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mmu_circKdm5a_1268
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm5a_1268
mm39_Chr. Position ID:
chr6|120375898|120392315|+
Gene name:
Kdm5a
Transcript:
ENSMUST00000135802.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
13,14,15,16,17,18,19
Exon/intron offsets:
0,3568,6027,6922,7637,13217,16278
Genomic length:
16417
Exon/intron sizes in nt:
12,01,95,18,21,25,15,10,00,000
Flanking exon/introns:
chr6:120371210-120375898|chr6:120392315-120395519
Splice length:
1268
Other database IDs:
CIRCpedia: MMU_CIRCpedia_227326, circAtlas: mmu-Kdm5a_0073
Human Ortholog IDs:
Mature spliced Sequence:
GTGTACAGGACTAATCAGTGTGCTGGAGAGTTTGTGGTGACGTTTCCTCGTGCCTATCACTCTGGATTTAACCAGGGATACAACTTTGCCGAAGCGGTGAACTTCTGTACTGCTGACTGGTTGCCCATTGGACGTCAGTGTGTAAATCACTATCGACGGCTCAGGCGCCATTGTGTCTTTTCACATGAGGAACTCATTTTCAAGATGGCAGCAGATCCAGAATGCTTAGATGTGGGGCTGGCTGCCATGGTATGCAAAGAGTTGACTCTCATGACTGAAGAAGAAACACGATTGAGAGAATCAGTTGTTCAAATGGGTGTCGTGATGTCAGAAGAAGAAGTCTTTGAACTTGTTCCTGATGATGAGCGGCAGTGTTCAGCATGCAGAACTACATGTTTTCTCTCAGCTCTCACATGCTCCTGTAATCCGGAGCGACTTGTATGTCTGTATCATCCAACTGATTTGTGCTCTTGCCCCATGCAGAACAAATGTCTTAGGTACCGCTATCCACTAGAAGACCTTCCATCTCTGCTTTATGGTGTCAAAGTGAGAGCACAATCCTATGACACTTGGGTCAATCGTGTTACAGAAGCATTGTCAGCTAGCTTCAACCATAAGAAAGATTTGATTGAATTGAGAGTAATGCTGGAAGATGCTGAGGATAGGAAATACCCAGAGAATGATCTCTTTCGAAAGCTCAGGGACGCGGTGAAAGAAGCTGAGACCTGTGGTTCTGTGGCTCAGCTGCTTCTGAGCAAAAAGCAAAAACACAGAATCTGCTGGATGATGTAGAAGAATTTCATGAACGTGCCCAGGAGGCCATGATGGATGAAACCCCAGATTCTTCCAAACTCCAAATGTTAATAGACATGGGCTCTAGTCTCTATGTGGAGCTACCTGAATTGCCCCGACTAAAGCAAGAGCTCCAGCAGGCTCGATGGCTGGATGAAGTAAGGCTAACTCTATCAGATCCACAACAAGTCACTTTGGATGTCATGAAGAAATTGATTGACTCTGGCGTAGGCTTGGCACCTCACCATGCTGTAGAAAAAGCAATGGCCGAACTACAGGAACTCCTTACAGTCTCTGAACGATGGGAAGAGAAGGCTAAGGTCTGCCTGCAAGCAAGACCTCGGCACAGTATGGCAAATTTAGAAAATATTGTGAATGAAGCCAAGAACATTCCAGCCTTTCTACCCAATGTGTTGTCCTTAAAAGAAGCCTTACAAAAGGCTCGTGAATGGACAGCTAAAGTGGAAGCTATTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCAAGAACATTCCAGCCT
59.59
TAGGCACGAGGAAACGTCAC
60.04
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCAAGAACATTCCAGCCT
59.59
ACGAGGAAACGTCACCACAA
59.82
148
PCR template sequence:
TGAAGCCAAGAACATTCCAGCCTTTCTACCCAATGTGTTGTCCTTAAAAGAAGCCTTACAAAAGGCTCGTGAATGGACAGCTAAAGTGGAAGCTATTCAGGTGTACAGGACTAATCAGTGTGCTGGAGAGTTTGTGGTGACGTTTCCTCGTGCCTATCACTCTGGATTTAACCAGGGATACAACTTTGCCGAAGCGGTGA
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-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-326-3p(1), mmu-miR-431-5p(1), mmu-miR-127-5p(1), mmu-miR-382-5p(1), mmu-miR-370-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAAGCTATTCAGGTGTACAGGACTA
siRNA sets
GTACACCTGAATAGCTTCC, TGTACACCTGAATAGCTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM5A_1268_ORF_1
0.9602
0.12076735
0.997316774
1239
ORF sequence:
ATGATGGATGAAACCCCAGATTCTTCCAAACTCCAAATGTTAATAGACATGGGCTCTAGTCTCTATGTGGAGCTACCTGAATTGCCCCGACTAAAGCAAGAGCTCCAGCAGGCTCGATGGCTGGATGAAGTAAGGCTAACTCTATCAGATCCACAACAAGTCACTTTGGATGTCATGAAGAAATTGATTGACTCTGGCGTAGGCTTGGCACCTCACCATGCTGTAGAAAAAGCAATGGCCGAACTACAGGAACTCCTTACAGTCTCTGAACGATGGGAAGAGAAGGCTAAGGTCTGCCTGCAAGCAAGACCTCGGCACAGTATGGCAAATTTAGAAAATATTGTGAATGAAGCCAAGAACATTCCAGCCTTTCTACCCAATGTGTTGTCCTTAAAAGAAGCCTTACAAAAGGCTCGTGAATGGACAGCTAAAGTGGAAGCTATTCAGGTGTACAGGACTAATCAGTGTGCTGGAGAGTTTGTGGTGACGTTTCCTCGTGCCTATCACTCTGGATTTAACCAGGGATACAACTTTGCCGAAGCGGTGAACTTCTGTACTGCTGACTGGTTGCCCATTGGACGTCAGTGTGTAAATCACTATCGACGGCTCAGGCGCCATTGTGTCTTTTCACATGAGGAACTCATTTTCAAGATGGCAGCAGATCCAGAATGCTTAGATGTGGGGCTGGCTGCCATGGTATGCAAAGAGTTGACTCTCATGACTGAAGAAGAAACACGATTGAGAGAATCAGTTGTTCAAATGGGTGTCGTGATGTCAGAAGAAGAAGTCTTTGAACTTGTTCCTGATGATGAGCGGCAGTGTTCAGCATGCAGAACTACATGTTTTCTCTCAGCTCTCACATGCTCCTGTAATCCGGAGCGACTTGTATGTCTGTATCATCCAACTGATTTGTGCTCTTGCCCCATGCAGAACAAATGTCTTAGGTACCGCTATCCACTAGAAGACCTTCCATCTCTGCTTTATGGTGTCAAAGTGAGAGCACAATCCTATGACACTTGGGTCAATCGTGTTACAGAAGCATTGTCAGCTAGCTTCAACCATAAGAAAGATTTGATTGAATTGAGAGTAATGCTGGAAGATGCTGAGGATAGGAAATACCCAGAGAATGATCTCTTTCGAAAGCTCAGGGACGCGGTGAAAGAAGCTGAGACCTGTGGTTCTGTGGCTCAGCTGCTTCTGAGCAAAAAGCAAAAACACAGAATCTGCTGGATGATGTAG
Peptide sequence:
MMDETPDSSKLQMLIDMGSSLYVELPELPRLKQELQQARWLDEVRLTLSDPQQVTLDVMKKLIDSGVGLAPHHAVEKAMAELQELLTVSERWEEKAKVCLQARPRHSMANLENIVNEAKNIPAFLPNVLSLKEALQKAREWTAKVEAIQVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCTADWLPIGRQCVNHYRRLRRHCVFSHEELIFKMAADPECLDVGLAAMVCKELTLMTEEETRLRESVVQMGVVMSEEEVFELVPDDERQCSACRTTCFLSALTCSCNPERLVCLYHPTDLCSCPMQNKCLRYRYPLEDLPSLLYGVKVRAQSYDTWVNRVTEALSASFNHKKDLIELRVMLEDAEDRKYPENDLFRKLRDAVKEAETCGSVAQLLLSKKQKHRICWMM
IRESfinder result
IRESfinder score
0.47850393
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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