709(1), mmu-miR-181b-5p(1), mmu-miR-190b-5p(1), mmu-miR-484(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCCATACTTAAGTGACGCCAACTGG
siRNA sets
TTGGCGTCACTTAAGTATG, TGGCGTCACTTAAGTATGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSTAM2_639_ORF_1
1.1063
0.220518003
0.996189509
1092
ORF sequence:
ATGGATAGAGCCCTGCAGATTCTCCAGAGCATAGATCCAAAAGAGTCAAAACCCGACTCCCAAGACCTCTTGGACTTGGAAGATGTTTGCCAACAGATGGGTCCGATGATAGATGAAAAACTTGAAGAGATTGATAGGAAGCATTCAGAACTGTCTGAGTTGAACGTAAAGGTGCTGGAAGCCCTGGACCTGTACAATAAGTTGGTGAATGAAGCGCCTGTGTACTCGGTCTATTCAAAGCTGCATCCCGCACATTACCCACCCGCAGCAGCTGGGGTTCCAGTGCAGACATATCCAGTCCAGTCGCATGGTGGAAACTACCTGGGCCACGGCATTCACCAAGTATCTGTTGCCCAGAACTATAACCTAGGACCTGATCCTATGGGCTCGCTGAGATCTCTGCCTCCAAATATGAACTCGGTAACAGCACACACCGTCCAACCTCCATACTTAAGTGACGCCAACTGGTGGCAAGGAGAAAATCACAGAGGAACAGGACTCTTCCCCTCCAACTTTGTAACGACTGACTTAAGCACAGAGGTTGAGACAGCAACGGTGGACAAATTGAATGTAATTGATGATGATGTGGAGGAAATTAAGAAATCAGAACCTGAGCCTGTTTATATAGATGAGGGTAAAATGGATAGAGCCCTGCAGATTCTCCAGAGCATAGATCCAAAAGAGTCAAAACCCGACTCCCAAGACCTCTTGGACTTGGAAGATGTTTGCCAACAGATGGGTCCGATGATAGATGAAAAACTTGAAGAGATTGATAGGAAGCATTCAGAACTGTCTGAGTTGAACGTAAAGGTGCTGGAAGCCCTGGACCTGTACAATAAGTTGGTGAATGAAGCGCCTGTGTACTCGGTCTATTCAAAGCTGCATCCCGCACATTACCCACCCGCAGCAGCTGGGGTTCCAGTGCAGACATATCCAGTCCAGTCGCATGGTGGAAACTACCTGGGCCACGGCATTCACCAAGTATCTGTTGCCCAGAACTATAACCTAGGACCTGATCCTATGGGCTCGCTGAGATCTCTGCCTCCAAATATGAACTCGGTAACAGCACACACCGTCCAACCTCCATACTTA
Peptide sequence:
MDRALQILQSIDPKESKPDSQDLLDLEDVCQQMGPMIDEKLEEIDRKHSELSELNVKVLEALDLYNKLVNEAPVYSVYSKLHPAHYPPAAAGVPVQTYPVQSHGGNYLGHGIHQVSVAQNYNLGPDPMGSLRSLPPNMNSVTAHTVQPPYLSDANWWQGENHRGTGLFPSNFVTTDLSTEVETATVDKLNVIDDDVEEIKKSEPEPVYIDEGKMDRALQILQSIDPKESKPDSQDLLDLEDVCQQMGPMIDEKLEEIDRKHSELSELNVKVLEALDLYNKLVNEAPVYSVYSKLHPAHYPPAAAGVPVQTYPVQSHGGNYLGHGIHQVSVAQNYNLGPDPMGSLRSLPPNMNSVTAHTVQPPYL
IRESfinder result
IRESfinder score
0.575209977
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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