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mmu_circCspp1_1402
Basic information of circular RNA
PanCircBase ID:
mmu_circCspp1_1402
mm39_Chr. Position ID:
chr1|10136650|10166238|+
Gene name:
Cspp1
Transcript:
ENSMUST00000071087.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
7,8,9,10,11,12,13,14,15,16
Exon/intron offsets:
0,8434,10746,15827,17075,19321,21625,22456,23762,29440
Genomic length:
29588
Exon/intron sizes in nt:
39,58,77,19,45,82,06,10,00,00,00,000
Flanking exon/introns:
chr1:10135646-10136650|chr1:10166238-10174436
Splice length:
1402
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_154653
Human Ortholog IDs:
Mature spliced Sequence:
CCTAAGAGTCAAAGAAATAAAAACCCTATTAGTCAAGGTAAATCTGATCTACCTTTACAAATACAGACTGCATACACACATTCAGAGGGACCCTGGCTAAGCCGGCAAGAGGAGGGCCTGTACCGACAGCTAGATGGTGAAATTGAATTAAGGAGCAGAAGACCGCTTAAACAAACAAAGGAAGAAGTAGGCATTTCTGGTGCAGAACATCCAAGCCTTTCTGGCAGCGCTGGTGTCCCAGAGAGAAGAGCCCGCAGGGCTAACGGGGAGCGGGTGCTTGACAGACAACATTGCAGAGCCGACCGAGACCCTGGTGTGAGTGAAGACATGGACGAGAGGTTTAGATTTGAAAGTGATTTTGATAGAAGACTTTTGAGAGTGTATACAAATGGCAGGCCGCATGGGAGCAGACGAGGGTATGTGGATGGGGATGATGTCCCAGAAGAGCCAAACACACAGATCTCAGCTGCTGAAAATAAAAGTGTTCACTGTAATGGACCACCCAGATCTGCTGATCTCGATATCACAAGTCCATTTGCAGGCATGCTCTTTGGAGGTGAAGATCGAGAACTTACCAAGAGAAGGAAGGAGAAATATAGGCAAGAACTACTAGAACAGATAGCTGAGCAACAGAAGAAGAAGAGACGAGAAAAAGATTTAGCATTTGGAATTACAACTTCTGGAGTACAAGACCCTGAAAAATCGCCTGATAGACTAAAGCAGTTTAGTTTGACACCAAGACACTTTGAAGAGATGCCACCTGAGAGGCCCAGAGTAGCTTTCCAGACACCTCCCCCTCCCTTCTCTGCCCCGTCTAGCCCATCCGTCCCACCAGTTCATTCCGCCCCTTCTCACAATGAAGACTTGCACAGTGGACTCGGCAGCACCCTTGGTGAACTGGCGCATCCCAGGGTTCTGCCTGTGCCTCTGAATCCACCCCCGCCTCCGCTCCTTGCCCCTCCAGCTTCTAACTATCGAACTCCTTACGATGATGCGTACTATTTTTACGGTGCCAGAAATACACTGGATCCCAATATTGTATACTATGGTTCAGGAATGATTGGAGGACAGCCTGCCCCTCATGTCTCTGCCCCTGTCACTCACCAGGTAGCACCGCCAGCTGTGAATACTGTTGGACAGAATGAACAGAAAGTTCTTAGTGATGGACTCAGGAATTCAGGACTGGTCTTTGAGGATAAGCCAAAACCTTCTACACAGTCGCTTCAGTCTTACCAAGAAGCTTTGCAGGAGCAGATTCGGGAAAGAGAAGCAAGAAGGAAGAAAGAACGTTTAGAAAAAGAAGAATATGAAGCTAAATTAGAAGCCGAAATGAGGATCTACAACCCCTGGGGGAAGGGCGGAGGTGGTGCTCCTCTCAGAGACGCCAAAGGAAATCTGATAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTGGTGCTCCTCTCAGAGA
60.61
TTAGCCAGGGTCCCTCTGAA
59.88
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGTGGTGCTCCTCTCAGA
60.61
TTAGCCAGGGTCCCTCTGAA
59.88
142
PCR template sequence:
GAATATGAAGCTAAATTAGAAGCCGAAATGAGGATCTACAACCCCTGGGGGAAGGGCGGAGGTGGTGCTCCTCTCAGAGACGCCAAAGGAAATCTGATAACCTAAGAGTCAAAGAAATAAAAACCCTATTAGTCAAGGTAAATCTGATCTACCTTTACAAATACAGACTGCATACACACATTCAGAGGGACCCTGGCTAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-29a-3p(1), mmu-miR-326-3p(1), mmu-miR-483-5p(1), mmu-miR-499-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-673-5p(1), mmu-miR-5101(1), mmu-miR-1904(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAAATCTGATAACCTAAGAGTCAAA
siRNA sets
TTTGACTCTTAGGTTATCA, TTGACTCTTAGGTTATCAG, CTTAGGTTATCAGATTTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCSPP1_1402_ORF_1
1.0638
0.12149975
0.993036278
1080
ORF sequence:
ATGGACGAGAGGTTTAGATTTGAAAGTGATTTTGATAGAAGACTTTTGAGAGTGTATACAAATGGCAGGCCGCATGGGAGCAGACGAGGGTATGTGGATGGGGATGATGTCCCAGAAGAGCCAAACACACAGATCTCAGCTGCTGAAAATAAAAGTGTTCACTGTAATGGACCACCCAGATCTGCTGATCTCGATATCACAAGTCCATTTGCAGGCATGCTCTTTGGAGGTGAAGATCGAGAACTTACCAAGAGAAGGAAGGAGAAATATAGGCAAGAACTACTAGAACAGATAGCTGAGCAACAGAAGAAGAAGAGACGAGAAAAAGATTTAGCATTTGGAATTACAACTTCTGGAGTACAAGACCCTGAAAAATCGCCTGATAGACTAAAGCAGTTTAGTTTGACACCAAGACACTTTGAAGAGATGCCACCTGAGAGGCCCAGAGTAGCTTTCCAGACACCTCCCCCTCCCTTCTCTGCCCCGTCTAGCCCATCCGTCCCACCAGTTCATTCCGCCCCTTCTCACAATGAAGACTTGCACAGTGGACTCGGCAGCACCCTTGGTGAACTGGCGCATCCCAGGGTTCTGCCTGTGCCTCTGAATCCACCCCCGCCTCCGCTCCTTGCCCCTCCAGCTTCTAACTATCGAACTCCTTACGATGATGCGTACTATTTTTACGGTGCCAGAAATACACTGGATCCCAATATTGTATACTATGGTTCAGGAATGATTGGAGGACAGCCTGCCCCTCATGTCTCTGCCCCTGTCACTCACCAGGTAGCACCGCCAGCTGTGAATACTGTTGGACAGAATGAACAGAAAGTTCTTAGTGATGGACTCAGGAATTCAGGACTGGTCTTTGAGGATAAGCCAAAACCTTCTACACAGTCGCTTCAGTCTTACCAAGAAGCTTTGCAGGAGCAGATTCGGGAAAGAGAAGCAAGAAGGAAGAAAGAACGTTTAGAAAAAGAAGAATATGAAGCTAAATTAGAAGCCGAAATGAGGATCTACAACCCCTGGGGGAAGGGCGGAGGTGGTGCTCCTCTCAGAGACGCCAAAGGAAATCTGATAACCTAA
Peptide sequence:
MDERFRFESDFDRRLLRVYTNGRPHGSRRGYVDGDDVPEEPNTQISAAENKSVHCNGPPRSADLDITSPFAGMLFGGEDRELTKRRKEKYRQELLEQIAEQQKKKRREKDLAFGITTSGVQDPEKSPDRLKQFSLTPRHFEEMPPERPRVAFQTPPPPFSAPSSPSVPPVHSAPSHNEDLHSGLGSTLGELAHPRVLPVPLNPPPPPLLAPPASNYRTPYDDAYYFYGARNTLDPNIVYYGSGMIGGQPAPHVSAPVTHQVAPPAVNTVGQNEQKVLSDGLRNSGLVFEDKPKPSTQSLQSYQEALQEQIREREARRKKERLEKEEYEAKLEAEMRIYNPWGKGGGGAPLRDAKGNLIT
IRESfinder result
IRESfinder score
0.524267089
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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