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mmu_circHdlbp_1119
Basic information of circular RNA
PanCircBase ID:
mmu_circHdlbp_1119
mm39_Chr. Position ID:
chr1|93340084|93345411|-
Gene name:
Hdlbp
Transcript:
ENSMUST00000170883.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
24,23,22,21,20,19,18
Exon/intron offsets:
0,1128,1464,2449,4138,4809,5105
Genomic length:
5327
Exon/intron sizes in nt:
14,41,35,10,51,55,13,90,00,000
Flanking exon/introns:
chr1:93336858-93340084|chr1:93345411-93347790
Splice length:
1119
Other database IDs:
CIRCpedia: HSA_CIRCpedia_94110
Human Ortholog IDs:
Mature spliced Sequence:
CAAACCAAGAGTTTTACTGTGGACATCCGAGCCAAGCCAGAATACCACAAATTCCTCATTGGCAAAGGGGGAGGTAAAATCCGAAAGGTGCGTGACAGTACTGGAGCCCGCATCATATTTCCGGCTGCTGAAGATAAGGACCAGGACCTGATCACAATCATAGGAAAGGAGGATGCTGTCCGTGAGGCCCAAAAGGAGCTGGAAGCATTGATCCAGAACCTGGAGAATGTGGTTGAAGACTATATGCTGGTGGACCCCAAACACCACCGCCATTTTGTCATCCGAAGAGGACAAGTTTTACGAGAAATTGCTGAAGAGTATGGCGGGGTGATGGTCAGCTTCCCACGCTCTGGCACGCAGAGTGATAAAGTCACTCTCAAGGGTGCCAAGGACTGTGTGGAGGCAGCCAAGAAACGCATTCAGGAAATCATTGAGGATCTGGAAGCTCAAGTGACAGTGGAATGTGCTATACCCCAGAAGTTTCACCGATCGGTCATGGGTCCCAAAGGTTCAAGAATCCAGCAGATCACTCGGGACTACAATGTTCAAATCAAGTTCCCAGATAGAGAGGAAAATCCAGTTCACAGTGTAGAGCCTTCCATCCAGGAGAATGGAGATGAGGCTGGAGAGGGCAGAGAGGCCAAGGAGACCGACCCTGGCTCTCCCAGGAGGTGTGACATCATAATCATCTCTGGCCGGAAAGAGAAATGCGAGGCTGCCAAGGAAGCCCTGGAGGCACTGGTTCCAGTCACCATCGAGGTAGAGGTACCCTTTGATCTTCACCGCTACATCATTGGGCAAAAAGGAAGTGGAATCCGCAAGATGATGGATGAGTTTGAGGTGAACATCCATGTACCAGCCCCCGAGCTGCAGTCAGACACCATCGCCATCACTGGCCTTGCAGCAAATTTGGACAGGGCTAAGGCGGGGCTACTGGATCGAGTAAAGGAGCTGCAGGCTGAGCAGGAAGATCGGGCTTTAAGGAGTTTTAAGCTGAGTGTCACTGTAGACCCCAAATACCATCCCAAAATTATCGGGAGAAAAGGAGCAGTGATCACCCAGATCCGCTTGGAACATGAAGTGAACATCCAATTTCCTGATAAGGATGATGGGAACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGAGCAGTGATCACCCAGA
60.25
TGTCACGCACCTTTCGGATT
60.25
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGAGCAGTGATCACCCAGA
60.25
CCCCCTTTGCCAATGAGGAA
60.25
147
PCR template sequence:
CCATCCCAAAATTATCGGGAGAAAAGGAGCAGTGATCACCCAGATCCGCTTGGAACATGAAGTGAACATCCAATTTCCTGATAAGGATGATGGGAACCAGCAAACCAAGAGTTTTACTGTGGACATCCGAGCCAAGCCAGAATACCACAAATTCCTCATTGGCAAAGGGGGAGGTAAAATCCGAAAGGTGCGTGACAGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-139-5p(1), mmu-miR-136-5p(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
TGATGGGAACCAGCAAACCAAGAGTT
siRNA sets
TCTTGGTTTGCTGGTTCCC,CTCTTGGTTTGCTGGTTCC,AACTCTTGGTTTGCTGGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHDLBP_1119_ORF_1
1.2523
0.440747805
0.999998208
1995
ORF sequence:
ATGCTGGTGGACCCCAAACACCACCGCCATTTTGTCATCCGAAGAGGACAAGTTTTACGAGAAATTGCTGAAGAGTATGGCGGGGTGATGGTCAGCTTCCCACGCTCTGGCACGCAGAGTGATAAAGTCACTCTCAAGGGTGCCAAGGACTGTGTGGAGGCAGCCAAGAAACGCATTCAGGAAATCATTGAGGATCTGGAAGCTCAAGTGACAGTGGAATGTGCTATACCCCAGAAGTTTCACCGATCGGTCATGGGTCCCAAAGGTTCAAGAATCCAGCAGATCACTCGGGACTACAATGTTCAAATCAAGTTCCCAGATAGAGAGGAAAATCCAGTTCACAGTGTAGAGCCTTCCATCCAGGAGAATGGAGATGAGGCTGGAGAGGGCAGAGAGGCCAAGGAGACCGACCCTGGCTCTCCCAGGAGGTGTGACATCATAATCATCTCTGGCCGGAAAGAGAAATGCGAGGCTGCCAAGGAAGCCCTGGAGGCACTGGTTCCAGTCACCATCGAGGTAGAGGTACCCTTTGATCTTCACCGCTACATCATTGGGCAAAAAGGAAGTGGAATCCGCAAGATGATGGATGAGTTTGAGGTGAACATCCATGTACCAGCCCCCGAGCTGCAGTCAGACACCATCGCCATCACTGGCCTTGCAGCAAATTTGGACAGGGCTAAGGCGGGGCTACTGGATCGAGTAAAGGAGCTGCAGGCTGAGCAGGAAGATCGGGCTTTAAGGAGTTTTAAGCTGAGTGTCACTGTAGACCCCAAATACCATCCCAAAATTATCGGGAGAAAAGGAGCAGTGATCACCCAGATCCGCTTGGAACATGAAGTGAACATCCAATTTCCTGATAAGGATGATGGGAACCAGCAAACCAAGAGTTTTACTGTGGACATCCGAGCCAAGCCAGAATACCACAAATTCCTCATTGGCAAAGGGGGAGGTAAAATCCGAAAGGTGCGTGACAGTACTGGAGCCCGCATCATATTTCCGGCTGCTGAAGATAAGGACCAGGACCTGATCACAATCATAGGAAAGGAGGATGCTGTCCGTGAGGCCCAAAAGGAGCTGGAAGCATTGATCCAGAACCTGGAGAATGTGGTTGAAGACTATATGCTGGTGGACCCCAAACACCACCGCCATTTTGTCATCCGAAGAGGACAAGTTTTACGAGAAATTGCTGAAGAGTATGGCGGGGTGATGGTCAGCTTCCCACGCTCTGGCACGCAGAGTGATAAAGTCACTCTCAAGGGTGCCAAGGACTGTGTGGAGGCAGCCAAGAAACGCATTCAGGAAATCATTGAGGATCTGGAAGCTCAAGTGACAGTGGAATGTGCTATACCCCAGAAGTTTCACCGATCGGTCATGGGTCCCAAAGGTTCAAGAATCCAGCAGATCACTCGGGACTACAATGTTCAAATCAAGTTCCCAGATAGAGAGGAAAATCCAGTTCACAGTGTAGAGCCTTCCATCCAGGAGAATGGAGATGAGGCTGGAGAGGGCAGAGAGGCCAAGGAGACCGACCCTGGCTCTCCCAGGAGGTGTGACATCATAATCATCTCTGGCCGGAAAGAGAAATGCGAGGCTGCCAAGGAAGCCCTGGAGGCACTGGTTCCAGTCACCATCGAGGTAGAGGTACCCTTTGATCTTCACCGCTACATCATTGGGCAAAAAGGAAGTGGAATCCGCAAGATGATGGATGAGTTTGAGGTGAACATCCATGTACCAGCCCCCGAGCTGCAGTCAGACACCATCGCCATCACTGGCCTTGCAGCAAATTTGGACAGGGCTAAGGCGGGGCTACTGGATCGAGTAAAGGAGCTGCAGGCTGAGCAGGAAGATCGGGCTTTAAGGAGTTTTAAGCTGAGTGTCACTGTAGACCCCAAATACCATCCCAAAATTATCGGGAGAAAAGGAGCAGTGATCACCCAGATCCGCTTGGAACATGAAGTGAACATCCAATTTCCTGATAAGGATGATGGGAACCAG
Peptide sequence:
MLVDPKHHRHFVIRRGQVLREIAEEYGGVMVSFPRSGTQSDKVTLKGAKDCVEAAKKRIQEIIEDLEAQVTVECAIPQKFHRSVMGPKGSRIQQITRDYNVQIKFPDREENPVHSVEPSIQENGDEAGEGREAKETDPGSPRRCDIIIISGRKEKCEAAKEALEALVPVTIEVEVPFDLHRYIIGQKGSGIRKMMDEFEVNIHVPAPELQSDTIAITGLAANLDRAKAGLLDRVKELQAEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHEVNIQFPDKDDGNQQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDSTGARIIFPAAEDKDQDLITIIGKEDAVREAQKELEALIQNLENVVEDYMLVDPKHHRHFVIRRGQVLREIAEEYGGVMVSFPRSGTQSDKVTLKGAKDCVEAAKKRIQEIIEDLEAQVTVECAIPQKFHRSVMGPKGSRIQQITRDYNVQIKFPDREENPVHSVEPSIQENGDEAGEGREAKETDPGSPRRCDIIIISGRKEKCEAAKEALEALVPVTIEVEVPFDLHRYIIGQKGSGIRKMMDEFEVNIHVPAPELQSDTIAITGLAANLDRAKAGLLDRVKELQAEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHEVNIQFPDKDDGNQ
IRESfinder result
IRESfinder score
0.438741485
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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