top of page
mmu_circCsde1_1249
Basic information of circular RNA
PanCircBase ID:
mmu_circCsde1_1249
mm39_Chr. Position ID:
chr3|102952074|102962828|+
Gene name:
Csde1
Transcript:
ENSMUST00000198174.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
4,5,6,7,8,9,10,11,12
Exon/intron offsets:
0,2026,2255,4862,5539,6281,8053,9896,10590
Genomic length:
10754
Exon/intron sizes in nt:
8,31,41,16,51,08,17,61,00,00,00,00,000
Flanking exon/introns:
chr3:102951247-102952074|chr3:102962828-102963660
Splice length:
1249
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ACCGACGTGACAAATTGGAACGAGCAACCAACATAGAGGTTCTATCAAATACATTTCAGTTCACTAATGAAGCCAGAGAGATGGGTGTGATTGCTGCCATGAGAGATGGTTTTGGTTTCATCAAGTGTGTGGATCGTGATGCTCGTATGTTCTTCCACTTCAGTGAGATTCTAGATGGGAACCAGCTCCACATTGCAGATGAAGTAGAGTTTACTGTGGTTCCTGATATGCTCTCTGCCCAAAGAAATCATGCTATTAGGATTAAAAAACTTCCCAAGGGCACGGTTTCATTCCATTCCCATTCAGATCATCGTTTTCTGGGCACCGTAGAAAAAGAAGCCACTTTTTCCAATCCTAAAACTACAAGCCCAAATAAAGGCAAAGACAAGGAGGCAGAAGATGGCATTATAGCTTATGACGACTGTGGGGTGAAACTGACGATTGCTTTTCAAGCCAAGGATGTGGAAGGATCTACTTCTCCTCAAATAGGAGATAAGGTTGAATTTAGTATTAGTGACAAACAGAGGCCTGGACAGCAGATTGCAACTTGCGTGAGACTTTTAGGTCGTAATTCTAACTCCAAACGTCTCTTGGGTTATGTGGCAACTCTGAAAGATAATTTTGGATTTATAGAAACAGCTAATCATGATAAGGAAATATTTTTCCACTATAGTGAGTTCTCTGGTGATGTTGATAGCCTGGAACTGGGAGACATGGTTGAATACAGCTTGTCCAAAGGCAAAGGCAATAAAGTCAGTGCTGAGAAAGTAAACAAAGCCCACTCAGTGAATGGCATTACTGAGGAAGCTAATCCCACCATCTACTCTGGTAAAGTCATTCGCCCTCTGAGAGGTGTTGATCCAACACAGATTGAGTACCAAGGAATGATTGAGATTGTGGAGGAGGGGGATATGAAAGGTGAAGTGTATCCTTTTGGCATAGTTGGGATGGCCAACAAAGGGGATTGCCTACAGAAAGGGGAGAGTGTCAAGTTCCAGTTGTGTGTACTTGGCCAAAATGCACAAACTATGGCCTACAACATCACACCCCTTCGTAGGGCTACTGTGGAGTGTGTGAAAGATCAGTTTGGCTTTATTAACTATGAAGTAGGAGATAGCAAGAAGCTCTTTTTCCATGTGAAAGAAGTTCAGGATGGCGTTGAGCTACAGGCAGGAGATGAGGTGGAATTCTCAGTGATCCTTAATCAGCGCACTGGGAAGTGCAGTGCCTGTAATGTCTGGCGAGTCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTTAATCAGCGCACTGGGA
60.11
TCACACCCATCTCTCTGGCT
60.25
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTTAATCAGCGCACTGGG
60.11
TCACACCCATCTCTCTGGCT
60.25
142
PCR template sequence:
AGGATGGCGTTGAGCTACAGGCAGGAGATGAGGTGGAATTCTCAGTGATCCTTAATCAGCGCACTGGGAAGTGCAGTGCCTGTAATGTCTGGCGAGTCTGACCGACGTGACAAATTGGAACGAGCAACCAACATAGAGGTTCTATCAAATACATTTCAGTTCACTAATGAAGCCAGAGAGATGGGTGTGATTGCTGCCAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-216a-5p(1), mmu-miR-203-3p(1), mmu-miR-433-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-382-3p(1), mmu-miR-96-5p(1), mmu-miR-3087-3p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
TCTGGCGAGTCTGACCGACGTGACAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCSDE1_1249_ORF_1
1.0835
0.18936009
0.998644022
1263
ORF sequence:
ATGTCTGGCGAGTCTGACCGACGTGACAAATTGGAACGAGCAACCAACATAGAGGTTCTATCAAATACATTTCAGTTCACTAATGAAGCCAGAGAGATGGGTGTGATTGCTGCCATGAGAGATGGTTTTGGTTTCATCAAGTGTGTGGATCGTGATGCTCGTATGTTCTTCCACTTCAGTGAGATTCTAGATGGGAACCAGCTCCACATTGCAGATGAAGTAGAGTTTACTGTGGTTCCTGATATGCTCTCTGCCCAAAGAAATCATGCTATTAGGATTAAAAAACTTCCCAAGGGCACGGTTTCATTCCATTCCCATTCAGATCATCGTTTTCTGGGCACCGTAGAAAAAGAAGCCACTTTTTCCAATCCTAAAACTACAAGCCCAAATAAAGGCAAAGACAAGGAGGCAGAAGATGGCATTATAGCTTATGACGACTGTGGGGTGAAACTGACGATTGCTTTTCAAGCCAAGGATGTGGAAGGATCTACTTCTCCTCAAATAGGAGATAAGGTTGAATTTAGTATTAGTGACAAACAGAGGCCTGGACAGCAGATTGCAACTTGCGTGAGACTTTTAGGTCGTAATTCTAACTCCAAACGTCTCTTGGGTTATGTGGCAACTCTGAAAGATAATTTTGGATTTATAGAAACAGCTAATCATGATAAGGAAATATTTTTCCACTATAGTGAGTTCTCTGGTGATGTTGATAGCCTGGAACTGGGAGACATGGTTGAATACAGCTTGTCCAAAGGCAAAGGCAATAAAGTCAGTGCTGAGAAAGTAAACAAAGCCCACTCAGTGAATGGCATTACTGAGGAAGCTAATCCCACCATCTACTCTGGTAAAGTCATTCGCCCTCTGAGAGGTGTTGATCCAACACAGATTGAGTACCAAGGAATGATTGAGATTGTGGAGGAGGGGGATATGAAAGGTGAAGTGTATCCTTTTGGCATAGTTGGGATGGCCAACAAAGGGGATTGCCTACAGAAAGGGGAGAGTGTCAAGTTCCAGTTGTGTGTACTTGGCCAAAATGCACAAACTATGGCCTACAACATCACACCCCTTCGTAGGGCTACTGTGGAGTGTGTGAAAGATCAGTTTGGCTTTATTAACTATGAAGTAGGAGATAGCAAGAAGCTCTTTTTCCATGTGAAAGAAGTTCAGGATGGCGTTGAGCTACAGGCAGGAGATGAGGTGGAATTCTCAGTGATCCTTAATCAGCGCACTGGGAAGTGCAGTGCCTGTAATGTCTGGCGAGTC
Peptide sequence:
MSGESDRRDKLERATNIEVLSNTFQFTNEAREMGVIAAMRDGFGFIKCVDRDARMFFHFSEILDGNQLHIADEVEFTVVPDMLSAQRNHAIRIKKLPKGTVSFHSHSDHRFLGTVEKEATFSNPKTTSPNKGKDKEAEDGIIAYDDCGVKLTIAFQAKDVEGSTSPQIGDKVEFSISDKQRPGQQIATCVRLLGRNSNSKRLLGYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGNKVSAEKVNKAHSVNGITEEANPTIYSGKVIRPLRGVDPTQIEYQGMIEIVEEGDMKGEVYPFGIVGMANKGDCLQKGESVKFQLCVLGQNAQTMAYNITPLRRATVECVKDQFGFINYEVGDSKKLFFHVKEVQDGVELQAGDEVEFSVILNQRTGKCSACNVWRV
IRESfinder result
IRESfinder score
0.57288132
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page