top of page
mmu_circSmchd1_1157
Basic information of circular RNA
PanCircBase ID:
mmu_circSmchd1_1157
mm39_Chr. Position ID:
chr17|71688326|71707193|-
Gene name:
Smchd1
Transcript:
ENSMUST00000127430.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
30,29,28,27,26,25,24,23
Exon/intron offsets:
0,5613,8411,9095,10020,13385,17220,18727
Genomic length:
18867
Exon/intron sizes in nt:
12,61,68,11,98,91,49,20,00,00,000
Flanking exon/introns:
chr17:71687203-71688326|chr17:71707193-71710092
Splice length:
1157
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTCCCCCTCATCAACTAAAGGTGAAACCTGACTCAGAAGTTCTGGTTATAGAGAATGGAACAGCTTTCCCATTTCAGGTGGAAGTTGTGGATGAGTCAGACAACATAACAGCACAACCAAAGCTGATCGTCCACTGTAAGTTTCTAGGTGCTCCAAACCTACCAGTCTATACTGTGGATTGCAGTAGCTCTGGAACTAGCATCCTAACAGGGTCACCCATTCAAGTTCAGAACATTAAGAAAGACCAGAAGACACTGACCGCCAGGATTGAGATACCTAGCTGTAAAGATGTGTCACCTGTTGAAAAGACGATCAAGTTACTTCCCAGTAGCCACGCTGCTTGCCTGCAGATCTTTAGTGTAGAGGAGCAAAAGGCGATCCAGATCAAACATCAGGATGAGGTTACTTGGGTAGCAGGTGATGTAATACGCAATCTAATTTTTCAAATGTATGACGAAGGAGAAAGAGAAATCAATATTACACCATCCTTGGCAGAAAAAATTAAGGTTAATTGGACTCCTGAGGTGAACAAAGAACATTTGGTACAAGGTCTCCTTCCTGATGTGCAAGTACCAACATCTGTGAAAGATGTCCGCTACTGCCATGTTTCTTTCCAAGATGACCACGTGTGTCTGGAGAGCGCCTTTACAGTAAGACCACTTCCTGATGATCCCAAACATTTAAAATGTGAATTAAAAGGAGGAAAAACAGTGCAGATGGGCCAAGAGCTTCAAGGAGAAATAGTTGTAATAATTGCAGATCAGTATGGAAATCAGATTTCATCATTTTCACCTGATTCCTTATCTACTTTGTCGATTACTGGAGATGGCCTTGACAGCTCAAACTTGAAAATCACCTTGGAGGCCAACTCACAGAGCGTAAGTGTGCAAGGCATCAGGTTTACTCCAGGGCCTCCTGGACCCAAGGATCTGTGTTTTACTTGGCGAGAGTTTTCTGACTTTCTGCGCGTGCAACTGGTTTCTGGACCTCCAACCAAGCTGCTGCTTATGGACTGGCCAGAGCTGAAAGAGTCCATTCCTGTGATTAATGGAAGACAATTAGAGAACCCTCTCATTGTTCAACTTTGTGATCAGTGGGATAATCCTGCTTTAGTCCCAAACGTTAAAATATGTCTCATAAAAGCAAGCAGCTTAAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGCTTTAGTCCCAAACGT
59.58
CTCATCCACAACTTCCACCTGA
59.96
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGCTTTAGTCCCAAACGT
59.58
GACTCATCCACAACTTCCACCT
59.96
152
PCR template sequence:
ATTAGAGAACCCTCTCATTGTTCAACTTTGTGATCAGTGGGATAATCCTGCTTTAGTCCCAAACGTTAAAATATGTCTCATAAAAGCAAGCAGCTTAAGGGTCCCCCTCATCAACTAAAGGTGAAACCTGACTCAGAAGTTCTGGTTATAGAGAATGGAACAGCTTTCCCATTTCAGGTGGAAGTTGTGGATGAGTCAGA
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-9-5p(1), mmu-miR-140-5p(1), mmu-miR-15a-5p(1), mmu-miR-15b-5p(1), mmu-miR-10a-5p(1), mmu-miR-127-5p(1), mmu-miR-362-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGCAGCTTAAGGGTCCCCCTCATCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMCHD1_1157_ORF_1
0.9814
0.075742125
0.995453741
1185
ORF sequence:
ATGTCTCATAAAAGCAAGCAGCTTAAGGGTCCCCCTCATCAACTAAAGGTGAAACCTGACTCAGAAGTTCTGGTTATAGAGAATGGAACAGCTTTCCCATTTCAGGTGGAAGTTGTGGATGAGTCAGACAACATAACAGCACAACCAAAGCTGATCGTCCACTGTAAGTTTCTAGGTGCTCCAAACCTACCAGTCTATACTGTGGATTGCAGTAGCTCTGGAACTAGCATCCTAACAGGGTCACCCATTCAAGTTCAGAACATTAAGAAAGACCAGAAGACACTGACCGCCAGGATTGAGATACCTAGCTGTAAAGATGTGTCACCTGTTGAAAAGACGATCAAGTTACTTCCCAGTAGCCACGCTGCTTGCCTGCAGATCTTTAGTGTAGAGGAGCAAAAGGCGATCCAGATCAAACATCAGGATGAGGTTACTTGGGTAGCAGGTGATGTAATACGCAATCTAATTTTTCAAATGTATGACGAAGGAGAAAGAGAAATCAATATTACACCATCCTTGGCAGAAAAAATTAAGGTTAATTGGACTCCTGAGGTGAACAAAGAACATTTGGTACAAGGTCTCCTTCCTGATGTGCAAGTACCAACATCTGTGAAAGATGTCCGCTACTGCCATGTTTCTTTCCAAGATGACCACGTGTGTCTGGAGAGCGCCTTTACAGTAAGACCACTTCCTGATGATCCCAAACATTTAAAATGTGAATTAAAAGGAGGAAAAACAGTGCAGATGGGCCAAGAGCTTCAAGGAGAAATAGTTGTAATAATTGCAGATCAGTATGGAAATCAGATTTCATCATTTTCACCTGATTCCTTATCTACTTTGTCGATTACTGGAGATGGCCTTGACAGCTCAAACTTGAAAATCACCTTGGAGGCCAACTCACAGAGCGTAAGTGTGCAAGGCATCAGGTTTACTCCAGGGCCTCCTGGACCCAAGGATCTGTGTTTTACTTGGCGAGAGTTTTCTGACTTTCTGCGCGTGCAACTGGTTTCTGGACCTCCAACCAAGCTGCTGCTTATGGACTGGCCAGAGCTGAAAGAGTCCATTCCTGTGATTAATGGAAGACAATTAGAGAACCCTCTCATTGTTCAACTTTGTGATCAGTGGGATAATCCTGCTTTAGTCCCAAACGTTAAAATATGTCTCATAAAAGCAAGCAGCTTAAGG
Peptide sequence:
MSHKSKQLKGPPHQLKVKPDSEVLVIENGTAFPFQVEVVDESDNITAQPKLIVHCKFLGAPNLPVYTVDCSSSGTSILTGSPIQVQNIKKDQKTLTARIEIPSCKDVSPVEKTIKLLPSSHAACLQIFSVEEQKAIQIKHQDEVTWVAGDVIRNLIFQMYDEGEREINITPSLAEKIKVNWTPEVNKEHLVQGLLPDVQVPTSVKDVRYCHVSFQDDHVCLESAFTVRPLPDDPKHLKCELKGGKTVQMGQELQGEIVVIIADQYGNQISSFSPDSLSTLSITGDGLDSSNLKITLEANSQSVSVQGIRFTPGPPGPKDLCFTWREFSDFLRVQLVSGPPTKLLLMDWPELKESIPVINGRQLENPLIVQLCDQWDNPALVPNVKICLIKASSLR
IRESfinder result
IRESfinder score
0.682202704
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page