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mmu_circHmgxb3_1074
Basic information of circular RNA
PanCircBase ID:
mmu_circHmgxb3_1074
mm39_Chr. Position ID:
chr18|61283440|61298655|-
Gene name:
Hmgxb3
Transcript:
ENSMUST00000091884.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
12,11,10,9,8,7,6,5
Exon/intron offsets:
0,1816,4659,4891,6974,7246,12528,15116
Genomic length:
15215
Exon/intron sizes in nt:
150,99,98,173,176,147,132,99
Flanking exon/introns:
chr18:61280620-61283440|chr18:61298655-61300267
Splice length:
1074
Other database IDs:
CIRCpedia: MMU_CIRCpedia_216045, circAtlas: mmu-Hmgxb3_0011
CIRCpedia: HSA_CIRCpedia_363383
Human Ortholog IDs:
Mature spliced Sequence:
GACTCCAGTGAGAGTAGCCCGTCTGCTCCAGCCACTCAGTTCATCATGCTGCCTCTGCCTGCTTACTCGGTCGTGGAGAACCCTTCTTCCATCAAGCTGACTACAACATACACCCGTCGGGGCCACGGGACATGCACAAGTCCAGGTTGTTCTTTTACCTATGTCACCAGGCACAAACCACCTAAGTGCCCTACTTGTGGTAACTTCCTAGGAGGGAAGTGGATCCCAAAGGAAAAGCCAGCCAAAGTCAAAGTGGAATTGGCTTCGGGTGTCTCCTCCAAAGGTTCTGTGATTAAAAGAAATCAGCAGTCTGTCACCACTGAGCAAAACCCCTCTAAGGAAAATGCTTCAAAACTGACTCTGGAGAACTCAGAAGCTGAAGTTCCTGGGAATCGTGGTACAGCGGTAACTAAGATGCCTGTTGTCAAGAGTGGTGCCCAGGCTGAGATCTCTCTGGGGACAACTGAGAATGACAGTCCTGGACCGGACATACTGCCATCGGCTGAGGGGACCAGCTCCTCCAGTTTACTCCAAGCTCACAAAAAGTCTCCAGGAGTTGACCTGTTCACCACTGGACCCAAAGCCCCAGAGCTGAAAGGCAGAGCACGAGGCAAGCCCTCCTTGCTGGCTGCAGCGAGACCTATGAGAGCAATCCTACCAGCCCCAACAAGTGTTGGGCGGGGCAGCGGCGTGGGACTGCCCAGGGCCAGGCAGGCTTTCCCCCTGGATAAGACTCCCTCGGTGAGGACTTGTGGCCTAAAGCCAAGCACGCTGAAACAGCTGGGCCAACCCATCCAGCAGCCACCTAGCACTGGTGAAGTAAAGCTATCCAACTGCGCAAGCAGCAGGACCCCACAGTTGAAAATCGTAGAGGTCAAGCCTGACCTGTTCCCTCCGTATAAGTATAGCTGCACTGTCACGCTGGATTTGGGCCTGGCTACATCGAGAGGACGGGGAAAGTGCAAAAATCCCTCCTGTAGCTATGTCTACACCAACCGACACAAACCTCGGATTTGTCCCAGCTGTGGTTTCAACCTTGCCAAAGACAGGACTGAGAAAACTCCAAAGGCCATT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACACCAACCGACACAAACCT
60.03
GACCGAGTAAGCAGGCAGAG
60.18
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACACCAACCGACACAAACCT
60.03
CTCCACGACCGAGTAAGCAG
60.18
164
PCR template sequence:
CTGTAGCTATGTCTACACCAACCGACACAAACCTCGGATTTGTCCCAGCTGTGGTTTCAACCTTGCCAAAGACAGGACTGAGAAAACTCCAAAGGCCATTGACTCCAGTGAGAGTAGCCCGTCTGCTCCAGCCACTCAGTTCATCATGCTGCCTCTGCCTGCTTACTCGGTCGTGGAGAACCCTTCTTCCATCAAGCTGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(1), mmu-miR-34c-5p(1), mmu-miR-223-3p(1), mmu-miR-92a-3p(1), mmu-miR-709(1), mmu-miR-326-3p(1), mmu-miR-25-3p(1), mmu-miR-214-3p(1), mmu-miR-182-5p(1), mmu-miR-107-3p(1), mmu-miR-98-5p(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCAAAGGCCATTGACTCCAGTGAGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHMGXB3_1074_ORF_1
0.8542
0.196258122
0.999995326
2103
ORF sequence:
ATGCTGCCTCTGCCTGCTTACTCGGTCGTGGAGAACCCTTCTTCCATCAAGCTGACTACAACATACACCCGTCGGGGCCACGGGACATGCACAAGTCCAGGTTGTTCTTTTACCTATGTCACCAGGCACAAACCACCTAAGTGCCCTACTTGTGGTAACTTCCTAGGAGGGAAGTGGATCCCAAAGGAAAAGCCAGCCAAAGTCAAAGTGGAATTGGCTTCGGGTGTCTCCTCCAAAGGTTCTGTGATTAAAAGAAATCAGCAGTCTGTCACCACTGAGCAAAACCCCTCTAAGGAAAATGCTTCAAAACTGACTCTGGAGAACTCAGAAGCTGAAGTTCCTGGGAATCGTGGTACAGCGGTAACTAAGATGCCTGTTGTCAAGAGTGGTGCCCAGGCTGAGATCTCTCTGGGGACAACTGAGAATGACAGTCCTGGACCGGACATACTGCCATCGGCTGAGGGGACCAGCTCCTCCAGTTTACTCCAAGCTCACAAAAAGTCTCCAGGAGTTGACCTGTTCACCACTGGACCCAAAGCCCCAGAGCTGAAAGGCAGAGCACGAGGCAAGCCCTCCTTGCTGGCTGCAGCGAGACCTATGAGAGCAATCCTACCAGCCCCAACAAGTGTTGGGCGGGGCAGCGGCGTGGGACTGCCCAGGGCCAGGCAGGCTTTCCCCCTGGATAAGACTCCCTCGGTGAGGACTTGTGGCCTAAAGCCAAGCACGCTGAAACAGCTGGGCCAACCCATCCAGCAGCCACCTAGCACTGGTGAAGTAAAGCTATCCAACTGCGCAAGCAGCAGGACCCCACAGTTGAAAATCGTAGAGGTCAAGCCTGACCTGTTCCCTCCGTATAAGTATAGCTGCACTGTCACGCTGGATTTGGGCCTGGCTACATCGAGAGGACGGGGAAAGTGCAAAAATCCCTCCTGTAGCTATGTCTACACCAACCGACACAAACCTCGGATTTGTCCCAGCTGTGGTTTCAACCTTGCCAAAGACAGGACTGAGAAAACTCCAAAGGCCATTGACTCCAGTGAGAGTAGCCCGTCTGCTCCAGCCACTCAGTTCATCATGCTGCCTCTGCCTGCTTACTCGGTCGTGGAGAACCCTTCTTCCATCAAGCTGACTACAACATACACCCGTCGGGGCCACGGGACATGCACAAGTCCAGGTTGTTCTTTTACCTATGTCACCAGGCACAAACCACCTAAGTGCCCTACTTGTGGTAACTTCCTAGGAGGGAAGTGGATCCCAAAGGAAAAGCCAGCCAAAGTCAAAGTGGAATTGGCTTCGGGTGTCTCCTCCAAAGGTTCTGTGATTAAAAGAAATCAGCAGTCTGTCACCACTGAGCAAAACCCCTCTAAGGAAAATGCTTCAAAACTGACTCTGGAGAACTCAGAAGCTGAAGTTCCTGGGAATCGTGGTACAGCGGTAACTAAGATGCCTGTTGTCAAGAGTGGTGCCCAGGCTGAGATCTCTCTGGGGACAACTGAGAATGACAGTCCTGGACCGGACATACTGCCATCGGCTGAGGGGACCAGCTCCTCCAGTTTACTCCAAGCTCACAAAAAGTCTCCAGGAGTTGACCTGTTCACCACTGGACCCAAAGCCCCAGAGCTGAAAGGCAGAGCACGAGGCAAGCCCTCCTTGCTGGCTGCAGCGAGACCTATGAGAGCAATCCTACCAGCCCCAACAAGTGTTGGGCGGGGCAGCGGCGTGGGACTGCCCAGGGCCAGGCAGGCTTTCCCCCTGGATAAGACTCCCTCGGTGAGGACTTGTGGCCTAAAGCCAAGCACGCTGAAACAGCTGGGCCAACCCATCCAGCAGCCACCTAGCACTGGTGAAGTAAAGCTATCCAACTGCGCAAGCAGCAGGACCCCACAGTTGAAAATCGTAGAGGTCAAGCCTGACCTGTTCCCTCCGTATAAGTATAGCTGCACTGTCACGCTGGATTTGGGCCTGGCTACATCGAGAGGACGGGGAAAGTGCAAAAATCCCTCCTGTAGCTATGTCTACACCAACCGACACAAACCTCGGATTTGTCCCAGCTGTGGTTTCAACCTTGCCAAAGACAGGACTGAGAAAACTCCAAAGGCCATT
Peptide sequence:
MLPLPAYSVVENPSSIKLTTTYTRRGHGTCTSPGCSFTYVTRHKPPKCPTCGNFLGGKWIPKEKPAKVKVELASGVSSKGSVIKRNQQSVTTEQNPSKENASKLTLENSEAEVPGNRGTAVTKMPVVKSGAQAEISLGTTENDSPGPDILPSAEGTSSSSLLQAHKKSPGVDLFTTGPKAPELKGRARGKPSLLAAARPMRAILPAPTSVGRGSGVGLPRARQAFPLDKTPSVRTCGLKPSTLKQLGQPIQQPPSTGEVKLSNCASSRTPQLKIVEVKPDLFPPYKYSCTVTLDLGLATSRGRGKCKNPSCSYVYTNRHKPRICPSCGFNLAKDRTEKTPKAIDSSESSPSAPATQFIMLPLPAYSVVENPSSIKLTTTYTRRGHGTCTSPGCSFTYVTRHKPPKCPTCGNFLGGKWIPKEKPAKVKVELASGVSSKGSVIKRNQQSVTTEQNPSKENASKLTLENSEAEVPGNRGTAVTKMPVVKSGAQAEISLGTTENDSPGPDILPSAEGTSSSSLLQAHKKSPGVDLFTTGPKAPELKGRARGKPSLLAAARPMRAILPAPTSVGRGSGVGLPRARQAFPLDKTPSVRTCGLKPSTLKQLGQPIQQPPSTGEVKLSNCASSRTPQLKIVEVKPDLFPPYKYSCTVTLDLGLATSRGRGKCKNPSCSYVYTNRHKPRICPSCGFNLAKDRTEKTPKAI
IRESfinder result
IRESfinder score
0.49787369
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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