top of page
mmu_circPatl1_994
Basic information of circular RNA
PanCircBase ID:
mmu_circPatl1_994
mm39_Chr. Position ID:
chr19|11897541|11902590|+
Gene name:
Patl1
Transcript:
ENSMUST00000061618.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
3,4,5,6,7,8,9
Exon/intron offsets:
0,627,1191,2289,3209,3623,4959
Genomic length:
5049
Exon/intron sizes in nt:
218,81,195,102,90,218,90
Flanking exon/introns:
chr19:11891823-11897541|chr19:11902590-11907238
Splice length:
994
Other database IDs:
circAtlas: mmu-Patl1_0002
Human Ortholog IDs:
Mature spliced Sequence:
ATGATGATTGGCAGGAAGCACATGAGCGCCTGGCTGAGTTGGAAGAGAAGCTACCTGTGGCAGCTGATGAACAAACAGGCAATGGAGAGAGAGATGAGATGGATTTGTTGGGTGACCATGAGGAGAATCTAGCAGAAAGGCTCAGTAAGATGGTGATTGAAAATGAGCTAGAAGATCCAGCTATCATGAGGGCAGTACAGACCAGGCCAGTTTTACAACCTCAACCAGGAAGTCTGAATTCCAGCATCTGGGATGGATCTGAAGTTCTGAGGCGAATCCGTGGACCACTACTTGCTCAGGAAATGCCTACAGTGTCTGTATTAGAGTATGCCTTGCCTCAGAGGCCCCTGCAGGGCCCAGAAGATGATCGGGACCTTTCTGAGCGAGCTTTACCAAGGCGGTCAACATCACCTATCATTGGAAGTCCTCCTGTTAGAGCCGTTCCTATAGGCACCCCACCTAAGCAGATGGCTGTTCCCAGCTTCAACCAACAGATCCTGTGTCCGAAGCCTGTTCATGTTCGGCCCCCAATGCCGCCACGCTATCCTGCTCCCTATGGCGAGAGGATATCTCCAAACCAGCTCTGCAGTGTCCCGAACTCCTCCCTCCTGGGCCACCCTTTTCCTCCTAATGTTCCTCCTGTACTTAGTCCCCTGCAGAGAGCACAGCTTCTTGGGGGAGCACAGCTACAGCCTGGACGAATGTCTCCCAGCCAGTTTGCACGGGTCCCTGGGTTTGTTGGTAGCCCACTGGCTGCCATGAATCCTAAGTTGCTACAAGGGCGCGTTGGGCAGATGCTTCCCCCAGCACCAAGCTTCCGTGCCTTCTTTAGTGCTCCACCCCCCGCTACGCCACCTCCACAGCAGCATCCCCCTGGCCCAGGACCTCACCTACAAAACCTCAGACCTCAGGCCCCAATGTTTAGAGCAGACACAACTCACCTTCATCCACAGCACCGGCGCCTGTTGCATCAGAGGCAGCTGCAGAGCAGAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACCTCAGGCCCCAATGTTT
60.25
TCATCAGCTGCCACAGGTAG
59.46
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACCTCAGGCCCCAATGTTT
60.25
TGTTCATCAGCTGCCACAGG
60.61
164
PCR template sequence:
AAAACCTCAGACCTCAGGCCCCAATGTTTAGAGCAGACACAACTCACCTTCATCCACAGCACCGGCGCCTGTTGCATCAGAGGCAGCTGCAGAGCAGAAAATGATGATTGGCAGGAAGCACATGAGCGCCTGGCTGAGTTGGAAGAGAAGCTACCTGTGGCAGCTGATGAACAAACAGGCAATGGAGAGAGAGATGAGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-3065-5p(2), mmu-miR-138-5p(1), mmu-miR-136-5p(1), mmu-miR-22-3p(1), mmu-miR-127-5p(1), mmu-miR-218-5p(1), mmu-miR-342-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCAGAGCAGAAAATGATGATTGGCA
siRNA sets
CATCATTTTCTGCTCTGCA, TCATCATTTTCTGCTCTGC, AATCATCATTTTCTGCTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPATL1_994_ORF_1
0.8687
0.117837941
0.964510158
900
ORF sequence:
ATGGATTTGTTGGGTGACCATGAGGAGAATCTAGCAGAAAGGCTCAGTAAGATGGTGATTGAAAATGAGCTAGAAGATCCAGCTATCATGAGGGCAGTACAGACCAGGCCAGTTTTACAACCTCAACCAGGAAGTCTGAATTCCAGCATCTGGGATGGATCTGAAGTTCTGAGGCGAATCCGTGGACCACTACTTGCTCAGGAAATGCCTACAGTGTCTGTATTAGAGTATGCCTTGCCTCAGAGGCCCCTGCAGGGCCCAGAAGATGATCGGGACCTTTCTGAGCGAGCTTTACCAAGGCGGTCAACATCACCTATCATTGGAAGTCCTCCTGTTAGAGCCGTTCCTATAGGCACCCCACCTAAGCAGATGGCTGTTCCCAGCTTCAACCAACAGATCCTGTGTCCGAAGCCTGTTCATGTTCGGCCCCCAATGCCGCCACGCTATCCTGCTCCCTATGGCGAGAGGATATCTCCAAACCAGCTCTGCAGTGTCCCGAACTCCTCCCTCCTGGGCCACCCTTTTCCTCCTAATGTTCCTCCTGTACTTAGTCCCCTGCAGAGAGCACAGCTTCTTGGGGGAGCACAGCTACAGCCTGGACGAATGTCTCCCAGCCAGTTTGCACGGGTCCCTGGGTTTGTTGGTAGCCCACTGGCTGCCATGAATCCTAAGTTGCTACAAGGGCGCGTTGGGCAGATGCTTCCCCCAGCACCAAGCTTCCGTGCCTTCTTTAGTGCTCCACCCCCCGCTACGCCACCTCCACAGCAGCATCCCCCTGGCCCAGGACCTCACCTACAAAACCTCAGACCTCAGGCCCCAATGTTTAGAGCAGACACAACTCACCTTCATCCACAGCACCGGCGCCTGTTGCATCAGAGGCAGCTGCAGAGCAGAAAATGA
Peptide sequence:
MDLLGDHEENLAERLSKMVIENELEDPAIMRAVQTRPVLQPQPGSLNSSIWDGSEVLRRIRGPLLAQEMPTVSVLEYALPQRPLQGPEDDRDLSERALPRRSTSPIIGSPPVRAVPIGTPPKQMAVPSFNQQILCPKPVHVRPPMPPRYPAPYGERISPNQLCSVPNSSLLGHPFPPNVPPVLSPLQRAQLLGGAQLQPGRMSPSQFARVPGFVGSPLAAMNPKLLQGRVGQMLPPAPSFRAFFSAPPPATPPPQQHPPGPGPHLQNLRPQAPMFRADTTHLHPQHRRLLHQRQLQSRK
IRESfinder result
IRESfinder score
0.456954623
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page