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mmu_circHdlbp_539
Basic information of circular RNA
PanCircBase ID:
mmu_circHdlbp_539
mm39_Chr. Position ID:
chr1|93340084|93342688|-
Gene name:
Hdlbp
Transcript:
ENSMUST00000170883.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
24,23,22,21
Exon/intron offsets:
0,1128,1464,2449
Genomic length:
2604
Exon/intron sizes in nt:
1,44,13,51,05,155
Flanking exon/introns:
chr1:93336858-93340084|chr1:93342688-93344222
Splice length:
539
Other database IDs:
circBase: hsa_circ_0119488, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_158161
Human Ortholog IDs:
Mature spliced Sequence:
TTCACAGTGTAGAGCCTTCCATCCAGGAGAATGGAGATGAGGCTGGAGAGGGCAGAGAGGCCAAGGAGACCGACCCTGGCTCTCCCAGGAGGTGTGACATCATAATCATCTCTGGCCGGAAAGAGAAATGCGAGGCTGCCAAGGAAGCCCTGGAGGCACTGGTTCCAGTCACCATCGAGGTAGAGGTACCCTTTGATCTTCACCGCTACATCATTGGGCAAAAAGGAAGTGGAATCCGCAAGATGATGGATGAGTTTGAGGTGAACATCCATGTACCAGCCCCCGAGCTGCAGTCAGACACCATCGCCATCACTGGCCTTGCAGCAAATTTGGACAGGGCTAAGGCGGGGCTACTGGATCGAGTAAAGGAGCTGCAGGCTGAGCAGGAAGATCGGGCTTTAAGGAGTTTTAAGCTGAGTGTCACTGTAGACCCCAAATACCATCCCAAAATTATCGGGAGAAAAGGAGCAGTGATCACCCAGATCCGCTTGGAACATGAAGTGAACATCCAATTTCCTGATAAGGATGATGGGAACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGAGCAGTGATCACCCAGA
60.25
ATGTCACACCTCCTGGGAGA
59.88
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATCACCCAGATCCGCTTGG
60.53
ATGTCACACCTCCTGGGAGA
59.88
167
PCR template sequence:
CCATCCCAAAATTATCGGGAGAAAAGGAGCAGTGATCACCCAGATCCGCTTGGAACATGAAGTGAACATCCAATTTCCTGATAAGGATGATGGGAACCAGTTCACAGTGTAGAGCCTTCCATCCAGGAGAATGGAGATGAGGCTGGAGAGGGCAGAGAGGCCAAGGAGACCGACCCTGGCTCTCCCAGGAGGTGTGACAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-139-5p(1), mmu-miR-136-5p(1), mmu-miR-207(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGATGGGAACCAGTTCACAGTGTAGA
siRNA sets
TACACTGTGAACTGGTTCC, ACACTGTGAACTGGTTCCC, CTACACTGTGAACTGGTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHDLBP_539_ORF_1
1.1641
0.393033118
0.675526306
309
ORF sequence:
ATGATGGATGAGTTTGAGGTGAACATCCATGTACCAGCCCCCGAGCTGCAGTCAGACACCATCGCCATCACTGGCCTTGCAGCAAATTTGGACAGGGCTAAGGCGGGGCTACTGGATCGAGTAAAGGAGCTGCAGGCTGAGCAGGAAGATCGGGCTTTAAGGAGTTTTAAGCTGAGTGTCACTGTAGACCCCAAATACCATCCCAAAATTATCGGGAGAAAAGGAGCAGTGATCACCCAGATCCGCTTGGAACATGAAGTGAACATCCAATTTCCTGATAAGGATGATGGGAACCAGTTCACAGTGTAG
Peptide sequence:
MMDEFEVNIHVPAPELQSDTIAITGLAANLDRAKAGLLDRVKELQAEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHEVNIQFPDKDDGNQFTV
IRESfinder result
IRESfinder score
0.443206633
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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