top of page
mmu_circArfgap3_1488
Basic information of circular RNA
PanCircBase ID:
mmu_circArfgap3_1488
mm39_Chr. Position ID:
chr15|83187303|83227341|-
Gene name:
Arfgap3
Transcript:
ENSMUST00000067215.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
14
Exon/intron indexes:
15,14,13,12,11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,3778,4950,7147,10366,11237,19471,21001,24502,27416,29583,31375,33551,39919
Genomic length:
40038
Exon/intron sizes in nt:
1,22,91,12,41,35,14,41,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr15:83184903-83187303|chr15:83227341-83234281
Splice length:
1488
Other database IDs:
circBase: hsa_circ_0116680, CIRCpedia: HSA_CIRCpedia_90978
Human Ortholog IDs:
Mature spliced Sequence:
GTGTGTTTTGACTGTGGTGCCAAAAATCCCAGCTGGGCCAGCATAAGCTATGGGGTGTTTCTCTGCATTGACTGCTCTGGATCACACCGGTCGCTCGGGGTTCACTTGAGTTTTATTCGGTCCACAGAGCTGGATTCAAACTGGTCGTGGTTCCAGCTTCGATGCATGCAAGTTGGAGGGAACTCAAATGCTTCTTCCTTCTTCCACCAACATGGGTGTGCCACCAAGGACACCAACGCCAAGTACAACAGCCGTGCGGCTCAGCTCTACAGGGAGAAGATCAAGACTCTGGCCACCCAGGCCACCCGCAGACACGGCACCGATCTGTGGCTGGACAGCTGTGCGGCTCCACCTGTGTCCCCTCCTCCAAAGGAGGAAGATTTTTTTGCTTCTCACGCCTCTCTGGAGGTCAGTGGTGCTATGCAGGCATCCGCACAGCCAGAGTCAGCCTCTTCAACACCGTGGGGCTTGGAAACCACTCCAGAAAAACATGAAGGTGGGCCAGGACAAGGGCCAAGCGTGGAAGGTCTGAACACCCCTGGAAAGGCTGCACCAGAGGTTTCATCGATTATAAAAAAGAAGCCAAATCAAGCAAAAAAAGGACTTGGAGCCAAAAAAGGAAGCTTGGGAGCCCAGAAACTGACAAATACATCCTTCACTGAGATCGAAAAGCAAGCTCAGGCTGTGGATAAGAGGAAGGAGCAGGAAGACCTTGCCAGGGGTGCCCCAAAGGAGGAGTCTATTGTTTCGTCCTTGCGACTGGCCTACAAGGATCTGGAAATCAGCAGGAAGAAAGATGAAAGACTGAACCTGAGTGGCCAGAAGAAGGTGGAAGCCGAGCGGCTGGGCATGGGCTTTGGAAGCTGCAGGAGTGGCATCTCCCACTCGGTGACTTCAGACATGCAGACCATTGAGCAGGAGTCGCCCACACTGGCAAAGCCGAGGAGGAAGTACCAGGAGGACCCAGAGGACTCGTACTTCAGCTCCAGCTCCAAGTGGTCTGAGCAGAGCAGCAGCAGGTACTTTGACGACCCCATGGAGTTAAGAAGCAGCTCCTTCTCTAGCTGGGATGATGGTGCCGATTCCTACTGGAAGAAAGACAGCAGCAGAGACCCCGAGCCTGCCATGAGAAGCACCGGCTCTTCAGACAGGCCCAGTGCTCGCCGGAAGCCAGAATATGAGCCCATTGGCAGCACAGATGAAGCCCAGAAGAAGTTTGGCAACGTCAAGGCCATCTCTTCAGACATGTACTTTGGAATTCAAGCCCAGACAGATTTTGAAACCCGGGCGCGGCTGGAGAGGCTCTCCACCAGCTCCTCCATAAGCTCTGCAGACCTTTTTGATGAGCAGAGGAAGCAGACTGCAGGAAACTACAACCTTTCCAATGTGCTGCCCAATGCCCCAGACATGGCGCAGTTCAAGCAAGGTGTGCGCTCCGTTGCTGGAAAACTTTCCGTCTTCGCCAATGGGGTCATGACGTCCATTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGACATGGCGCAGTTCAAG
59.83
CGGTGTGATCCAGAGCAGTC
60.46
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGCAGTTCAAGCAAGGTGTG
60.32
CGGTGTGATCCAGAGCAGTC
60.46
166
PCR template sequence:
GCTGCCCAATGCCCCAGACATGGCGCAGTTCAAGCAAGGTGTGCGCTCCGTTGCTGGAAAACTTTCCGTCTTCGCCAATGGGGTCATGACGTCCATTCAGGTGTGTTTTGACTGTGGTGCCAAAAATCCCAGCTGGGCCAGCATAAGCTATGGGGTGTTTCTCTGCATTGACTGCTCTGGATCACACCGGTCGCTCGGGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-199a-5p(1), mmu-miR-205-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-328-3p(1), mmu-miR-326-3p(1), mmu-miR-370-3p(1), mmu-miR-362-5p(1), mmu-miR-224-5p(1), mmu-miR-705(1), mmu-miR-129-5p(1), mmu-miR-335-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GACGTCCATTCAGGTGTGTTTTGACT
siRNA sets
AAAACACACCTGAATGGAC, TCAAAACACACCTGAATGG, AACACACCTGAATGGACGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARFGAP3_1488_ORF_1
0.8821
0.34182857
0.999999985
2811
ORF sequence:
ATGCAAGTTGGAGGGAACTCAAATGCTTCTTCCTTCTTCCACCAACATGGGTGTGCCACCAAGGACACCAACGCCAAGTACAACAGCCGTGCGGCTCAGCTCTACAGGGAGAAGATCAAGACTCTGGCCACCCAGGCCACCCGCAGACACGGCACCGATCTGTGGCTGGACAGCTGTGCGGCTCCACCTGTGTCCCCTCCTCCAAAGGAGGAAGATTTTTTTGCTTCTCACGCCTCTCTGGAGGTCAGTGGTGCTATGCAGGCATCCGCACAGCCAGAGTCAGCCTCTTCAACACCGTGGGGCTTGGAAACCACTCCAGAAAAACATGAAGGTGGGCCAGGACAAGGGCCAAGCGTGGAAGGTCTGAACACCCCTGGAAAGGCTGCACCAGAGGTTTCATCGATTATAAAAAAGAAGCCAAATCAAGCAAAAAAAGGACTTGGAGCCAAAAAAGGAAGCTTGGGAGCCCAGAAACTGACAAATACATCCTTCACTGAGATCGAAAAGCAAGCTCAGGCTGTGGATAAGAGGAAGGAGCAGGAAGACCTTGCCAGGGGTGCCCCAAAGGAGGAGTCTATTGTTTCGTCCTTGCGACTGGCCTACAAGGATCTGGAAATCAGCAGGAAGAAAGATGAAAGACTGAACCTGAGTGGCCAGAAGAAGGTGGAAGCCGAGCGGCTGGGCATGGGCTTTGGAAGCTGCAGGAGTGGCATCTCCCACTCGGTGACTTCAGACATGCAGACCATTGAGCAGGAGTCGCCCACACTGGCAAAGCCGAGGAGGAAGTACCAGGAGGACCCAGAGGACTCGTACTTCAGCTCCAGCTCCAAGTGGTCTGAGCAGAGCAGCAGCAGGTACTTTGACGACCCCATGGAGTTAAGAAGCAGCTCCTTCTCTAGCTGGGATGATGGTGCCGATTCCTACTGGAAGAAAGACAGCAGCAGAGACCCCGAGCCTGCCATGAGAAGCACCGGCTCTTCAGACAGGCCCAGTGCTCGCCGGAAGCCAGAATATGAGCCCATTGGCAGCACAGATGAAGCCCAGAAGAAGTTTGGCAACGTCAAGGCCATCTCTTCAGACATGTACTTTGGAATTCAAGCCCAGACAGATTTTGAAACCCGGGCGCGGCTGGAGAGGCTCTCCACCAGCTCCTCCATAAGCTCTGCAGACCTTTTTGATGAGCAGAGGAAGCAGACTGCAGGAAACTACAACCTTTCCAATGTGCTGCCCAATGCCCCAGACATGGCGCAGTTCAAGCAAGGTGTGCGCTCCGTTGCTGGAAAACTTTCCGTCTTCGCCAATGGGGTCATGACGTCCATTCAGGTGTGTTTTGACTGTGGTGCCAAAAATCCCAGCTGGGCCAGCATAAGCTATGGGGTGTTTCTCTGCATTGACTGCTCTGGATCACACCGGTCGCTCGGGGTTCACTTGAGTTTTATTCGGTCCACAGAGCTGGATTCAAACTGGTCGTGGTTCCAGCTTCGATGCATGCAAGTTGGAGGGAACTCAAATGCTTCTTCCTTCTTCCACCAACATGGGTGTGCCACCAAGGACACCAACGCCAAGTACAACAGCCGTGCGGCTCAGCTCTACAGGGAGAAGATCAAGACTCTGGCCACCCAGGCCACCCGCAGACACGGCACCGATCTGTGGCTGGACAGCTGTGCGGCTCCACCTGTGTCCCCTCCTCCAAAGGAGGAAGATTTTTTTGCTTCTCACGCCTCTCTGGAGGTCAGTGGTGCTATGCAGGCATCCGCACAGCCAGAGTCAGCCTCTTCAACACCGTGGGGCTTGGAAACCACTCCAGAAAAACATGAAGGTGGGCCAGGACAAGGGCCAAGCGTGGAAGGTCTGAACACCCCTGGAAAGGCTGCACCAGAGGTTTCATCGATTATAAAAAAGAAGCCAAATCAAGCAAAAAAAGGACTTGGAGCCAAAAAAGGAAGCTTGGGAGCCCAGAAACTGACAAATACATCCTTCACTGAGATCGAAAAGCAAGCTCAGGCTGTGGATAAGAGGAAGGAGCAGGAAGACCTTGCCAGGGGTGCCCCAAAGGAGGAGTCTATTGTTTCGTCCTTGCGACTGGCCTACAAGGATCTGGAAATCAGCAGGAAGAAAGATGAAAGACTGAACCTGAGTGGCCAGAAGAAGGTGGAAGCCGAGCGGCTGGGCATGGGCTTTGGAAGCTGCAGGAGTGGCATCTCCCACTCGGTGACTTCAGACATGCAGACCATTGAGCAGGAGTCGCCCACACTGGCAAAGCCGAGGAGGAAGTACCAGGAGGACCCAGAGGACTCGTACTTCAGCTCCAGCTCCAAGTGGTCTGAGCAGAGCAGCAGCAGGTACTTTGACGACCCCATGGAGTTAAGAAGCAGCTCCTTCTCTAGCTGGGATGATGGTGCCGATTCCTACTGGAAGAAAGACAGCAGCAGAGACCCCGAGCCTGCCATGAGAAGCACCGGCTCTTCAGACAGGCCCAGTGCTCGCCGGAAGCCAGAATATGAGCCCATTGGCAGCACAGATGAAGCCCAGAAGAAGTTTGGCAACGTCAAGGCCATCTCTTCAGACATGTACTTTGGAATTCAAGCCCAGACAGATTTTGAAACCCGGGCGCGGCTGGAGAGGCTCTCCACCAGCTCCTCCATAAGCTCTGCAGACCTTTTTGATGAGCAGAGGAAGCAGACTGCAGGAAACTACAACCTTTCCAATGTGCTGCCCAATGCCCCAGACATGGCGCAGTTCAAGCAAGGTGTGCGCTCCGTTGCTGGAAAACTTTCCGTCTTCGCCAATGGGGTCATGACGTCCATTCAG
Peptide sequence:
MQVGGNSNASSFFHQHGCATKDTNAKYNSRAAQLYREKIKTLATQATRRHGTDLWLDSCAAPPVSPPPKEEDFFASHASLEVSGAMQASAQPESASSTPWGLETTPEKHEGGPGQGPSVEGLNTPGKAAPEVSSIIKKKPNQAKKGLGAKKGSLGAQKLTNTSFTEIEKQAQAVDKRKEQEDLARGAPKEESIVSSLRLAYKDLEISRKKDERLNLSGQKKVEAERLGMGFGSCRSGISHSVTSDMQTIEQESPTLAKPRRKYQEDPEDSYFSSSSKWSEQSSSRYFDDPMELRSSSFSSWDDGADSYWKKDSSRDPEPAMRSTGSSDRPSARRKPEYEPIGSTDEAQKKFGNVKAISSDMYFGIQAQTDFETRARLERLSTSSSISSADLFDEQRKQTAGNYNLSNVLPNAPDMAQFKQGVRSVAGKLSVFANGVMTSIQVCFDCGAKNPSWASISYGVFLCIDCSGSHRSLGVHLSFIRSTELDSNWSWFQLRCMQVGGNSNASSFFHQHGCATKDTNAKYNSRAAQLYREKIKTLATQATRRHGTDLWLDSCAAPPVSPPPKEEDFFASHASLEVSGAMQASAQPESASSTPWGLETTPEKHEGGPGQGPSVEGLNTPGKAAPEVSSIIKKKPNQAKKGLGAKKGSLGAQKLTNTSFTEIEKQAQAVDKRKEQEDLARGAPKEESIVSSLRLAYKDLEISRKKDERLNLSGQKKVEAERLGMGFGSCRSGISHSVTSDMQTIEQESPTLAKPRRKYQEDPEDSYFSSSSKWSEQSSSRYFDDPMELRSSSFSSWDDGADSYWKKDSSRDPEPAMRSTGSSDRPSARRKPEYEPIGSTDEAQKKFGNVKAISSDMYFGIQAQTDFETRARLERLSTSSSISSADLFDEQRKQTAGNYNLSNVLPNAPDMAQFKQGVRSVAGKLSVFANGVMTSIQ
IRESfinder result
IRESfinder score
0.462314286
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page