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mmu_circHdlbp_1497
Basic information of circular RNA
PanCircBase ID:
mmu_circHdlbp_1497
mm39_Chr. Position ID:
chr1|93341548|93351596|-
Gene name:
Hdlbp
Transcript:
ENSMUST00000170883.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
22,21,20,19,18,17,16,15,14,13
Exon/intron offsets:
0,985,2674,3345,3641,6242,7257,7516,9437,9943
Genomic length:
10048
Exon/intron sizes in nt:
10,51,55,13,92,19,22,20,00,00,00,00,00,000
Flanking exon/introns:
chr1:93341347-93341548|chr1:93351596-93352988
Splice length:
1497
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GAAAATGAGCGCACCAAGGATCTAATCATCGAGCAAAGATTTCATCGCACAATCATTGGGCAGAAAGGTGAACGGATTCGAGAAATTCGTGACAAATTCCCAGAGGTTATCATCAACTTTCCAGACCCAGCACAAAAAAGTGATATTGTACAACTCAGAGGCCCCAAGAATGAGGTGGAGAAGTGCACTAAGTATATGCAGAAGATGGTCGCAGACCTGGTGGAAAATAGCTATTCAATTTCTGTACCAATCTTCAAACAGTTTCACAAGAATATCATCGGGAAAGGAGGCGCAAACATTAAAAAGATCCGTGAAGAGAGCAACACCAAGATTGACCTTCCTGCAGAGAACAGCAACTCTGAGACCATTATTATCACTGGCAAGCGAGCCAACTGTGAAGCTGCCCGCAGCCGGATTCTGTCTATCCAGAAAGATCTGGCCAACATAGCTGAAGTGGAGGTCTCAATTCCTGCCAAACTACACAACTCTCTCATTGGCACAAAGGGCCGTCTGATCCGCTCCATCATGGAGGAATGTGGTGGCGTCCATATTCACTTTCCTGTGGAAGGTTCTGGAAGCGACACTGTTGTCATCAGGGGTCCTTCCTCAGATGTAGAGAAGGCCAAGAAGCAGCTCCTGCACCTGGCTGAGGAGAAGCAAACCAAGAGTTTTACTGTGGACATCCGAGCCAAGCCAGAATACCACAAATTCCTCATTGGCAAAGGGGGAGGTAAAATCCGAAAGGTGCGTGACAGTACTGGAGCCCGCATCATATTTCCGGCTGCTGAAGATAAGGACCAGGACCTGATCACAATCATAGGAAAGGAGGATGCTGTCCGTGAGGCCCAAAAGGAGCTGGAAGCATTGATCCAGAACCTGGAGAATGTGGTTGAAGACTATATGCTGGTGGACCCCAAACACCACCGCCATTTTGTCATCCGAAGAGGACAAGTTTTACGAGAAATTGCTGAAGAGTATGGCGGGGTGATGGTCAGCTTCCCACGCTCTGGCACGCAGAGTGATAAAGTCACTCTCAAGGGTGCCAAGGACTGTGTGGAGGCAGCCAAGAAACGCATTCAGGAAATCATTGAGGATCTGGAAGCTCAAGTGACAGTGGAATGTGCTATACCCCAGAAGTTTCACCGATCGGTCATGGGTCCCAAAGGTTCAAGAATCCAGCAGATCACTCGGGACTACAATGTTCAAATCAAGTTCCCAGATAGAGAGGAAAATCCAGTTCACAGTGTAGAGCCTTCCATCCAGGAGAATGGAGATGAGGCTGGAGAGGGCAGAGAGGCCAAGGAGACCGACCCTGGCTCTCCCAGGAGGTGTGACATCATAATCATCTCTGGCCGGAAAGAGAAATGCGAGGCTGCCAAGGAAGCCCTGGAGGCACTGGTTCCAGTCACCATCGAGGTAGAGGTACCCTTTGATCTTCACCGCTACATCATTGGGCAAAAAGGAAGTGGAATCCGCAAGATGATGGATGAGTTTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTTCCAGTCACCATCGAGG
60.11
TCTGCCCAATGATTGTGCGA
60.32
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTTCCAGTCACCATCGAGG
60.11
ATCCGTTCACCTTTCTGCCC
60.32
177
PCR template sequence:
GGTTCCAGTCACCATCGAGGTAGAGGTACCCTTTGATCTTCACCGCTACATCATTGGGCAAAAAGGAAGTGGAATCCGCAAGATGATGGATGAGTTTGAGGAAAATGAGCGCACCAAGGATCTAATCATCGAGCAAAGATTTCATCGCACAATCATTGGGCAGAAAGGTGAACGGATTCGAGAAATTCGTGACAAATTCC
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-134-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-136-5p(1), mmu-miR-383-5p(1), mmu-miR-1198-5p(1), mmu-miR-207(1), mmu-miR-452-3p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
GGATGAGTTTGAGGAAAATGAGCGCA
siRNA sets
ATTTTCCTCAAACTCATCC, CATTTTCCTCAAACTCATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHDLBP_1497_ORF_1
1.2559
0.438344531
0.999999994
2799
ORF sequence:
ATGCAGAAGATGGTCGCAGACCTGGTGGAAAATAGCTATTCAATTTCTGTACCAATCTTCAAACAGTTTCACAAGAATATCATCGGGAAAGGAGGCGCAAACATTAAAAAGATCCGTGAAGAGAGCAACACCAAGATTGACCTTCCTGCAGAGAACAGCAACTCTGAGACCATTATTATCACTGGCAAGCGAGCCAACTGTGAAGCTGCCCGCAGCCGGATTCTGTCTATCCAGAAAGATCTGGCCAACATAGCTGAAGTGGAGGTCTCAATTCCTGCCAAACTACACAACTCTCTCATTGGCACAAAGGGCCGTCTGATCCGCTCCATCATGGAGGAATGTGGTGGCGTCCATATTCACTTTCCTGTGGAAGGTTCTGGAAGCGACACTGTTGTCATCAGGGGTCCTTCCTCAGATGTAGAGAAGGCCAAGAAGCAGCTCCTGCACCTGGCTGAGGAGAAGCAAACCAAGAGTTTTACTGTGGACATCCGAGCCAAGCCAGAATACCACAAATTCCTCATTGGCAAAGGGGGAGGTAAAATCCGAAAGGTGCGTGACAGTACTGGAGCCCGCATCATATTTCCGGCTGCTGAAGATAAGGACCAGGACCTGATCACAATCATAGGAAAGGAGGATGCTGTCCGTGAGGCCCAAAAGGAGCTGGAAGCATTGATCCAGAACCTGGAGAATGTGGTTGAAGACTATATGCTGGTGGACCCCAAACACCACCGCCATTTTGTCATCCGAAGAGGACAAGTTTTACGAGAAATTGCTGAAGAGTATGGCGGGGTGATGGTCAGCTTCCCACGCTCTGGCACGCAGAGTGATAAAGTCACTCTCAAGGGTGCCAAGGACTGTGTGGAGGCAGCCAAGAAACGCATTCAGGAAATCATTGAGGATCTGGAAGCTCAAGTGACAGTGGAATGTGCTATACCCCAGAAGTTTCACCGATCGGTCATGGGTCCCAAAGGTTCAAGAATCCAGCAGATCACTCGGGACTACAATGTTCAAATCAAGTTCCCAGATAGAGAGGAAAATCCAGTTCACAGTGTAGAGCCTTCCATCCAGGAGAATGGAGATGAGGCTGGAGAGGGCAGAGAGGCCAAGGAGACCGACCCTGGCTCTCCCAGGAGGTGTGACATCATAATCATCTCTGGCCGGAAAGAGAAATGCGAGGCTGCCAAGGAAGCCCTGGAGGCACTGGTTCCAGTCACCATCGAGGTAGAGGTACCCTTTGATCTTCACCGCTACATCATTGGGCAAAAAGGAAGTGGAATCCGCAAGATGATGGATGAGTTTGAGGAAAATGAGCGCACCAAGGATCTAATCATCGAGCAAAGATTTCATCGCACAATCATTGGGCAGAAAGGTGAACGGATTCGAGAAATTCGTGACAAATTCCCAGAGGTTATCATCAACTTTCCAGACCCAGCACAAAAAAGTGATATTGTACAACTCAGAGGCCCCAAGAATGAGGTGGAGAAGTGCACTAAGTATATGCAGAAGATGGTCGCAGACCTGGTGGAAAATAGCTATTCAATTTCTGTACCAATCTTCAAACAGTTTCACAAGAATATCATCGGGAAAGGAGGCGCAAACATTAAAAAGATCCGTGAAGAGAGCAACACCAAGATTGACCTTCCTGCAGAGAACAGCAACTCTGAGACCATTATTATCACTGGCAAGCGAGCCAACTGTGAAGCTGCCCGCAGCCGGATTCTGTCTATCCAGAAAGATCTGGCCAACATAGCTGAAGTGGAGGTCTCAATTCCTGCCAAACTACACAACTCTCTCATTGGCACAAAGGGCCGTCTGATCCGCTCCATCATGGAGGAATGTGGTGGCGTCCATATTCACTTTCCTGTGGAAGGTTCTGGAAGCGACACTGTTGTCATCAGGGGTCCTTCCTCAGATGTAGAGAAGGCCAAGAAGCAGCTCCTGCACCTGGCTGAGGAGAAGCAAACCAAGAGTTTTACTGTGGACATCCGAGCCAAGCCAGAATACCACAAATTCCTCATTGGCAAAGGGGGAGGTAAAATCCGAAAGGTGCGTGACAGTACTGGAGCCCGCATCATATTTCCGGCTGCTGAAGATAAGGACCAGGACCTGATCACAATCATAGGAAAGGAGGATGCTGTCCGTGAGGCCCAAAAGGAGCTGGAAGCATTGATCCAGAACCTGGAGAATGTGGTTGAAGACTATATGCTGGTGGACCCCAAACACCACCGCCATTTTGTCATCCGAAGAGGACAAGTTTTACGAGAAATTGCTGAAGAGTATGGCGGGGTGATGGTCAGCTTCCCACGCTCTGGCACGCAGAGTGATAAAGTCACTCTCAAGGGTGCCAAGGACTGTGTGGAGGCAGCCAAGAAACGCATTCAGGAAATCATTGAGGATCTGGAAGCTCAAGTGACAGTGGAATGTGCTATACCCCAGAAGTTTCACCGATCGGTCATGGGTCCCAAAGGTTCAAGAATCCAGCAGATCACTCGGGACTACAATGTTCAAATCAAGTTCCCAGATAGAGAGGAAAATCCAGTTCACAGTGTAGAGCCTTCCATCCAGGAGAATGGAGATGAGGCTGGAGAGGGCAGAGAGGCCAAGGAGACCGACCCTGGCTCTCCCAGGAGGTGTGACATCATAATCATCTCTGGCCGGAAAGAGAAATGCGAGGCTGCCAAGGAAGCCCTGGAGGCACTGGTTCCAGTCACCATCGAGGTAGAGGTACCCTTTGATCTTCACCGCTACATCATTGGGCAAAAAGGAAGTGGAATCCGCAAGATGATGGATGAGTTTGAG
Peptide sequence:
MQKMVADLVENSYSISVPIFKQFHKNIIGKGGANIKKIREESNTKIDLPAENSNSETIIITGKRANCEAARSRILSIQKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDSTGARIIFPAAEDKDQDLITIIGKEDAVREAQKELEALIQNLENVVEDYMLVDPKHHRHFVIRRGQVLREIAEEYGGVMVSFPRSGTQSDKVTLKGAKDCVEAAKKRIQEIIEDLEAQVTVECAIPQKFHRSVMGPKGSRIQQITRDYNVQIKFPDREENPVHSVEPSIQENGDEAGEGREAKETDPGSPRRCDIIIISGRKEKCEAAKEALEALVPVTIEVEVPFDLHRYIIGQKGSGIRKMMDEFEENERTKDLIIEQRFHRTIIGQKGERIREIRDKFPEVIINFPDPAQKSDIVQLRGPKNEVEKCTKYMQKMVADLVENSYSISVPIFKQFHKNIIGKGGANIKKIREESNTKIDLPAENSNSETIIITGKRANCEAARSRILSIQKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDSTGARIIFPAAEDKDQDLITIIGKEDAVREAQKELEALIQNLENVVEDYMLVDPKHHRHFVIRRGQVLREIAEEYGGVMVSFPRSGTQSDKVTLKGAKDCVEAAKKRIQEIIEDLEAQVTVECAIPQKFHRSVMGPKGSRIQQITRDYNVQIKFPDREENPVHSVEPSIQENGDEAGEGREAKETDPGSPRRCDIIIISGRKEKCEAAKEALEALVPVTIEVEVPFDLHRYIIGQKGSGIRKMMDEFE
IRESfinder result
IRESfinder score
0.481107562
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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