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mmu_circHdlbp_843
Basic information of circular RNA
PanCircBase ID:
mmu_circHdlbp_843
mm39_Chr. Position ID:
chr1|93355869|93359240|-
Gene name:
Hdlbp
Transcript:
ENSMUST00000170883.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
10,9,8,7,6
Exon/intron offsets:
0,1230,1950,2807,3164
Genomic length:
3371
Exon/intron sizes in nt:
105,108,207,216,207
Flanking exon/introns:
chr1:93355358-93355869|chr1:93359240-93364815
Splice length:
843
Other database IDs:
circAtlas: mmu-Hdlbp_0004
circAtlas: hsa-HDLBP_0043
Human Ortholog IDs:
Mature spliced Sequence:
GCCTCAGCAACTGTTCCCATTCCTAAAGAGCACCATCGCTTTGTTATTGGCAAAAACGGAGAGAAACTGCAAGACTTAGAACTAAAAACTGCAACCAAAATCCAGATCCCACGCCCAGATGACCCCAGTAATCAGATCAAGATCACTGGCACCAAAGAAGGCATCGAGAAAGCTCGCCATGAAGTCCTCCTAATCTCTGCTGAGCAGGACAAGCGTGCTGTAGAGAGGCTAGAAGTGGAGAAGGCTTTCCACCCCTTCATCGCTGGGCCGTACAACAGACTTGTGGGTGAAATCATGCAGGAGACAGGGACGCGAATCAACATCCCTCCACCCAGTGTTAACCGTACAGAAATCGTCTTCACTGGAGAGAAGGAGCAGCTGGCTCAGGCTGTGGCTCGCATTAAGAAGATTTATGAGGAAAAGAAGAAGAAGACTACAACCATTGCGGTAGAGGTGAAGAAGTCTCAGCACAAGTATGTTATTGGGCCAAAGGGCAATTCACTGCAAGAAATCCTGGAAAGAACTGGAGTTTCTGTTGAGATCCCACCCTCCGACAGCATCTCTGAGACTGTGATACTTAGAGGCGAACCTGAAAAGTTGGGACAGGCGTTGACTGAAGTCTATGCCAAGGCCAACAGTTTTACAGTCTCCTCAGTCTCTGCCCCTTCCTGGCTTCATCGTTTCATCATTGGTAAGAAAGGGCAGAACCTGGCCAAAATCACTCAGCAAATGCCAAAGGTTCACATTGAGTTCACAGAAGGTGAGGACAAGATCACCCTGGAGGGCCCCACAGAGGATGTGAATGTAGCCCAAGAACAGATTGAAGGAATGGTCAAAGACCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGACAAGATCACCCTGGAGG
59.46
AGTCTTGCAGTTTCTCTCCGT
59.31
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGACAAGATCACCCTGGAGG
59.46
AGTCTTGCAGTTTCTCTCCGTT
59.9
155
PCR template sequence:
CATTGAGTTCACAGAAGGTGAGGACAAGATCACCCTGGAGGGCCCCACAGAGGATGTGAATGTAGCCCAAGAACAGATTGAAGGAATGGTCAAAGACCTGGCCTCAGCAACTGTTCCCATTCCTAAAGAGCACCATCGCTTTGTTATTGGCAAAAACGGAGAGAAACTGCAAGACTTAGAACTAAAAACTGCAACCAAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-181a-5p(1), mmu-miR-221-3p(1), mmu-miR-339-5p(1), mmu-miR-139-5p(1), mmu-miR-181b-5p(1), mmu-miR-431-5p(1), mmu-miR-207(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGTCAAAGACCTGGCCTCAGCAACTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHDLBP_843_ORF_1
1.2176
0.38323823
0.999814787
1392
ORF sequence:
ATGCAGGAGACAGGGACGCGAATCAACATCCCTCCACCCAGTGTTAACCGTACAGAAATCGTCTTCACTGGAGAGAAGGAGCAGCTGGCTCAGGCTGTGGCTCGCATTAAGAAGATTTATGAGGAAAAGAAGAAGAAGACTACAACCATTGCGGTAGAGGTGAAGAAGTCTCAGCACAAGTATGTTATTGGGCCAAAGGGCAATTCACTGCAAGAAATCCTGGAAAGAACTGGAGTTTCTGTTGAGATCCCACCCTCCGACAGCATCTCTGAGACTGTGATACTTAGAGGCGAACCTGAAAAGTTGGGACAGGCGTTGACTGAAGTCTATGCCAAGGCCAACAGTTTTACAGTCTCCTCAGTCTCTGCCCCTTCCTGGCTTCATCGTTTCATCATTGGTAAGAAAGGGCAGAACCTGGCCAAAATCACTCAGCAAATGCCAAAGGTTCACATTGAGTTCACAGAAGGTGAGGACAAGATCACCCTGGAGGGCCCCACAGAGGATGTGAATGTAGCCCAAGAACAGATTGAAGGAATGGTCAAAGACCTGGCCTCAGCAACTGTTCCCATTCCTAAAGAGCACCATCGCTTTGTTATTGGCAAAAACGGAGAGAAACTGCAAGACTTAGAACTAAAAACTGCAACCAAAATCCAGATCCCACGCCCAGATGACCCCAGTAATCAGATCAAGATCACTGGCACCAAAGAAGGCATCGAGAAAGCTCGCCATGAAGTCCTCCTAATCTCTGCTGAGCAGGACAAGCGTGCTGTAGAGAGGCTAGAAGTGGAGAAGGCTTTCCACCCCTTCATCGCTGGGCCGTACAACAGACTTGTGGGTGAAATCATGCAGGAGACAGGGACGCGAATCAACATCCCTCCACCCAGTGTTAACCGTACAGAAATCGTCTTCACTGGAGAGAAGGAGCAGCTGGCTCAGGCTGTGGCTCGCATTAAGAAGATTTATGAGGAAAAGAAGAAGAAGACTACAACCATTGCGGTAGAGGTGAAGAAGTCTCAGCACAAGTATGTTATTGGGCCAAAGGGCAATTCACTGCAAGAAATCCTGGAAAGAACTGGAGTTTCTGTTGAGATCCCACCCTCCGACAGCATCTCTGAGACTGTGATACTTAGAGGCGAACCTGAAAAGTTGGGACAGGCGTTGACTGAAGTCTATGCCAAGGCCAACAGTTTTACAGTCTCCTCAGTCTCTGCCCCTTCCTGGCTTCATCGTTTCATCATTGGTAAGAAAGGGCAGAACCTGGCCAAAATCACTCAGCAAATGCCAAAGGTTCACATTGAGTTCACAGAAGGTGAGGACAAGATCACCCTGGAGGGCCCCACAGAGGATGTGAATGTAGCCCAAGAACAGATTGAAGGAATGGTCAAAGACCTG
Peptide sequence:
MQETGTRINIPPPSVNRTEIVFTGEKEQLAQAVARIKKIYEEKKKKTTTIAVEVKKSQHKYVIGPKGNSLQEILERTGVSVEIPPSDSISETVILRGEPEKLGQALTEVYAKANSFTVSSVSAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDKITLEGPTEDVNVAQEQIEGMVKDLASATVPIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISAEQDKRAVERLEVEKAFHPFIAGPYNRLVGEIMQETGTRINIPPPSVNRTEIVFTGEKEQLAQAVARIKKIYEEKKKKTTTIAVEVKKSQHKYVIGPKGNSLQEILERTGVSVEIPPSDSISETVILRGEPEKLGQALTEVYAKANSFTVSSVSAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDKITLEGPTEDVNVAQEQIEGMVKDL
IRESfinder result
IRESfinder score
0.500278287
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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