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mmu_circHdlbp_922
Basic information of circular RNA
PanCircBase ID:
mmu_circHdlbp_922
mm39_Chr. Position ID:
chr1|93355279|93359240|-
Gene name:
Hdlbp
Transcript:
ENSMUST00000170883.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
11,10,9,8,7,6
Exon/intron offsets:
0,590,1820,2540,3397,3754
Genomic length:
3961
Exon/intron sizes in nt:
79,10,51,08,20,72,16,200
Flanking exon/introns:
chr1:93353128-93355279|chr1:93359240-93364815
Splice length:
922
Other database IDs:
circAtlas: mmu-Hdlbp_0009
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_94121
Human Ortholog IDs:
Mature spliced Sequence:
GCCTCAGCAACTGTTCCCATTCCTAAAGAGCACCATCGCTTTGTTATTGGCAAAAACGGAGAGAAACTGCAAGACTTAGAACTAAAAACTGCAACCAAAATCCAGATCCCACGCCCAGATGACCCCAGTAATCAGATCAAGATCACTGGCACCAAAGAAGGCATCGAGAAAGCTCGCCATGAAGTCCTCCTAATCTCTGCTGAGCAGGACAAGCGTGCTGTAGAGAGGCTAGAAGTGGAGAAGGCTTTCCACCCCTTCATCGCTGGGCCGTACAACAGACTTGTGGGTGAAATCATGCAGGAGACAGGGACGCGAATCAACATCCCTCCACCCAGTGTTAACCGTACAGAAATCGTCTTCACTGGAGAGAAGGAGCAGCTGGCTCAGGCTGTGGCTCGCATTAAGAAGATTTATGAGGAAAAGAAGAAGAAGACTACAACCATTGCGGTAGAGGTGAAGAAGTCTCAGCACAAGTATGTTATTGGGCCAAAGGGCAATTCACTGCAAGAAATCCTGGAAAGAACTGGAGTTTCTGTTGAGATCCCACCCTCCGACAGCATCTCTGAGACTGTGATACTTAGAGGCGAACCTGAAAAGTTGGGACAGGCGTTGACTGAAGTCTATGCCAAGGCCAACAGTTTTACAGTCTCCTCAGTCTCTGCCCCTTCCTGGCTTCATCGTTTCATCATTGGTAAGAAAGGGCAGAACCTGGCCAAAATCACTCAGCAAATGCCAAAGGTTCACATTGAGTTCACAGAAGGTGAGGACAAGATCACCCTGGAGGGCCCCACAGAGGATGTGAATGTAGCCCAAGAACAGATTGAAGGAATGGTCAAAGACCTGATTAATAGGATGGACTATGTAGAGATCAACATTGACCATAAATTCCACAGACACCTCATTGGAAAGAGCGGAGCCAACA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGATGGACTATGTAGAGATCAACA
58.62
AGTCTTGCAGTTTCTCTCCGT
59.31
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGATGGACTATGTAGAGATCAACA
57.34
AGTCTTGCAGTTTCTCTCCGT
59.31
148
PCR template sequence:
GAAGGAATGGTCAAAGACCTGATTAATAGGATGGACTATGTAGAGATCAACATTGACCATAAATTCCACAGACACCTCATTGGAAAGAGCGGAGCCAACAGCCTCAGCAACTGTTCCCATTCCTAAAGAGCACCATCGCTTTGTTATTGGCAAAAACGGAGAGAAACTGCAAGACTTAGAACTAAAAACTGCAACCAAAA
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
AGCGGAGCCAACAGCCTCAGCAACTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHDLBP_922_ORF_1
1.1739
0.342770375
0.953369604
654
ORF sequence:
ATGCAGGAGACAGGGACGCGAATCAACATCCCTCCACCCAGTGTTAACCGTACAGAAATCGTCTTCACTGGAGAGAAGGAGCAGCTGGCTCAGGCTGTGGCTCGCATTAAGAAGATTTATGAGGAAAAGAAGAAGAAGACTACAACCATTGCGGTAGAGGTGAAGAAGTCTCAGCACAAGTATGTTATTGGGCCAAAGGGCAATTCACTGCAAGAAATCCTGGAAAGAACTGGAGTTTCTGTTGAGATCCCACCCTCCGACAGCATCTCTGAGACTGTGATACTTAGAGGCGAACCTGAAAAGTTGGGACAGGCGTTGACTGAAGTCTATGCCAAGGCCAACAGTTTTACAGTCTCCTCAGTCTCTGCCCCTTCCTGGCTTCATCGTTTCATCATTGGTAAGAAAGGGCAGAACCTGGCCAAAATCACTCAGCAAATGCCAAAGGTTCACATTGAGTTCACAGAAGGTGAGGACAAGATCACCCTGGAGGGCCCCACAGAGGATGTGAATGTAGCCCAAGAACAGATTGAAGGAATGGTCAAAGACCTGATTAATAGGATGGACTATGTAGAGATCAACATTGACCATAAATTCCACAGACACCTCATTGGAAAGAGCGGAGCCAACAGCCTCAGCAACTGTTCCCATTCCTAA
Peptide sequence:
MQETGTRINIPPPSVNRTEIVFTGEKEQLAQAVARIKKIYEEKKKKTTTIAVEVKKSQHKYVIGPKGNSLQEILERTGVSVEIPPSDSISETVILRGEPEKLGQALTEVYAKANSFTVSSVSAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDKITLEGPTEDVNVAQEQIEGMVKDLINRMDYVEINIDHKFHRHLIGKSGANSLSNCSHS
IRESfinder result
IRESfinder score
0.519007477
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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