top of page
mmu_circArfgef1_778
Basic information of circular RNA
PanCircBase ID:
mmu_circArfgef1_778
mm39_Chr. Position ID:
chr1|10229792|10243209|-
Gene name:
Arfgef1
Transcript:
ENSMUST00000088615.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
26,25,24,23,22,21
Exon/intron offsets:
0,309,1133,1395,4129,13266
Genomic length:
13417
Exon/intron sizes in nt:
1,73,15,21,70,41,91,150
Flanking exon/introns:
chr1:10228285-10229792|chr1:10243209-10243418
Splice length:
778
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATCCTGAAGTGCATCAGTCAGTTAGAGCTGGCACAACTTATAGGAACTGGAGTGAAGCCTCGGTACATTTCTGGGACTGTGAGAGGCAGAGAAGGGTCTCTCACTGGGACAAAAGATCAGGCTCCAGATGAATTTGTTGGTCTAGGGCTAGTTGGAGGAAATGTGGACTGGAAGCAGATAGCCAGTATTCAGGAGTCTATTGGAGAAACCAGCTCTCAAAGTGTGGTAGTTGCTGTGGATAGAATATTCACCGGATCCACAAGGCTAGATGGAAATGCTATTGTTGATTTTGTCCGTTGGCTATGTGCTGTGTCTATGGATGAATTGCTTTCTACTACACACCCAAGAATGTTTAGTCTACAAAAAATAGTAGAAATATCATACTATAACATGGGAAGAATAAGACTGCAGTGGTCTCGGATTTGGGAAGTTATTGGAGATCATTTTAATAAGGTTGGTTGCAATCCTAATGAAGATGTAGCCATATTTGCAGTAGACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTGAACATATAATGAAACGAAACAGGTCTCCAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCATCTAGCTGCATCAGACCA
59.58
ACCCTTCTCTGCCTCTCACA
60.18
168
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTGCATCAGACCAAGATGA
59.44
ACCCTTCTCTGCCTCTCACA
60.18
162
PCR template sequence:
TCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCAATCCTGAAGTGCATCAGTCAGTTAGAGCTGGCACAACTTATAGGAACTGGAGTGAAGCCTCGGTACATTTCTGGGACTGTGAGAGGCAGAGAAGGGTCTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-221-3p(1), mmu-miR-200c-3p(1), mmu-miR-222-3p(1), mmu-miR-203-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGGCACATTGTCAATCCTGAAGTGCA
siRNA sets
TTCAGGATTGACAATGTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARFGEF1_778_ORF_1
0.716
-0.09556568
0.486949496
594
ORF sequence:
ATGGATGAATTGCTTTCTACTACACACCCAAGAATGTTTAGTCTACAAAAAATAGTAGAAATATCATACTATAACATGGGAAGAATAAGACTGCAGTGGTCTCGGATTTGGGAAGTTATTGGAGATCATTTTAATAAGGTTGGTTGCAATCCTAATGAAGATGTAGCCATATTTGCAGTAGACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTGAACATATAATGAAACGAAACAGGTCTCCAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCAATCCTGAAGTGCATCAGTCAGTTAGAGCTGGCACAACTTATAGGAACTGGAGTGAAGCCTCGGTACATTTCTGGGACTGTGAGAGGCAGAGAAGGGTCTCTCACTGGGACAAAAGATCAGGCTCCAGATGA
Peptide sequence:
MDELLSTTHPRMFSLQKIVEISYYNMGRIRLQWSRIWEVIGDHFNKVGCNPNEDVAIFAVDSLRQLSMKFLEKGELANFRFQKDFLRPFEHIMKRNRSPTIRDMVVRCIAQMVNSQAANIRSGWKNIFSVFHLAASDQDESIVELAFQTTGHIVNPEVHQSVRAGTTYRNWSEASVHFWDCERQRRVSHWDKRSGSR
IRESfinder result
IRESfinder score
0.649116594
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page