top of page
mmu_circPatj_1859
Basic information of circular RNA
PanCircBase ID:
mmu_circPatj_1859
mm39_Chr. Position ID:
chr4|98379774|98480261|+
Gene name:
Patj
Transcript:
ENSMUST00000041284.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
18,19,20,21,22,23,24,25,26,27,28,29
Exon/intron offsets:
0,3487,5336,14144,22061,27393,29205,31853,43972,47421,77401,100395
Genomic length:
100487
Exon/intron sizes in nt:
210,114,408,124,175,72,178,111,78,100,197,92
Flanking exon/introns:
chr4:98357841-98379774|chr4:98480261-98499304
Splice length:
1859
Other database IDs:
circAtlas: mmu-Inadl_0006
circAtlas: hsa-PATJ_0012
Human Ortholog IDs:
Mature spliced Sequence:
GACCCCCTGGATCCCACGCGGTCAGTGATTGTGATTCGCTCCTTGGTGGCAGATGGTGTAGCGGAAAGAAGTGGAGAACTTTTACCTGGAGATCGCCTAGTCTCCGTCAATGAGTTCTCCTTGGACAATGCCACTCTTGCTGAGGCTGTGGAAGTGTTGAAGGCTGTACCCCCAGGTGTGGTGCATCTTGGCATCTGTAAGCCTTTGGTGGAAGATGAGAAGGAAGAGCGTTTTAGTTTACATTCAAACAACAATGGTGACAGCAGCGAGCCTGCAGACGCTGTTCATGAGATCCACTCATCTTTAATCCTTGAGGCACCCCAGGGATTTAGAGATGAGCCATATCTTGAAGAACTCGTGGATGAACCTTTTCTAGATTTGGGAAAGTCTTTGCAGTTCCAACAAAAAGACGTGGACAGCAGCTCGGAAGCTTGGGAAATGCATGAGTTCCTGAGTCCTCCGCTGGACGGCAGGGGTGAGGAGAGAGAGATGCTTGTCGATGAGGAGTATGAACTTTATCAAGATCACCTCCGGGCCATGGAGTCAAACCCACCACCACCACACATTCGGGAGGCCGCTCCTGCATCTCCCGTGCTGGAACTCCAGGCTGGTACACAGTGGCTGCATGCTAACCTCTCAGGAGGCGAAAGGCTGGAGTGTCACGATGCAGAGTCCATGATGAGTGCCTATCCCCAGGAGATGCAGCAGTATAGCTACAGCACTGCAGACATGATGGAAGAAACGTTTGGCCTTGATTCCCGGGCCCCCATACCGTCCTCTGAAGGAAATGGTCAACACGGCAGATTTGATGACATGGGACACCTTCATTCACTAACGAGCAGCAGCCTGGATTTAGGCATGATGATTCCAAGTGATCTGCAAGGTCCTGGCGTGCTTGTCGATCTTCCAGCTGTTGCTCAAAGAAGAGAACAGGAAGATTTGCCTCTGTACCGACTCCCCAGCGCCCGCGTTGTCACCAAGCCGTCATCACACATGGGACTGGTGTCTTCACGGCATGCAAATGCTGCATGTGAATTACCGGAGAGAGAGGAAGGTGAAGGAGAGGAGACACCGAACTTCAGCCACTGGGGTCCACCAAGAATAGTTGAAATTTTTAGAGAACCTAATGTGTCTCTTGGCATCAGCATCGTTGGTGGACAAACAGTTATAAAACGCCTCAAGAATGGAGAGGAACTCAAGGGGATATTCATCAAACAAGTGTTAGAGGACAGTCCTGCCGGGAAGACCAATGCGCTGAAAACCGGAGATAAAATTCTTGAGGTGTCTGGTGTAGACCTGCAGAATGCCTCCCATGCAGAAGCCGTGGAGGCAATCAAGAGTGCGGGAAACCCTGTGGTATTCGTGGTACAGAGCCTGTCATCCACCCCAAGGGTCATCCCAACTGTGAATAACAAAGGCAAAACACCTGCCCCGAACCAGGATCAAAACACTCAAGAAAGGAAAGCTAAGAGGCACGGAACAGCTCCACCTCCAATGAAGCTGCCCCCGCCCTACAGAGCTCCATCTGCAGACATGGAGGGAAGTGAAGAAGACTGTGCGCTGACCGACAAAAAGATCAGGCAAAGATATGCAGACCTGCCGGGAGAACTACACATTATCGAACTGGAAAAGGACAAGAATGGACTGGGGCTCAGTCTCGCTGGCAATAAGGACAGGTCACGGATGAGCATCTTCGTGGTGGGGATTAATCCGGAGGGACCTGCTGCTGCAGACGGACGGATGCGGATTGGAGACGAGCTGCTAGAGATAAACAATCAGATTCTTTATGGAAGAAGTCATCAGAACGCATCTGCCATTATTAAGACTGCCCCAACCAGGGTCAAACTGGTTTTCATTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAAGAAGTCATCAGAACGCA
59.96
TCCACTTCTTTCCGCTACACC
60
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAAGAAGTCATCAGAACGCA
59.96
CTTTCCGCTACACCATCTGC
58.99
140
PCR template sequence:
TGCTAGAGATAAACAATCAGATTCTTTATGGAAGAAGTCATCAGAACGCATCTGCCATTATTAAGACTGCCCCAACCAGGGTCAAACTGGTTTTCATTAGGACCCCCTGGATCCCACGCGGTCAGTGATTGTGATTCGCTCCTTGGTGGCAGATGGTGTAGCGGAAAGAAGTGGAGAACTTTTACCTGGAGATCGCCTAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-27a-3p(1), mmu-miR-103-3p(1), mmu-miR-221-3p(1), mmu-miR-339-5p(1), mmu-miR-107-3p(1), mmu-miR-342-5p(1), mmu-miR-1187(1), mmu-miR-484(1), mmu-miR-1199-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGGTTTTCATTAGGACCCCCTGGATC
siRNA sets
ATCCAGGGGGTCCTAATGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPATJ_1859_ORF_1
1.0158
0.257880412
0.999687268
1449
ORF sequence:
ATGCATGAGTTCCTGAGTCCTCCGCTGGACGGCAGGGGTGAGGAGAGAGAGATGCTTGTCGATGAGGAGTATGAACTTTATCAAGATCACCTCCGGGCCATGGAGTCAAACCCACCACCACCACACATTCGGGAGGCCGCTCCTGCATCTCCCGTGCTGGAACTCCAGGCTGGTACACAGTGGCTGCATGCTAACCTCTCAGGAGGCGAAAGGCTGGAGTGTCACGATGCAGAGTCCATGATGAGTGCCTATCCCCAGGAGATGCAGCAGTATAGCTACAGCACTGCAGACATGATGGAAGAAACGTTTGGCCTTGATTCCCGGGCCCCCATACCGTCCTCTGAAGGAAATGGTCAACACGGCAGATTTGATGACATGGGACACCTTCATTCACTAACGAGCAGCAGCCTGGATTTAGGCATGATGATTCCAAGTGATCTGCAAGGTCCTGGCGTGCTTGTCGATCTTCCAGCTGTTGCTCAAAGAAGAGAACAGGAAGATTTGCCTCTGTACCGACTCCCCAGCGCCCGCGTTGTCACCAAGCCGTCATCACACATGGGACTGGTGTCTTCACGGCATGCAAATGCTGCATGTGAATTACCGGAGAGAGAGGAAGGTGAAGGAGAGGAGACACCGAACTTCAGCCACTGGGGTCCACCAAGAATAGTTGAAATTTTTAGAGAACCTAATGTGTCTCTTGGCATCAGCATCGTTGGTGGACAAACAGTTATAAAACGCCTCAAGAATGGAGAGGAACTCAAGGGGATATTCATCAAACAAGTGTTAGAGGACAGTCCTGCCGGGAAGACCAATGCGCTGAAAACCGGAGATAAAATTCTTGAGGTGTCTGGTGTAGACCTGCAGAATGCCTCCCATGCAGAAGCCGTGGAGGCAATCAAGAGTGCGGGAAACCCTGTGGTATTCGTGGTACAGAGCCTGTCATCCACCCCAAGGGTCATCCCAACTGTGAATAACAAAGGCAAAACACCTGCCCCGAACCAGGATCAAAACACTCAAGAAAGGAAAGCTAAGAGGCACGGAACAGCTCCACCTCCAATGAAGCTGCCCCCGCCCTACAGAGCTCCATCTGCAGACATGGAGGGAAGTGAAGAAGACTGTGCGCTGACCGACAAAAAGATCAGGCAAAGATATGCAGACCTGCCGGGAGAACTACACATTATCGAACTGGAAAAGGACAAGAATGGACTGGGGCTCAGTCTCGCTGGCAATAAGGACAGGTCACGGATGAGCATCTTCGTGGTGGGGATTAATCCGGAGGGACCTGCTGCTGCAGACGGACGGATGCGGATTGGAGACGAGCTGCTAGAGATAAACAATCAGATTCTTTATGGAAGAAGTCATCAGAACGCATCTGCCATTATTAAGACTGCCCCAACCAGGGTCAAACTGGTTTTCATTAGGACCCCCTGGATCCCACGCGGTCAGTGA
Peptide sequence:
MHEFLSPPLDGRGEEREMLVDEEYELYQDHLRAMESNPPPPHIREAAPASPVLELQAGTQWLHANLSGGERLECHDAESMMSAYPQEMQQYSYSTADMMEETFGLDSRAPIPSSEGNGQHGRFDDMGHLHSLTSSSLDLGMMIPSDLQGPGVLVDLPAVAQRREQEDLPLYRLPSARVVTKPSSHMGLVSSRHANAACELPEREEGEGEETPNFSHWGPPRIVEIFREPNVSLGISIVGGQTVIKRLKNGEELKGIFIKQVLEDSPAGKTNALKTGDKILEVSGVDLQNASHAEAVEAIKSAGNPVVFVVQSLSSTPRVIPTVNNKGKTPAPNQDQNTQERKAKRHGTAPPPMKLPPPYRAPSADMEGSEEDCALTDKKIRQRYADLPGELHIIELEKDKNGLGLSLAGNKDRSRMSIFVVGINPEGPAAADGRMRIGDELLEINNQILYGRSHQNASAIIKTAPTRVKLVFIRTPWIPRGQ
IRESfinder result
IRESfinder score
0.464291162
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page