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mmu_circArhgap21_805
Basic information of circular RNA
PanCircBase ID:
mmu_circArhgap21_805
mm39_Chr. Position ID:
chr2|20860391|20865918|-
Gene name:
Arhgap21
Transcript:
ENSMUST00000154230.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
21,20,19,18,17,16,15
Exon/intron offsets:
0,3320,3486,4137,4300,4723,5390
Genomic length:
5527
Exon/intron sizes in nt:
1,26,90,74,79,15,61,43,000
Flanking exon/introns:
chr2:20860206-20860391|chr2:20865918-20865996
Splice length:
805
Other database IDs:
CIRCpedia: MMU_CIRCpedia_224765, circAtlas: mmu-Arhgap21_0037
Human Ortholog IDs:
Mature spliced Sequence:
CAAAACAGAACAGTTGCCAAAAACACCTCGCCAGAGTCTTAGCATCAGGCAAACTTTGCTTGGTGCTAAATCAGAGCCAAAGACTCAAAGCCCACATTCTCCAAAGGAGGAGTCCGAGAGGAAGCTTCTCAGTAAAGATGATACCAGTCCCCCTAAAGACAAAGGTACTTGGAGAAGAGGCATTCCAAGCATCGTGAGGAAGACGTTTGAGAAAAAGCCGGCCGCCACAGGGACCTTTGGAGTTAGGCTGGATGACTGCCCACCCGCCCACACCAACAGGTACATTCCATTAATCGTTGACATATGTTGCAAATTAGTTGAAGAAAGGGGTCTTGAATATACAGGTATTTACCGAGTTCCCGGCAACAACGCAGCCATTTCAAGCATGCAGGAAGAACTCAACAAGGGGATGGCAGACATTGACATACAAGATGATAAATGGCGAGATTTGAATGTGATAAGCAGTTTACTAAAATCCTTCTTCAGAAAGCTCCCTGAGCCTCTCTTTACGAATGACAAATATGCTGACTTCATTGAGGCCAATCGCAAAGAGGACCCACTGGATCGGCTACGAACATTAAAGAGACTAATTCATGACCTGCCTGAGCATCATTTTGAGACGCTCAAGTTTCTCTCGGCTCATCTGAAGACAGTGGCAGAGAACTCAGAAAAGAATAAGATGGAACCCAGAAACCTAGCGATCGTTTTTGGTCCAACTCTAGTGAGAACATCAGAAGACAACATGACCCACATGGTCACGCACATGCCTGACCAGTATAAGATCGTAGAGACTCTCATCCAGCAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGCACATGCCTGACCAGTAT
60.46
TGGGCTTTGAGTCTTTGGCT
59.81
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGCACATGCCTGACCAGTAT
60.46
GTGGGCTTTGAGTCTTTGGC
59.68
142
PCR template sequence:
TTTTGGTCCAACTCTAGTGAGAACATCAGAAGACAACATGACCCACATGGTCACGCACATGCCTGACCAGTATAAGATCGTAGAGACTCTCATCCAGCATCAAAACAGAACAGTTGCCAAAAACACCTCGCCAGAGTCTTAGCATCAGGCAAACTTTGCTTGGTGCTAAATCAGAGCCAAAGACTCAAAGCCCACATTCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-206-3p(1), mmu-miR-181a-5p(1), mmu-miR-96-5p(1), mmu-miR-499-5p(1), mmu-miR-325-3p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-669d-5p(1), mmu-miR-3105-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTCATCCAGCATCAAAACAGAACAG
siRNA sets
TGTTTTGATGCTGGATGAG,GTTTTGATGCTGGATGAGA,TGTTCTGTTTTGATGCTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARHGAP21_805_ORF_1
1.0454
0.255829272
0.739475955
462
ORF sequence:
ATGCAGGAAGAACTCAACAAGGGGATGGCAGACATTGACATACAAGATGATAAATGGCGAGATTTGAATGTGATAAGCAGTTTACTAAAATCCTTCTTCAGAAAGCTCCCTGAGCCTCTCTTTACGAATGACAAATATGCTGACTTCATTGAGGCCAATCGCAAAGAGGACCCACTGGATCGGCTACGAACATTAAAGAGACTAATTCATGACCTGCCTGAGCATCATTTTGAGACGCTCAAGTTTCTCTCGGCTCATCTGAAGACAGTGGCAGAGAACTCAGAAAAGAATAAGATGGAACCCAGAAACCTAGCGATCGTTTTTGGTCCAACTCTAGTGAGAACATCAGAAGACAACATGACCCACATGGTCACGCACATGCCTGACCAGTATAAGATCGTAGAGACTCTCATCCAGCATCAAAACAGAACAGTTGCCAAAAACACCTCGCCAGAGTCTTAG
Peptide sequence:
MQEELNKGMADIDIQDDKWRDLNVISSLLKSFFRKLPEPLFTNDKYADFIEANRKEDPLDRLRTLKRLIHDLPEHHFETLKFLSAHLKTVAENSEKNKMEPRNLAIVFGPTLVRTSEDNMTHMVTHMPDQYKIVETLIQHQNRTVAKNTSPES
IRESfinder result
IRESfinder score
0.462880099
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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