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mmu_circSec61a2_1237
Basic information of circular RNA
PanCircBase ID:
mmu_circSec61a2_1237
mm39_Chr. Position ID:
chr2|5878553|5898032|-
Gene name:
Sec61a2
Transcript:
ENSMUST00000102981.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,484,2621,3098,4112,8838,9075,12756,17547,19411
Genomic length:
19479
Exon/intron sizes in nt:
77,192,198,161,154,110,132,79,66,68
Flanking exon/introns:
chr2:5876832-5878553|chr2:5898032-5900067
Splice length:
1237
Other database IDs:
circAtlas: mmu-Sec61a2_0002
circBase: hsa_circ_0092934, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_128785
Human Ortholog IDs:
Mature spliced Sequence:
TCAAGTTTTTAGAAGTTATTAAACCTTTCTGTGCAGTTCTACCAGAAATTCAGAAGCCTGAAAGGAAAATTCAGTTTAGAGAGAAGGTACTATGGACTGCTATAACACTCTTCATTTTCTTAGTATGCTGTCAGATTCCGCTGTTTGGGATCATGTCATCGGACTCTGCAGATCCCTTCTACTGGATGAGAGTTATTCTTGCATCCAACAGAGGAACATTGATGGAATTGGGTATTTCCCCAATTGTAACGTCTGGTTTGATTATGCAGTTGTTAGCTGGAGCCAAAATCATTGAAGTTGGAGACACACCCAAAGATAGAGCTCTGTTCAATGGAGCCCAGAAATTATTTGGTATGATCATTACCATTGGGCAAGCCATTGTGTATGTCATGACGGGGATGTACGGGGACCCTGCGGAAATGGGTGCTGGGATCTGTCTCCTTATCATTATTCAGTTGTTTGTTGCTGGTTTGATTGTGCTGCTGTTAGATGAGCTGCTACAGAAGGGTTACGGCTTGGGGTCTGGGATTTCCCTCTTTATTGCCACCAACATCTGTGAAACCATTGTCTGGAAGGCCTTTAGTCCCACTACCATTAACACTGGCAGAGGTACGGAGTTTGAAGGTGCAGTCATAGCTCTGTTTCATTTGCTGGCCACCAGGACAGACAAGGTGCGAGCCTTGAGGGAGGCTTTCTATAGGCAGAACCTCCCCAACCTCATGAACCTCATCGCCACAGTGTTCGTGTTTGCTGTCGTCATCTATTTTCAGGGGTTTCGTGTTGACTTGCCCATTAAGTCGGCACGGTATCGTGGACAGTACAGTAGCTATCCTATCAAGCTCTTCTACACGTCGAATATTCCCATAATCCTCCAGTCTGCCCTAGTTTCAAACTTGTACGTCATTTCCCAGATGCTGTCTGTTCGATTTAGTGGCAACTTCTTAGTAAACTTACTAGGACAGTGGGCCGATGTCAGTGGGGGAGGGCCTGCTCGCTCCTACCCTGTTGGCGGCCTTTGTTACTATCTGTCTCCTCCTGAGTCTATGGGAGCCATATTTGAGGATCCTGTTCATGTAGTTGTATATATTATCTTCATGTTGGGGTCATGTGCATTCTTTTCTAAGACGTGGATAGAAGTTTCTGGTTCTTCAGCCAAAGATGTGGCCAAGCAACTTAAAGAACAGCAGATGGTGATGAGGGGTCACAGAGATACCTCCATGGTCCATGAGCTGAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTGATGAGGGGTCACAGA
60.18
GCAGTCCATAGTACCTTCTCTCT
58.79
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCAGATGGTGATGAGGGG
60.18
GCAGTCCATAGTACCTTCTCTCT
58.79
156
PCR template sequence:
TTTCTGGTTCTTCAGCCAAAGATGTGGCCAAGCAACTTAAAGAACAGCAGATGGTGATGAGGGGTCACAGAGATACCTCCATGGTCCATGAGCTGAACAGTCAAGTTTTTAGAAGTTATTAAACCTTTCTGTGCAGTTCTACCAGAAATTCAGAAGCCTGAAAGGAAAATTCAGTTTAGAGAGAAGGTACTATGGACTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-15b-5p(1), mmu-miR-217-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-300-3p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGAGCTGAACAGTCAAGTTTTTAGA
siRNA sets
TAAAAACTTGACTGTTCAG, AAAAACTTGACTGTTCAGC, AAAACTTGACTGTTCAGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC61A2_1237_ORF_1
1.1071
0.111173737
0.994518679
1107
ORF sequence:
ATGTCATCGGACTCTGCAGATCCCTTCTACTGGATGAGAGTTATTCTTGCATCCAACAGAGGAACATTGATGGAATTGGGTATTTCCCCAATTGTAACGTCTGGTTTGATTATGCAGTTGTTAGCTGGAGCCAAAATCATTGAAGTTGGAGACACACCCAAAGATAGAGCTCTGTTCAATGGAGCCCAGAAATTATTTGGTATGATCATTACCATTGGGCAAGCCATTGTGTATGTCATGACGGGGATGTACGGGGACCCTGCGGAAATGGGTGCTGGGATCTGTCTCCTTATCATTATTCAGTTGTTTGTTGCTGGTTTGATTGTGCTGCTGTTAGATGAGCTGCTACAGAAGGGTTACGGCTTGGGGTCTGGGATTTCCCTCTTTATTGCCACCAACATCTGTGAAACCATTGTCTGGAAGGCCTTTAGTCCCACTACCATTAACACTGGCAGAGGTACGGAGTTTGAAGGTGCAGTCATAGCTCTGTTTCATTTGCTGGCCACCAGGACAGACAAGGTGCGAGCCTTGAGGGAGGCTTTCTATAGGCAGAACCTCCCCAACCTCATGAACCTCATCGCCACAGTGTTCGTGTTTGCTGTCGTCATCTATTTTCAGGGGTTTCGTGTTGACTTGCCCATTAAGTCGGCACGGTATCGTGGACAGTACAGTAGCTATCCTATCAAGCTCTTCTACACGTCGAATATTCCCATAATCCTCCAGTCTGCCCTAGTTTCAAACTTGTACGTCATTTCCCAGATGCTGTCTGTTCGATTTAGTGGCAACTTCTTAGTAAACTTACTAGGACAGTGGGCCGATGTCAGTGGGGGAGGGCCTGCTCGCTCCTACCCTGTTGGCGGCCTTTGTTACTATCTGTCTCCTCCTGAGTCTATGGGAGCCATATTTGAGGATCCTGTTCATGTAGTTGTATATATTATCTTCATGTTGGGGTCATGTGCATTCTTTTCTAAGACGTGGATAGAAGTTTCTGGTTCTTCAGCCAAAGATGTGGCCAAGCAACTTAAAGAACAGCAGATGGTGATGAGGGGTCACAGAGATACCTCCATGGTCCATGAGCTGAACAGTCAAGTTTTTAGAAGTTATTAA
Peptide sequence:
MSSDSADPFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLFGMIITIGQAIVYVMTGMYGDPAEMGAGICLLIIIQLFVAGLIVLLLDELLQKGYGLGSGISLFIATNICETIVWKAFSPTTINTGRGTEFEGAVIALFHLLATRTDKVRALREAFYRQNLPNLMNLIATVFVFAVVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNLYVISQMLSVRFSGNFLVNLLGQWADVSGGGPARSYPVGGLCYYLSPPESMGAIFEDPVHVVVYIIFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHRDTSMVHELNSQVFRSY
IRESfinder result
IRESfinder score
0.723590649
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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