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mmu_circHsd17b4_636
Basic information of circular RNA
PanCircBase ID:
mmu_circHsd17b4_636
mm39_Chr. Position ID:
chr18|50288193|50300002|+
Gene name:
Hsd17b4
Transcript:
ENSMUST00000025385.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
9,10,11,12,13,14
Exon/intron offsets:
0,3258,5008,6975,9488,11757
Genomic length:
11809
Exon/intron sizes in nt:
92,25,129,101,237,52
Flanking exon/introns:
chr18:50279644-50288193|chr18:50300002-50303786
Splice length:
636
Other database IDs:
circAtlas: mmu-Hsd17b4_0002
Human Ortholog IDs:
Mature spliced Sequence:
ATCTTGTTGAAGCCCTGAAGCCAGAGTATGTGGCCCCTCTGGTGCTTTGGCTTTGCCATGAGAGCTGTGAGGAAAATGGTGGCCTATTTGAGGTTGGAGCAGGATGGATTGGAAAATTGCGCTGGGAGAGGACCCTGGGCGCCATCGTCAGAAAGCGGAATCAGCCCATGACTCCCGAGGCAGTGAGGGACAACTGGGAGAAGATCTGTGACTTCAGCAATGCCAGCAAGCCGCAGACCATTCAAGAATCAACAGGTGGTATAGTCGAAGTTTTACATAAGGTAGATTCAGAAGGAATCTCACCAAACCGTACCAGTCACGCGGCACCTGCAGCCACGTCAGGATTCGTTGGTGCTGTTGGCCATAAACTTCCTTCATTTTCTTCTTCGTATACGGAGCTGCAGAGTATTATGTATGCCCTCGGAGTGGGAGCGTCAGTCAAAAATCCAAAGGATTTGAAGTTTGTTTATGAAGGCAGTGCTGACTTCTCCTGTTTGCCCACCTTCGGAGTCATTGTCGCTCAGAAGTCCATGATGAATGGAGGGCTGGCAGAGGTTCCTGGGCTGTCATTCAACTTTGCAAAGGCTCTTCACGGGGAGCAGTACTTGGAGCTGTATAAGCCACTTCCTCGATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTTCCTGGGCTGTCATTCA
59.96
CCTCACAGCTCTCATGGCAA
60.04
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTTCCTGGGCTGTCATTCA
59.96
CACAGCTCTCATGGCAAAGC
59.83
152
PCR template sequence:
AATGGAGGGCTGGCAGAGGTTCCTGGGCTGTCATTCAACTTTGCAAAGGCTCTTCACGGGGAGCAGTACTTGGAGCTGTATAAGCCACTTCCTCGATCAGATCTTGTTGAAGCCCTGAAGCCAGAGTATGTGGCCCCTCTGGTGCTTTGGCTTTGCCATGAGAGCTGTGAGGAAAATGGTGGCCTATTTGAGGTTGGAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-29a-3p(1), mmu-miR-222-3p(1), mmu-miR-136-5p(1), mmu-miR-324-3p(1), mmu-miR-207(1), mmu-miR-673-5p(1), mmu-miR-369-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTCCTCGATCAGATCTTGTTGAAGC
siRNA sets
CTTCAACAAGATCTGATCG, AACAAGATCTGATCGAGGA, TTCAACAAGATCTGATCGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHSD17B4_636_ORF_1
0.9115
0.201902754
0.994592417
1104
ORF sequence:
ATGACTCCCGAGGCAGTGAGGGACAACTGGGAGAAGATCTGTGACTTCAGCAATGCCAGCAAGCCGCAGACCATTCAAGAATCAACAGGTGGTATAGTCGAAGTTTTACATAAGGTAGATTCAGAAGGAATCTCACCAAACCGTACCAGTCACGCGGCACCTGCAGCCACGTCAGGATTCGTTGGTGCTGTTGGCCATAAACTTCCTTCATTTTCTTCTTCGTATACGGAGCTGCAGAGTATTATGTATGCCCTCGGAGTGGGAGCGTCAGTCAAAAATCCAAAGGATTTGAAGTTTGTTTATGAAGGCAGTGCTGACTTCTCCTGTTTGCCCACCTTCGGAGTCATTGTCGCTCAGAAGTCCATGATGAATGGAGGGCTGGCAGAGGTTCCTGGGCTGTCATTCAACTTTGCAAAGGCTCTTCACGGGGAGCAGTACTTGGAGCTGTATAAGCCACTTCCTCGATCAGATCTTGTTGAAGCCCTGAAGCCAGAGTATGTGGCCCCTCTGGTGCTTTGGCTTTGCCATGAGAGCTGTGAGGAAAATGGTGGCCTATTTGAGGTTGGAGCAGGATGGATTGGAAAATTGCGCTGGGAGAGGACCCTGGGCGCCATCGTCAGAAAGCGGAATCAGCCCATGACTCCCGAGGCAGTGAGGGACAACTGGGAGAAGATCTGTGACTTCAGCAATGCCAGCAAGCCGCAGACCATTCAAGAATCAACAGGTGGTATAGTCGAAGTTTTACATAAGGTAGATTCAGAAGGAATCTCACCAAACCGTACCAGTCACGCGGCACCTGCAGCCACGTCAGGATTCGTTGGTGCTGTTGGCCATAAACTTCCTTCATTTTCTTCTTCGTATACGGAGCTGCAGAGTATTATGTATGCCCTCGGAGTGGGAGCGTCAGTCAAAAATCCAAAGGATTTGAAGTTTGTTTATGAAGGCAGTGCTGACTTCTCCTGTTTGCCCACCTTCGGAGTCATTGTCGCTCAGAAGTCCATGATGAATGGAGGGCTGGCAGAGGTTCCTGGGCTGTCATTCAACTTTGCAAAGGCTCTTCACGGGGAGCAGTACTTGGAGCTGTATAAGCCACTTCCTCGATCA
Peptide sequence:
MTPEAVRDNWEKICDFSNASKPQTIQESTGGIVEVLHKVDSEGISPNRTSHAAPAATSGFVGAVGHKLPSFSSSYTELQSIMYALGVGASVKNPKDLKFVYEGSADFSCLPTFGVIVAQKSMMNGGLAEVPGLSFNFAKALHGEQYLELYKPLPRSDLVEALKPEYVAPLVLWLCHESCEENGGLFEVGAGWIGKLRWERTLGAIVRKRNQPMTPEAVRDNWEKICDFSNASKPQTIQESTGGIVEVLHKVDSEGISPNRTSHAAPAATSGFVGAVGHKLPSFSSSYTELQSIMYALGVGASVKNPKDLKFVYEGSADFSCLPTFGVIVAQKSMMNGGLAEVPGLSFNFAKALHGEQYLELYKPLPRS
IRESfinder result
IRESfinder score
0.483564948
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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