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mmu_circRcc1l_993
Basic information of circular RNA
PanCircBase ID:
mmu_circRcc1l_993
mm39_Chr. Position ID:
chr5|134182962|134200815|-
Gene name:
Rcc1l
Transcript:
ENSMUST00000076228.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,1616,3467,9500,11215,12541,14088,15094,17723
Genomic length:
17853
Exon/intron sizes in nt:
86,174,88,182,85,52,67,129,130
Flanking exon/introns:
chr5:134177845-134182962|chr5:134200815-134205238
Splice length:
993
Other database IDs:
CIRCpedia: MMU_CIRCpedia_8049, circAtlas: mmu-Wbscr16_0003
circAtlas: hsa-RCC1L_0001, CIRCpedia: HSA_CIRCpedia_343652
Human Ortholog IDs:
Mature spliced Sequence:
ATTTCCTCTGCTGCCTGTGGCTATGGATTCACATTGCTGTCCTCGAAAACCAAGGATGTTACAAAAGTCTGGGGCATGGGACTCAACAAAGATTCCCAGCTGGGATTCCACAGGAGCCGGAAGGATAAAACCAGGGGCTATGAGTACGTTTTGGAGCCCTCGCCTGTCCCGCTGCCGCTGGACAGACCTCAGGAGACAAAGGTGTTGCAGGTGTCCTGCGGTCGAGCACACTCCCTTGTCCTGACAGACAGAGAAGGTGTCTTCAGCATGGGCAACAATTCCCACGGGCAGTGTGGCCGGAAGGTGGTGGAGGATGAAGTATACAGCGAGAGTCACAAAGTGCACAGGATGCAGGACTTCGATGGACAGGTGGTCCAGGTTGTCTGTGGTCAGGACCACAGCCTGTTCCTCACAGACAAAGGTGAAGTCTATTCTTGTGGCTGGGGTGCCGATGGACAGACAGGCCTGGGTCACTACAACATCACCAGCACACCCAGCAAGCTGGGCGGAGACCTTGCCGGGGTGACCGTTGTCCAGGTCGCCACCTACGGTGACTGCTGCTTAGCTTTGTCCGCTGATGGAGGTGTCTTTGGCTGGGGAAATTCCGAGTACCTGCAGTTGGCCTCTGTCACAGACTCCACACAGGTGAATGTCCCTCGGTGCCTGCCTTTCTCTGGAGTAGGCAAGGTGAAGCAGGTGGCTTGTGGTGGCACAGGCTGTGCTGTACTGAACGCGGAGGGACATGTTTTCGTCTGGGGCTATGGAATTCTTGGGAAAGGACCAAAGCTCTTGGAAACGGCAATTCCAGAAATGATTCCACCCACGCTCTTTGGTTTGACGGAGTTTAACCCTGAAGTCCAGGTTTCCCAGATCCGATGTGGGCTTAGCCACTTTGCCGCACTCACCAACAAGGGTGAGCTGTTCGTGTGGGGCAAGAACATCCGAGGGTGCTTGGGGATTGGCCGCCTGGAAGACCAGTACTTCCCATGGAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAACATCCGAGGGTGCTTG
60.04
TCCCATGCCCCAGACTTTTG
60.25
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAAGAACATCCGAGGGTGCT
60.04
TCCCATGCCCCAGACTTTTG
60.25
142
PCR template sequence:
TGCCGCACTCACCAACAAGGGTGAGCTGTTCGTGTGGGGCAAGAACATCCGAGGGTGCTTGGGGATTGGCCGCCTGGAAGACCAGTACTTCCCATGGAGGATTTCCTCTGCTGCCTGTGGCTATGGATTCACATTGCTGTCCTCGAAAACCAAGGATGTTACAAAAGTCTGGGGCATGGGACTCAACAAAGATTCCCAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-181a-5p(1), mmu-miR-15b-5p(1), mmu-miR-216a-5p(1), mmu-miR-138-5p(1), mmu-miR-181b-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-342-3p(1), mmu-miR-697(1), mmu-miR-490-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTCCCATGGAGGATTTCCTCTGCTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRCC1L_993_ORF_1
0.9007
0.304818603
0.99998905
1911
ORF sequence:
ATGGGACTCAACAAAGATTCCCAGCTGGGATTCCACAGGAGCCGGAAGGATAAAACCAGGGGCTATGAGTACGTTTTGGAGCCCTCGCCTGTCCCGCTGCCGCTGGACAGACCTCAGGAGACAAAGGTGTTGCAGGTGTCCTGCGGTCGAGCACACTCCCTTGTCCTGACAGACAGAGAAGGTGTCTTCAGCATGGGCAACAATTCCCACGGGCAGTGTGGCCGGAAGGTGGTGGAGGATGAAGTATACAGCGAGAGTCACAAAGTGCACAGGATGCAGGACTTCGATGGACAGGTGGTCCAGGTTGTCTGTGGTCAGGACCACAGCCTGTTCCTCACAGACAAAGGTGAAGTCTATTCTTGTGGCTGGGGTGCCGATGGACAGACAGGCCTGGGTCACTACAACATCACCAGCACACCCAGCAAGCTGGGCGGAGACCTTGCCGGGGTGACCGTTGTCCAGGTCGCCACCTACGGTGACTGCTGCTTAGCTTTGTCCGCTGATGGAGGTGTCTTTGGCTGGGGAAATTCCGAGTACCTGCAGTTGGCCTCTGTCACAGACTCCACACAGGTGAATGTCCCTCGGTGCCTGCCTTTCTCTGGAGTAGGCAAGGTGAAGCAGGTGGCTTGTGGTGGCACAGGCTGTGCTGTACTGAACGCGGAGGGACATGTTTTCGTCTGGGGCTATGGAATTCTTGGGAAAGGACCAAAGCTCTTGGAAACGGCAATTCCAGAAATGATTCCACCCACGCTCTTTGGTTTGACGGAGTTTAACCCTGAAGTCCAGGTTTCCCAGATCCGATGTGGGCTTAGCCACTTTGCCGCACTCACCAACAAGGGTGAGCTGTTCGTGTGGGGCAAGAACATCCGAGGGTGCTTGGGGATTGGCCGCCTGGAAGACCAGTACTTCCCATGGAGGATTTCCTCTGCTGCCTGTGGCTATGGATTCACATTGCTGTCCTCGAAAACCAAGGATGTTACAAAAGTCTGGGGCATGGGACTCAACAAAGATTCCCAGCTGGGATTCCACAGGAGCCGGAAGGATAAAACCAGGGGCTATGAGTACGTTTTGGAGCCCTCGCCTGTCCCGCTGCCGCTGGACAGACCTCAGGAGACAAAGGTGTTGCAGGTGTCCTGCGGTCGAGCACACTCCCTTGTCCTGACAGACAGAGAAGGTGTCTTCAGCATGGGCAACAATTCCCACGGGCAGTGTGGCCGGAAGGTGGTGGAGGATGAAGTATACAGCGAGAGTCACAAAGTGCACAGGATGCAGGACTTCGATGGACAGGTGGTCCAGGTTGTCTGTGGTCAGGACCACAGCCTGTTCCTCACAGACAAAGGTGAAGTCTATTCTTGTGGCTGGGGTGCCGATGGACAGACAGGCCTGGGTCACTACAACATCACCAGCACACCCAGCAAGCTGGGCGGAGACCTTGCCGGGGTGACCGTTGTCCAGGTCGCCACCTACGGTGACTGCTGCTTAGCTTTGTCCGCTGATGGAGGTGTCTTTGGCTGGGGAAATTCCGAGTACCTGCAGTTGGCCTCTGTCACAGACTCCACACAGGTGAATGTCCCTCGGTGCCTGCCTTTCTCTGGAGTAGGCAAGGTGAAGCAGGTGGCTTGTGGTGGCACAGGCTGTGCTGTACTGAACGCGGAGGGACATGTTTTCGTCTGGGGCTATGGAATTCTTGGGAAAGGACCAAAGCTCTTGGAAACGGCAATTCCAGAAATGATTCCACCCACGCTCTTTGGTTTGACGGAGTTTAACCCTGAAGTCCAGGTTTCCCAGATCCGATGTGGGCTTAGCCACTTTGCCGCACTCACCAACAAGGGTGAGCTGTTCGTGTGGGGCAAGAACATCCGAGGGTGCTTGGGGATTGGCCGCCTGGAAGACCAGTACTTCCCATGGAGG
Peptide sequence:
MGLNKDSQLGFHRSRKDKTRGYEYVLEPSPVPLPLDRPQETKVLQVSCGRAHSLVLTDREGVFSMGNNSHGQCGRKVVEDEVYSESHKVHRMQDFDGQVVQVVCGQDHSLFLTDKGEVYSCGWGADGQTGLGHYNITSTPSKLGGDLAGVTVVQVATYGDCCLALSADGGVFGWGNSEYLQLASVTDSTQVNVPRCLPFSGVGKVKQVACGGTGCAVLNAEGHVFVWGYGILGKGPKLLETAIPEMIPPTLFGLTEFNPEVQVSQIRCGLSHFAALTNKGELFVWGKNIRGCLGIGRLEDQYFPWRISSAACGYGFTLLSSKTKDVTKVWGMGLNKDSQLGFHRSRKDKTRGYEYVLEPSPVPLPLDRPQETKVLQVSCGRAHSLVLTDREGVFSMGNNSHGQCGRKVVEDEVYSESHKVHRMQDFDGQVVQVVCGQDHSLFLTDKGEVYSCGWGADGQTGLGHYNITSTPSKLGGDLAGVTVVQVATYGDCCLALSADGGVFGWGNSEYLQLASVTDSTQVNVPRCLPFSGVGKVKQVACGGTGCAVLNAEGHVFVWGYGILGKGPKLLETAIPEMIPPTLFGLTEFNPEVQVSQIRCGLSHFAALTNKGELFVWGKNIRGCLGIGRLEDQYFPWR
IRESfinder result
IRESfinder score
0.446854423
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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