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mmu_circSrpk1_1740
Basic information of circular RNA
PanCircBase ID:
mmu_circSrpk1_1740
mm39_Chr. Position ID:
chr17|28811191|28825368|-
Gene name:
Srpk1
Transcript:
ENSMUST00000233440.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
13,12,11,10,9,8,7,6,5
Exon/intron offsets:
0,1952,6684,7253,8651,10470,11220,13081,14089
Genomic length:
14177
Exon/intron sizes in nt:
70,108,101,986,26,166,107,88,88
Flanking exon/introns:
chr17:28810267-28811191|chr17:28825368-28826057
Splice length:
1740
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGGAAAGAAGTTTGTAGCAATGAAAGTAGTTAAAAGTGCTGAGCATTACACAGAAACAGCACTAGATGAAATCCGGCTGCTGAAATCGGTTCGCAACTCAGACCCGAATGATCCAAATGGAGAAATGGTTGTTCAACTACTAGATGACTTTAAAATATCAGGCGTTAATGGAACACATATCTGCATGGTGTTTGAGGTTTTGGGGCATCATCTACTCAAGTGGATCATCAAGTCCAACTATCAGGGGCTTCCGCTGCCTTGTGTCAAAAAAATTATTCAGCAAGTGCTACAGGGCCTGGATTACTTACACACCAAGTGCCGGATCATCCACACGGACATCAAACCAGAGAACATCTTGTTGTCTGTGAATGAGCAGTACATTCGAAGGCTGGCTGCAGAGGCCACAGAGTGGCAGCGCTCAGGAGCTCCCCCACCATCGGGGTCTGCAGTCAGCACTGCTCCACAGCCTAAGCCAGCTGACAAAATGTCAAAGAATAAGAAGAAGAAATTGAAGAAGAAGCAGAAGCGCCAGGCAGAATTACTAGAGAAGCGAATGCAGGAAATTGAGGAAATGGAGAAAGAGTCGGGCCCTGGGCAAAAAAGACCTAACAAGCAAGAAGAATCAGAGAGTCCTGTTGACAGACCCCTGACAGAGAACCCACCTAATAAAATGACCCAAGAGAAACTTGGTATAAAAGAGCATTGCAGCAGTGACTTGATGGCACACTTGACACTGGGTTATCTTGTTTGTAATGTTTGCTTTCATGTATGCAGCTCATCTCTGGGGGTGTCCTGTAAGAGTTCACATTGCTCTAATGGAGGCAGCTGGTAGACACTGCAGGGTAACTTGGTGCTTTCTCCTCAGAAGTGGAGATAAGACTTTGTAGCCACTGGGTAAAGATGAGGTCTTTGTCCTTCCATCAGGAGGTGGTAGAGGGCTGTTGTGTTAGTCTTGTTTTTCTGCCACTCAGGATAAGCTCAGGAGAGTGTTTTGATGATGTGAGAATTGTCCTGCTGCTCACTAGCACATACACACATGCATCCTTTTCTGTTTGTTCTTAGAAGAGTCAAATTCCATTGGCCAGGACCAGACACTCACGGAGCGTGGTGGAGAGGGTGGTGCGCCAGAGATTAATTGCAATGGAGTGATTGGAGTCGTTAATTACCCTGAGAACAGTAATAATGAGACACTGAGGCATAAAGAGGATCTGCATAATGCTAATGACTGTGATGTCCACACTTTGAAGCAGGAACCTAGTTTCCTAAACTCTTCAAATGGAGACAGCAGTCCATCTCAAGACACAGACTCTTGCACACCCACGGCCTCTGAGACCATGGTGTGCCAATCCTCTGCAGAGCAGTCACTCACCCGACAGGACATCACCCAGCTGGAGGAGAGCATTCGGGCAGATACACCTTCTGGGGATGAGCAGGAGCCCAATGGAGCCCTGGACAGCAAAGGAAAATTCTCTGCTGGAAATTTTCTTATTAATCCCCTTGAGCCAAAAAATGCAGAGAAGCTCCAAGTGAAGATCGCAGACCTCGGGAACGCCTGCTGGGTGCACAAGCATTTCACTGAAGATATCCAGACACGGCAGTATCGGTCTTTGGAAGTCCTGATAGGATCTGGCTACAACACCCCTGCTGACATCTGGAGCACAGCATGCATGGCCTTTGAACTAGCCACAGGGGACTATTTGTTTGAGCCTCATTCAGGGGAGGATTACACACGAGATGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGAACTAGCCACAGGGGACT
60.18
GTTGCGAACCGATTTCAGCA
59.76
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCATGCATGGCCTTTGAA
59.75
GTTGCGAACCGATTTCAGCA
59.76
178
PCR template sequence:
CCTGCTGACATCTGGAGCACAGCATGCATGGCCTTTGAACTAGCCACAGGGGACTATTTGTTTGAGCCTCATTCAGGGGAGGATTACACACGAGATGAAGGGGAAAGAAGTTTGTAGCAATGAAAGTAGTTAAAAGTGCTGAGCATTACACAGAAACAGCACTAGATGAAATCCGGCTGCTGAAATCGGTTCGCAACTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-136-5p(4), mmu-miR-134-5p(1), mmu-miR-16-5p(1), mmu-miR-199a-5p(1), mmu-miR-34a-5p(1), mmu-miR-29b-3p(1), mmu-miR-203-3p(1), mmu-miR-503-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-382-3p(1), mmu-miR-297a-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-1198-5p(1), mmu-miR-466p-5p(1), mmu-miR-190b-5p(1), mmu-miR-129-5p(1), mmu-miR-3470b(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
ACACGAGATGAAGGGGAAAGAAGTTT
siRNA sets
TTCTTTCCCCTTCATCTCG, CTTCTTTCCCCTTCATCTC, AACTTCTTTCCCCTTCATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSRPK1_1740_ORF_3
0.8312
0.293822866
0.616590149
423
ORF sequence:
ATGGTGTGCCAATCCTCTGCAGAGCAGTCACTCACCCGACAGGACATCACCCAGCTGGAGGAGAGCATTCGGGCAGATACACCTTCTGGGGATGAGCAGGAGCCCAATGGAGCCCTGGACAGCAAAGGAAAATTCTCTGCTGGAAATTTTCTTATTAATCCCCTTGAGCCAAAAAATGCAGAGAAGCTCCAAGTGAAGATCGCAGACCTCGGGAACGCCTGCTGGGTGCACAAGCATTTCACTGAAGATATCCAGACACGGCAGTATCGGTCTTTGGAAGTCCTGATAGGATCTGGCTACAACACCCCTGCTGACATCTGGAGCACAGCATGCATGGCCTTTGAACTAGCCACAGGGGACTATTTGTTTGAGCCTCATTCAGGGGAGGATTACACACGAGATGAAGGGGAAAGAAGTTTGTAG
Peptide sequence:
MVCQSSAEQSLTRQDITQLEESIRADTPSGDEQEPNGALDSKGKFSAGNFLINPLEPKNAEKLQVKIADLGNACWVHKHFTEDIQTRQYRSLEVLIGSGYNTPADIWSTACMAFELATGDYLFEPHSGEDYTRDEGERSL
IRESfinder result
IRESfinder score
0.554627954
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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