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mmu_circKatnal2_1163
Basic information of circular RNA
PanCircBase ID:
mmu_circKatnal2_1163
mm39_Chr. Position ID:
chr18|77082089|77106951|-
Gene name:
Katnal2
Transcript:
ENSMUST00000126153.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
13,12,11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,3205,8037,8343,10329,13114,13391,16553,17590,21608,23067,24791
Genomic length:
24862
Exon/intron sizes in nt:
111,92,119,64,99,78,99,99,121,43,167,71
Flanking exon/introns:
chr18:77067857-77082089|chr18:77106951-77134869
Splice length:
1163
Other database IDs:
circAtlas: mmu-Katnal2_0001
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_156960
Human Ortholog IDs:
Mature spliced Sequence:
TACGAGATGAGAACAGAAGCACGGCGAAAAAATCTTCTCATTCTGATTTTGCATTACTTAACACAAGAAGGCTACATGGATGCAGCTAAGGCTTTGGAGGAGGAGACCAAACTGGGATTACGGCGCTTTGAAGTTTGTGACAACGTTGACCTGGAAACTATTTTGATGGAATATGAGAGCTATTATTTTGTAAAGTTCCAGAAGTACCCCAAAGTGGTTAAGAAGGCCCCGGACCCAGTGGAAAATAATTTACCGTCACGAAGTGGAGGGAAGAACAAAAGGCTGACGAATGACAGTTGTCAAAATCTCCCCAAGATATGTCACCAGAAGTCACGACCTAAAACTTCAGCAGTGAAGACAGGGGACACCAAATCTGTCAAGGAACACCTTAAACAGGTCAAGGAGAGTGTCACTGACACTCAAGCAGAGAGCACTGACTTCGGCCTGAACATATCAAAAATCCACAAAGACCAGCCAGAGGAAAAGGCCCAACCACGAAGAGGCCAAATCATTGACTTCCGAGGACTGCTCTCAGACGCTATCAAAGGAGCCACAAGTGAATTTGCATTGAACACCTTTGAATGTAACCCAGACCCTTCAGAGCGATTGCTGAAACCTCTGAGTGCATTTATTGGCATGAACAGTGAGATGCGAGAACTGGCAGCGGTGGTGAGCCGGGACATTTATCTCCATAATCCCAACATAAAGTGGAATGACATTATTGGACTGGACGCAGCCAAGCAGCTAGTCAAAGAAGCCGTTGTGTACCCAATAAGATACCCGCAGCTCTTCACAGGAATTCTTTCCCCGTGGAAAGGACTGCTGCTTTACGGCCCCCCAGGCACAGGGAAGACTTTGCTGGCCAAAGCGGTGGCCACCGAATGCAAAACCACCTTCTTTAACATTTCTGCATCCACTATTGTCAGCAAATGGAGAGGAGATTCCGAAAAACTGGTCCGGGTGCTGTTTGAACTTGCGCGATATCATGCCCCCTCCACGATCTTCCTGGATGAGCTGGAGTCGGTGATGAGTCAGAGAGGCATGGTTCCTGGGGGGGAACATGAAGGGAGCCTTCGGATGAAGACGGAGTTACTGGTGCAGATGGATGGCTTAGCACGCTCGGAGGATCTCGTGTTTGTCTTAGCAGCCTCAAACCTGCCATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TACTGGTGCAGATGGATGGC
59.82
TGCATCCATGTAGCCTTCTTGT
60.03
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TACTGGTGCAGATGGATGGC
59.82
GCCTTAGCTGCATCCATGTAG
58.85
165
PCR template sequence:
AAGGGAGCCTTCGGATGAAGACGGAGTTACTGGTGCAGATGGATGGCTTAGCACGCTCGGAGGATCTCGTGTTTGTCTTAGCAGCCTCAAACCTGCCATGTACGAGATGAGAACAGAAGCACGGCGAAAAAATCTTCTCATTCTGATTTTGCATTACTTAACACAAGAAGGCTACATGGATGCAGCTAAGGCTTTGGAGG
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-1a-3p(1), mmu-miR-206-3p(1), mmu-miR-181a-5p(1), mmu-miR-205-5p(1), mmu-miR-322-5p(1), mmu-miR-181b-5p(1), mmu-miR-136-5p(1), mmu-miR-802-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAAACCTGCCATGTACGAGATGAGAA
siRNA sets
TTCTCATCTCGTACATGGC, TCTCATCTCGTACATGGCA, CTCATCTCGTACATGGCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKATNAL2_1163_ORF_1
0.9899
0.250473912
0.997499897
1167
ORF sequence:
ATGAGAACAGAAGCACGGCGAAAAAATCTTCTCATTCTGATTTTGCATTACTTAACACAAGAAGGCTACATGGATGCAGCTAAGGCTTTGGAGGAGGAGACCAAACTGGGATTACGGCGCTTTGAAGTTTGTGACAACGTTGACCTGGAAACTATTTTGATGGAATATGAGAGCTATTATTTTGTAAAGTTCCAGAAGTACCCCAAAGTGGTTAAGAAGGCCCCGGACCCAGTGGAAAATAATTTACCGTCACGAAGTGGAGGGAAGAACAAAAGGCTGACGAATGACAGTTGTCAAAATCTCCCCAAGATATGTCACCAGAAGTCACGACCTAAAACTTCAGCAGTGAAGACAGGGGACACCAAATCTGTCAAGGAACACCTTAAACAGGTCAAGGAGAGTGTCACTGACACTCAAGCAGAGAGCACTGACTTCGGCCTGAACATATCAAAAATCCACAAAGACCAGCCAGAGGAAAAGGCCCAACCACGAAGAGGCCAAATCATTGACTTCCGAGGACTGCTCTCAGACGCTATCAAAGGAGCCACAAGTGAATTTGCATTGAACACCTTTGAATGTAACCCAGACCCTTCAGAGCGATTGCTGAAACCTCTGAGTGCATTTATTGGCATGAACAGTGAGATGCGAGAACTGGCAGCGGTGGTGAGCCGGGACATTTATCTCCATAATCCCAACATAAAGTGGAATGACATTATTGGACTGGACGCAGCCAAGCAGCTAGTCAAAGAAGCCGTTGTGTACCCAATAAGATACCCGCAGCTCTTCACAGGAATTCTTTCCCCGTGGAAAGGACTGCTGCTTTACGGCCCCCCAGGCACAGGGAAGACTTTGCTGGCCAAAGCGGTGGCCACCGAATGCAAAACCACCTTCTTTAACATTTCTGCATCCACTATTGTCAGCAAATGGAGAGGAGATTCCGAAAAACTGGTCCGGGTGCTGTTTGAACTTGCGCGATATCATGCCCCCTCCACGATCTTCCTGGATGAGCTGGAGTCGGTGATGAGTCAGAGAGGCATGGTTCCTGGGGGGGAACATGAAGGGAGCCTTCGGATGAAGACGGAGTTACTGGTGCAGATGGATGGCTTAGCACGCTCGGAGGATCTCGTGTTTGTCTTAGCAGCCTCAAACCTGCCATGTACGAGATGA
Peptide sequence:
MRTEARRKNLLILILHYLTQEGYMDAAKALEEETKLGLRRFEVCDNVDLETILMEYESYYFVKFQKYPKVVKKAPDPVENNLPSRSGGKNKRLTNDSCQNLPKICHQKSRPKTSAVKTGDTKSVKEHLKQVKESVTDTQAESTDFGLNISKIHKDQPEEKAQPRRGQIIDFRGLLSDAIKGATSEFALNTFECNPDPSERLLKPLSAFIGMNSEMRELAAVVSRDIYLHNPNIKWNDIIGLDAAKQLVKEAVVYPIRYPQLFTGILSPWKGLLLYGPPGTGKTLLAKAVATECKTTFFNISASTIVSKWRGDSEKLVRVLFELARYHAPSTIFLDELESVMSQRGMVPGGEHEGSLRMKTELLVQMDGLARSEDLVFVLAASNLPCTR
IRESfinder result
IRESfinder score
0.467046145
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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