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mmu_circSclt1_584
Basic information of circular RNA
PanCircBase ID:
mmu_circSclt1_584
mm39_Chr. Position ID:
chr3|41657820|41685354|-
Gene name:
Sclt1
Transcript:
ENSMUST00000026866.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
9,8,7,6,5,4,3
Exon/intron offsets:
0,6083,7697,14343,23707,26905,27475
Genomic length:
27534
Exon/intron sizes in nt:
71,66,123,136,56,73,59
Flanking exon/introns:
chr3:41636807-41657820|chr3:41685354-41688602
Splice length:
584
Other database IDs:
circBase: mmu_circ_0010672, CIRCpedia: MMU_CIRCpedia_19705, circAtlas: mmu-Sclt1_0028
circBase: hsa_circ_0070961, circAtlas: hsa-SCLT1_0048, CIRCpedia: HSA_CIRCpedia_103579
Human Ortholog IDs:
Mature spliced Sequence:
AACAGCATGTCCAAAGGAGGCAGAGGTGACACACTAGTAGACTCAATAAATGAGCAAAGTTCTTTACCTCCTCTCATTGCTGAGTATGAGAAACATCTGGAAGAGCTAAACAGGCAGCTGACCTATTACCAGAAGCACATGGGTGAGATGAAACTACAACTTGAAACTGTCATCACAGAAAATGAAAGGTTGCACAGTAAATTAAAAGATGCTGTTGAAAAGCAATTGGAAGCCCTTCCCTTTGGCACAGGGATAGGAAATGACATCTGTGCAGATGATGAGACCGTGAGGATCCTTCAAGAACAATTGCAACTAGCCAATCAAGAGAAAACTTGGGCTCTGGAACTCTGGCAGACTGCTTCTCAGGAGTTGCAAAGTGTACAGAAACTCTATCAGGAGCATATGACTGAAGCCCAGATTCATGAATTTGAAAACCGAAAGCAAAAAGATCAGCTGAACAATTTTCAACAACTAACCAAGAAACTCCATGTTGCTAATGAGAACATAGAAATGACTAACCACCACTTCCTGAAAACAGTAACTGAACAAAACATGGAGATTGAGAAACTTCGAAAACATCTTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCACCACTTCCTGAAAACAGT
60.03
ACTCAGCAATGAGAGGAGGT
58.05
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCACCACTTCCTGAAAACAGT
58.35
ACTCAGCAATGAGAGGAGGT
58.05
151
PCR template sequence:
TCCATGTTGCTAATGAGAACATAGAAATGACTAACCACCACTTCCTGAAAACAGTAACTGAACAAAACATGGAGATTGAGAAACTTCGAAAACATCTTAGAACAGCATGTCCAAAGGAGGCAGAGGTGACACACTAGTAGACTCAATAAATGAGCAAAGTTCTTTACCTCCTCTCATTGCTGAGTATGAGAAACATCTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-22-3p(1), mmu-miR-325-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAAACATCTTAGAACAGCATGTCCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSCLT1_584_ORF_1
1.1364
0.137794801
0.863459187
615
ORF sequence:
ATGTCCAAAGGAGGCAGAGGTGACACACTAGTAGACTCAATAAATGAGCAAAGTTCTTTACCTCCTCTCATTGCTGAGTATGAGAAACATCTGGAAGAGCTAAACAGGCAGCTGACCTATTACCAGAAGCACATGGGTGAGATGAAACTACAACTTGAAACTGTCATCACAGAAAATGAAAGGTTGCACAGTAAATTAAAAGATGCTGTTGAAAAGCAATTGGAAGCCCTTCCCTTTGGCACAGGGATAGGAAATGACATCTGTGCAGATGATGAGACCGTGAGGATCCTTCAAGAACAATTGCAACTAGCCAATCAAGAGAAAACTTGGGCTCTGGAACTCTGGCAGACTGCTTCTCAGGAGTTGCAAAGTGTACAGAAACTCTATCAGGAGCATATGACTGAAGCCCAGATTCATGAATTTGAAAACCGAAAGCAAAAAGATCAGCTGAACAATTTTCAACAACTAACCAAGAAACTCCATGTTGCTAATGAGAACATAGAAATGACTAACCACCACTTCCTGAAAACAGTAACTGAACAAAACATGGAGATTGAGAAACTTCGAAAACATCTTAGAACAGCATGTCCAAAGGAGGCAGAGGTGACACACTAG
Peptide sequence:
MSKGGRGDTLVDSINEQSSLPPLIAEYEKHLEELNRQLTYYQKHMGEMKLQLETVITENERLHSKLKDAVEKQLEALPFGTGIGNDICADDETVRILQEQLQLANQEKTWALELWQTASQELQSVQKLYQEHMTEAQIHEFENRKQKDQLNNFQQLTKKLHVANENIEMTNHHFLKTVTEQNMEIEKLRKHLRTACPKEAEVTH
IRESfinder result
IRESfinder score
0.537899006
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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