top of page
mmu_circAtf1_671
Basic information of circular RNA
PanCircBase ID:
mmu_circAtf1_671
mm39_Chr. Position ID:
chr15|100130613|100152394|+
Gene name:
Atf1
Transcript:
ENSMUST00000023769.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
2,3,4,5,6
Exon/intron offsets:
0,12512,19336,21361,21621
Genomic length:
21781
Exon/intron sizes in nt:
99,101,131,180,160
Flanking exon/introns:
chr15:100125963-100130613|chr15:100152394-100157695
Splice length:
671
Other database IDs:
CIRCpedia: MMU_CIRCpedia_76, circAtlas: mmu-Atf1_0003
circBase: hsa_circ_0026282, circAtlas: hsa-ATF1_0002, CIRCpedia: HSA_CIRCpedia_8751
Human Ortholog IDs:
Mature spliced Sequence:
TTGATTATGGAAGATTCCCACAAGAGTAACACGACAGAGACTGCATCTCAGCCTGGTTCAACCGTTGCGGGGCCTCACGTTTCTCAGATAGTACATCAGGTGTCATCGTTATCAGAAAGTGAGGAGTCTCAGGACTCATCTGACAGCATAGGCTCCTCACAGAAAGCTCACGGGATCCTGGCCCGGCGCCCATCCTACAGGAAAATTTTGAAAGACCTCTCTTCTGAAGATACACGGGGCAGAAAAGGGGAAGGAGAAAATCCCAGCATTTCTGCCATCACGTCTATGTCTGTTCCAGCCCCCATCTATCAGACGAGCAGCGGACAGTACATTGCCATTGCCCCAAACGGAGCCTTACAGTTGGCCAGTCCAAGCACGGATGGAGTGCAGGCACTGCAGACATTAACCATGACAAATTCAAGCAGTACTCAGCAGGGGACGATCCTCCAGTATGCACAGACCTCTGACGGACAGCAGATACTCGTCCCGAGCAACCAGGTGGTTGTACAGACTGCATCAGGAGATATGCAGACCTACCAGATCCGTACCACGCCGTCTGCCACGTCTCTCCCGCAGACCGTGGTGATGACTTCTCCTGTGACTCTTGCATCTCAGACAACAAAGACAGATGACCCTCAACTAAGAAGAGAAATACGACTGATGAAAAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGACCGTGGTGATGACTT
60.32
GAACCAGGCTGAGATGCAGT
60.04
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGACCGTGGTGATGACTT
60.32
CGGTTGAACCAGGCTGAGAT
60.04
163
PCR template sequence:
CGCAGACCGTGGTGATGACTTCTCCTGTGACTCTTGCATCTCAGACAACAAAGACAGATGACCCTCAACTAAGAAGAGAAATACGACTGATGAAAAACAGTTGATTATGGAAGATTCCCACAAGAGTAACACGACAGAGACTGCATCTCAGCCTGGTTCAACCGTTGCGGGGCCTCACGTTTCTCAGATAGTACATCAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-34c-5p(1), mmu-miR-125b-5p(1), mmu-miR-185-5p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGATGAAAAACAGTTGATTATGGAAG
siRNA sets
TAATCAACTGTTTTTCATC, CATAATCAACTGTTTTTCA, ATAATCAACTGTTTTTCAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATF1_671_ORF_1
0.9258
0.208490371
0.893530237
669
ORF sequence:
ATGGAAGATTCCCACAAGAGTAACACGACAGAGACTGCATCTCAGCCTGGTTCAACCGTTGCGGGGCCTCACGTTTCTCAGATAGTACATCAGGTGTCATCGTTATCAGAAAGTGAGGAGTCTCAGGACTCATCTGACAGCATAGGCTCCTCACAGAAAGCTCACGGGATCCTGGCCCGGCGCCCATCCTACAGGAAAATTTTGAAAGACCTCTCTTCTGAAGATACACGGGGCAGAAAAGGGGAAGGAGAAAATCCCAGCATTTCTGCCATCACGTCTATGTCTGTTCCAGCCCCCATCTATCAGACGAGCAGCGGACAGTACATTGCCATTGCCCCAAACGGAGCCTTACAGTTGGCCAGTCCAAGCACGGATGGAGTGCAGGCACTGCAGACATTAACCATGACAAATTCAAGCAGTACTCAGCAGGGGACGATCCTCCAGTATGCACAGACCTCTGACGGACAGCAGATACTCGTCCCGAGCAACCAGGTGGTTGTACAGACTGCATCAGGAGATATGCAGACCTACCAGATCCGTACCACGCCGTCTGCCACGTCTCTCCCGCAGACCGTGGTGATGACTTCTCCTGTGACTCTTGCATCTCAGACAACAAAGACAGATGACCCTCAACTAAGAAGAGAAATACGACTGATGAAAAACAGTTGA
Peptide sequence:
MEDSHKSNTTETASQPGSTVAGPHVSQIVHQVSSLSESEESQDSSDSIGSSQKAHGILARRPSYRKILKDLSSEDTRGRKGEGENPSISAITSMSVPAPIYQTSSGQYIAIAPNGALQLASPSTDGVQALQTLTMTNSSSTQQGTILQYAQTSDGQQILVPSNQVVVQTASGDMQTYQIRTTPSATSLPQTVVMTSPVTLASQTTKTDDPQLRREIRLMKNS
IRESfinder result
IRESfinder score
0.500434458
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page