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mmu_circHspa4_1135
Basic information of circular RNA
PanCircBase ID:
mmu_circHspa4_1135
mm39_Chr. Position ID:
chr11|53155860|53166046|-
Gene name:
Hspa4
Transcript:
ENSMUST00000020630.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
16,15,14,13,12,11,10,9,8
Exon/intron offsets:
0,890,1932,3456,4654,5912,6980,7693,10109
Genomic length:
10186
Exon/intron sizes in nt:
108,126,153,96,182,134,107,152,77
Flanking exon/introns:
chr11:53153826-53155860|chr11:53166046-53171294
Splice length:
1135
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
AGGCAAATTTTTGGAGATGTGTGATGATCTCCTAGCAAGAGTGGAGCCGCCACTTCGAAGCGTCTTGGAGCAATCCAAGTTAAAGAAAGAAGATATTTATGCAGTGGAGATAGTTGGTGGTGCCACACGAATCCCTGCAGTGAAAGAGAAGATCAGCAAGTTTTTTGGTAAAGAACTCAGCACAACATTAAATGCAGATGAAGCTGTCACTCGAGGCTGTGCTCTGCAGTGTGCAATTTTATCACCTGCTTTCAAAGTCAGAGAATTTTCTATCACTGATGTGGTACCATATCCAATATCTTTGCGATGGAATTCTCCAGCTGAAGAGGGGTTAAGTGACTGTGAAGTCTTCCCCAAAAACCATGCTGCTCCTTTCTCCAAAGTCCTCACCTTCTACAGAAAGGAACCTTTCACTCTTGAGGCCTACTATAGTTCTCCTCAGGATTTGCCCTATCCAGATCCTGCTATAGCTCAGTTCTCAGTTCAGAAAGTCACTCCACAGTCTGATGGCTCCAGCTCAAAAGTGAAAGTCAAGGTCCGGGTGAACGTGCACGGCATCTTCAGTGTGTCCAGTGCGGCCTTGGTGGAGGTGCACAAGTCTGAAGAGAGTGAGGAGCCCATGGAGACGGATCAGAATGCAAAGGAAGAGGAGAAGATGCAAGTGGACCAGGAAGAACCACATACTGAAGAGCAGCAGCAGCAGCCACAGACACCAGCAGAAAACAAGGCGGAGTCTGAGGAGATGGAGACATCTCAAGCTGGATCAAAAGATAAAAAGACGGACCAACCACCTCAAGCAAAGAAGGCAAAAGTGAAGACCAGCACTGTGGACCTGCCCATTGAGAGCCAGCTGCTCTGGCAGCTGGACCGGGAGATGCTCGGCCTGTACACAGAGAATGAGGGTAAGATGATCATGCAGGATAAACTGGAGAAGGAACGGAATGACGCCAAGAATGCTGTGGAAGAGTATGTGTATGAGATGAGAGACAAGCTTAGTGGTGAATATGAGAAGTTTGTGAGTGAAGATGATCGTAATACTTTTACCTTAAAATTAGAGGATACTGAAAATTGGCTGTATGAAGATGGAGAAGATCAACCAAAGCAAGTTTATGTAGACAAATTGGCTGAATTAAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCTGTATGAAGATGGAGAAGA
58.97
ATTGCTCCAAGACGCTTCGA
60.04
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCTGTATGAAGATGGAGAAGA
58.97
GATTGCTCCAAGACGCTTCG
59.63
141
PCR template sequence:
TACTTTTACCTTAAAATTAGAGGATACTGAAAATTGGCTGTATGAAGATGGAGAAGATCAACCAAAGCAAGTTTATGTAGACAAATTGGCTGAATTAAAAAGGCAAATTTTTGGAGATGTGTGATGATCTCCTAGCAAGAGTGGAGCCGCCACTTCGAAGCGTCTTGGAGCAATCCAAGTTAAAGAAAGAAGATATTTAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-207(2), mmu-miR-9-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-32-5p(1), mmu-miR-7b-5p(1), mmu-miR-146a-5p(1), mmu-miR-217-5p(1), mmu-miR-7a-5p(1), mmu-miR-138-5p(1), mmu-miR-128-3p(1), mmu-miR-22-3p(1), mmu-miR-541-5p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCTGAATTAAAAAGGCAAATTTTTG
siRNA sets
ATTTGCCTTTTTAATTCAG, AAATTTGCCTTTTTAATTC, AATTTGCCTTTTTAATTCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHSPA4_1135_ORF_1
0.9947
0.322231001
0.997804928
1143
ORF sequence:
ATGTGTGATGATCTCCTAGCAAGAGTGGAGCCGCCACTTCGAAGCGTCTTGGAGCAATCCAAGTTAAAGAAAGAAGATATTTATGCAGTGGAGATAGTTGGTGGTGCCACACGAATCCCTGCAGTGAAAGAGAAGATCAGCAAGTTTTTTGGTAAAGAACTCAGCACAACATTAAATGCAGATGAAGCTGTCACTCGAGGCTGTGCTCTGCAGTGTGCAATTTTATCACCTGCTTTCAAAGTCAGAGAATTTTCTATCACTGATGTGGTACCATATCCAATATCTTTGCGATGGAATTCTCCAGCTGAAGAGGGGTTAAGTGACTGTGAAGTCTTCCCCAAAAACCATGCTGCTCCTTTCTCCAAAGTCCTCACCTTCTACAGAAAGGAACCTTTCACTCTTGAGGCCTACTATAGTTCTCCTCAGGATTTGCCCTATCCAGATCCTGCTATAGCTCAGTTCTCAGTTCAGAAAGTCACTCCACAGTCTGATGGCTCCAGCTCAAAAGTGAAAGTCAAGGTCCGGGTGAACGTGCACGGCATCTTCAGTGTGTCCAGTGCGGCCTTGGTGGAGGTGCACAAGTCTGAAGAGAGTGAGGAGCCCATGGAGACGGATCAGAATGCAAAGGAAGAGGAGAAGATGCAAGTGGACCAGGAAGAACCACATACTGAAGAGCAGCAGCAGCAGCCACAGACACCAGCAGAAAACAAGGCGGAGTCTGAGGAGATGGAGACATCTCAAGCTGGATCAAAAGATAAAAAGACGGACCAACCACCTCAAGCAAAGAAGGCAAAAGTGAAGACCAGCACTGTGGACCTGCCCATTGAGAGCCAGCTGCTCTGGCAGCTGGACCGGGAGATGCTCGGCCTGTACACAGAGAATGAGGGTAAGATGATCATGCAGGATAAACTGGAGAAGGAACGGAATGACGCCAAGAATGCTGTGGAAGAGTATGTGTATGAGATGAGAGACAAGCTTAGTGGTGAATATGAGAAGTTTGTGAGTGAAGATGATCGTAATACTTTTACCTTAAAATTAGAGGATACTGAAAATTGGCTGTATGAAGATGGAGAAGATCAACCAAAGCAAGTTTATGTAGACAAATTGGCTGAATTAAAAAGGCAAATTTTTGGAGATGTGTGA
Peptide sequence:
MCDDLLARVEPPLRSVLEQSKLKKEDIYAVEIVGGATRIPAVKEKISKFFGKELSTTLNADEAVTRGCALQCAILSPAFKVREFSITDVVPYPISLRWNSPAEEGLSDCEVFPKNHAAPFSKVLTFYRKEPFTLEAYYSSPQDLPYPDPAIAQFSVQKVTPQSDGSSSKVKVKVRVNVHGIFSVSSAALVEVHKSEESEEPMETDQNAKEEEKMQVDQEEPHTEEQQQQPQTPAENKAESEEMETSQAGSKDKKTDQPPQAKKAKVKTSTVDLPIESQLLWQLDREMLGLYTENEGKMIMQDKLEKERNDAKNAVEEYVYEMRDKLSGEYEKFVSEDDRNTFTLKLEDTENWLYEDGEDQPKQVYVDKLAELKRQIFGDV
IRESfinder result
IRESfinder score
0.450844694
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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