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mmu_circSecisbp2l_964
Basic information of circular RNA
PanCircBase ID:
mmu_circSecisbp2l_964
mm39_Chr. Position ID:
chr2|125602191|125615420|-
Gene name:
Secisbp2l
Transcript:
ENSMUST00000053699.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
8,7,6,5,4,3
Exon/intron offsets:
0,7103,7537,7835,11137,12904
Genomic length:
13229
Exon/intron sizes in nt:
13,51,16,25,22,71,36,300
Flanking exon/introns:
chr2:125600166-125602191|chr2:125615420-125617472
Splice length:
964
Other database IDs:
CIRCpedia: MMU_CIRCpedia_6545, circAtlas: mmu-Secisbp2l_0007
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_130630
Human Ortholog IDs:
Mature spliced Sequence:
ACAATTTCCTTTATATAACAACGATATACGATGGCAGCAGCCCAGCCCAAGTCCTACCGGACCCTACCTTGCCTACCCCATTATATCTGCTCAGCCACCTGTTTCCACAGAGTACACCTATTACCAGCTGATGCCAGCACCCTGTGCCCAAGTTATGGGCTTCTATCATCCTTTTCCTACCCCTTACTCCAGCACCTTCCAGGCTGCAAACACTGTCAATGCCATAAGCACAGAATGCACCGAGCGTCCAAATCAGCTGGGGCAGGCCTTCCCGCTGTCCAGTCATCGGAGCAGGAATGGTAACAGAGGGCCAGTGGTGCCAAAACCGCAGCTTTTACAACAACATATAAAAAACAAAAGACCACAGGTGAAGAATGTGGCTACTCAGAAAGAAACAAGCGCAACAGGTCCTGATAGCCGATCAAAAATTGTGCTTCTGGTAGATGCTTCACAGCAAACTGATTTCCCATCAGACATCGCTAATAAGTCTCTCTCGGAGAGCACAGCCACAATGCTCTGGAAAGCCAAAGGCAGGAGGAGAAGAGCGTCCCACCCTGCTGTAGAGTCCTCCAGTGAGCAGGGCGCCAGTGAAGCTGACATCGACAGCGACAGCGGCTACTGCAGTCCCAAGCACAACAACCAGTCTGCGCCAGGGGCTCTGCGCGACCCTGCCTCTGGGACCATGAACCGTTTGGAGTCATCGGGCTGTTCAGGTGGTGTAAACTGGCCCAAAGTAACTTGCCAGGCAACTCAGAAAAGACCTTGGATGGAAAAGAACCAAGCATTTTCTAGAGGTGGAAGGCAAACTGAACAAAGAAATAATTTACAGGTTGGATTCAGATGCAGAGGGCACAGTACTTCCTCAGAAAGAAGACAGAATTTGCAAAAGAGACAAGACAATAAGCACTTAAACTCTACTCAGTCTCACAGAAGTGACCCAAATTCCGAGTCTTTATATTTTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAAAAGAGACAAGACAATAAGCA
59.7
CAAGGTAGGGTCCGGTAGGA
60.03
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAAAAGAGACAAGACAATAAGCAC
59.37
CAAGGTAGGGTCCGGTAGGA
60.03
153
PCR template sequence:
AGAAAGAAGACAGAATTTGCAAAAGAGACAAGACAATAAGCACTTAAACTCTACTCAGTCTCACAGAAGTGACCCAAATTCCGAGTCTTTATATTTTGAGACAATTTCCTTTATATAACAACGATATACGATGGCAGCAGCCCAGCCCAAGTCCTACCGGACCCTACCTTGCCTACCCCATTATATCTGCTCAGCCACCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-328-3p(1), mmu-miR-320-3p(1), mmu-miR-96-5p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTATATTTTGAGACAATTTCCTTTA
siRNA sets
AAATTGTCTCAAAATATAA, AAAGGAAATTGTCTCAAAA, TAAAGGAAATTGTCTCAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSECISBP2L_964_ORF_1
0.7311
0.067605628
0.923869175
852
ORF sequence:
ATGCCAGCACCCTGTGCCCAAGTTATGGGCTTCTATCATCCTTTTCCTACCCCTTACTCCAGCACCTTCCAGGCTGCAAACACTGTCAATGCCATAAGCACAGAATGCACCGAGCGTCCAAATCAGCTGGGGCAGGCCTTCCCGCTGTCCAGTCATCGGAGCAGGAATGGTAACAGAGGGCCAGTGGTGCCAAAACCGCAGCTTTTACAACAACATATAAAAAACAAAAGACCACAGGTGAAGAATGTGGCTACTCAGAAAGAAACAAGCGCAACAGGTCCTGATAGCCGATCAAAAATTGTGCTTCTGGTAGATGCTTCACAGCAAACTGATTTCCCATCAGACATCGCTAATAAGTCTCTCTCGGAGAGCACAGCCACAATGCTCTGGAAAGCCAAAGGCAGGAGGAGAAGAGCGTCCCACCCTGCTGTAGAGTCCTCCAGTGAGCAGGGCGCCAGTGAAGCTGACATCGACAGCGACAGCGGCTACTGCAGTCCCAAGCACAACAACCAGTCTGCGCCAGGGGCTCTGCGCGACCCTGCCTCTGGGACCATGAACCGTTTGGAGTCATCGGGCTGTTCAGGTGGTGTAAACTGGCCCAAAGTAACTTGCCAGGCAACTCAGAAAAGACCTTGGATGGAAAAGAACCAAGCATTTTCTAGAGGTGGAAGGCAAACTGAACAAAGAAATAATTTACAGGTTGGATTCAGATGCAGAGGGCACAGTACTTCCTCAGAAAGAAGACAGAATTTGCAAAAGAGACAAGACAATAAGCACTTAAACTCTACTCAGTCTCACAGAAGTGACCCAAATTCCGAGTCTTTATATTTTGAGACAATTTCCTTTATATAA
Peptide sequence:
MPAPCAQVMGFYHPFPTPYSSTFQAANTVNAISTECTERPNQLGQAFPLSSHRSRNGNRGPVVPKPQLLQQHIKNKRPQVKNVATQKETSATGPDSRSKIVLLVDASQQTDFPSDIANKSLSESTATMLWKAKGRRRRASHPAVESSSEQGASEADIDSDSGYCSPKHNNQSAPGALRDPASGTMNRLESSGCSGGVNWPKVTCQATQKRPWMEKNQAFSRGGRQTEQRNNLQVGFRCRGHSTSSERRQNLQKRQDNKHLNSTQSHRSDPNSESLYFETISFI
IRESfinder result
IRESfinder score
0.504650189
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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