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mmu_circHerc1_1143
Basic information of circular RNA
PanCircBase ID:
mmu_circHerc1_1143
mm39_Chr. Position ID:
chr9|66323465|66340773|+
Gene name:
Herc1
Transcript:
ENSMUST00000042824.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
22,23,24,25,26,27
Exon/intron offsets:
0,2212,2945,4813,12627,17092
Genomic length:
17308
Exon/intron sizes in nt:
17,23,13,12,15,22,69,200
Flanking exon/introns:
chr9:66321681-66323465|chr9:66340773-66341005
Splice length:
1143
Other database IDs:
circAtlas: mmu-Herc1_0154
circBase: hsa_circ_0035796, circAtlas: hsa-HERC1_0035, CIRCpedia: HSA_CIRCpedia_15098
Human Ortholog IDs:
Mature spliced Sequence:
ATCACAGATAACCAAGACTCTGCAGATGTTGATCCTCAAGAACATTCCTTTACCCGGACCATTGATGAAGAAGCTGAAATGGAAGAGCTGGCTGAGAGAGACAGGGAGGATGGCCACCCAGAGCCAGAAGATGAGGAAGAAGAGCGGGAACATGAAGTAATGACAGCTGGCAAAATCTTTCAGTGTTTCCTCTCAGCCCGAGAAGTAGCTCGTAGCCGAGACCGAGATAGAATGAACAGTGGGGCAGGGTCTGGGGTCCGAGCTGATGACCCACCTCCACAGTCTCAGCAGGAACGACGGGTCAGCACAGACCTTCCTGAGGGGCAGGATGTGTACACTGCTGCCTGCAACTCTGTGATCCACCGCTGTGCGCTCCTAATATTAGGAGTAAGTCCTGTGATTGATGAGCTTCAGAAGCGAAGGGAAGAAGGGCAGTTACAGCAGCCTTCTGTGAGTGCCTCTGAAGGCACCGGACTTATGACCAGGAGTGAAAGTCTCACTGCTGAGAGCCGCCTAGTTCATGCAAGTCCAAGTTACAGACTGATCAAATCAAGGAGTGAATCTGATCTGTCTCAGCCTGAATCAGATGAAGAGGGTTATGCACTGAGTGGCCGACGAAATGTTGACTTTGATTTGGCATCATCTCATAGGAAGAGAGGTCCTATGCATAGTCAATTAGAATCTCTGAGTGACTCTTGGACTCGCCTGAAACATACCAGAGATTGGTTCTACAACTCCTCTTACTCCTTTGAGTCTGATTTTGACCTTACCAAGTCTTTGGGAGTTCACACATTGATTGAAAATGTTGTAAGTTTTGTGAGTGGAGATGTGGGGAATGCTCCAGGTTTCAAGGAGCCGGAAGAAAGTATGTCTACAAGTCCCCAGGCCTCCATCATTGCAATGGAGCAGCAACAGCTAAGGGCAGAGCTTCGTTTGGAGGCACTTCACCAGATCCTCACTCTATTGTCTGGCATGGAAGAAAAGGGTAACGTCTTGCTGACAGGAAGCAGATCAAGTTCAGGCTTTCAGTCATCCACCCTGCTCACATCTGTGAGATTGCAGTTTCTAGCAGGGTGTTTCGGTTTAGGTACTGTTGGACACACGGGAACCAAAGGAGAGAGTGGCCGACTGCATCACTATCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTACTGTTGGACACACGGGA
59.61
TCTCTCAGCCAGCTCTTCCA
60.25
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGTACTGTTGGACACACGG
59.61
TCTCTCAGCCAGCTCTTCCA
60.25
157
PCR template sequence:
CACATCTGTGAGATTGCAGTTTCTAGCAGGGTGTTTCGGTTTAGGTACTGTTGGACACACGGGAACCAAAGGAGAGAGTGGCCGACTGCATCACTATCAAATCACAGATAACCAAGACTCTGCAGATGTTGATCCTCAAGAACATTCCTTTACCCGGACCATTGATGAAGAAGCTGAAATGGAAGAGCTGGCTGAGAGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-326-3p(1), mmu-miR-339-5p(1), mmu-miR-149-5p(1), mmu-miR-136-5p(1), mmu-miR-127-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-370-3p(1), mmu-miR-362-5p(1), mmu-miR-335-3p(1), mmu-miR-350-3p(1), mmu-miR-697(1), mmu-miR-490-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GCATCACTATCAAATCACAGATAACC
siRNA sets
TGTGATTTGATAGTGATGC,ATCTGTGATTTGATAGTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHERC1_1143_ORF_1
0.9541
0.196745338
0.999998178
2208
ORF sequence:
ATGGAAGAGCTGGCTGAGAGAGACAGGGAGGATGGCCACCCAGAGCCAGAAGATGAGGAAGAAGAGCGGGAACATGAAGTAATGACAGCTGGCAAAATCTTTCAGTGTTTCCTCTCAGCCCGAGAAGTAGCTCGTAGCCGAGACCGAGATAGAATGAACAGTGGGGCAGGGTCTGGGGTCCGAGCTGATGACCCACCTCCACAGTCTCAGCAGGAACGACGGGTCAGCACAGACCTTCCTGAGGGGCAGGATGTGTACACTGCTGCCTGCAACTCTGTGATCCACCGCTGTGCGCTCCTAATATTAGGAGTAAGTCCTGTGATTGATGAGCTTCAGAAGCGAAGGGAAGAAGGGCAGTTACAGCAGCCTTCTGTGAGTGCCTCTGAAGGCACCGGACTTATGACCAGGAGTGAAAGTCTCACTGCTGAGAGCCGCCTAGTTCATGCAAGTCCAAGTTACAGACTGATCAAATCAAGGAGTGAATCTGATCTGTCTCAGCCTGAATCAGATGAAGAGGGTTATGCACTGAGTGGCCGACGAAATGTTGACTTTGATTTGGCATCATCTCATAGGAAGAGAGGTCCTATGCATAGTCAATTAGAATCTCTGAGTGACTCTTGGACTCGCCTGAAACATACCAGAGATTGGTTCTACAACTCCTCTTACTCCTTTGAGTCTGATTTTGACCTTACCAAGTCTTTGGGAGTTCACACATTGATTGAAAATGTTGTAAGTTTTGTGAGTGGAGATGTGGGGAATGCTCCAGGTTTCAAGGAGCCGGAAGAAAGTATGTCTACAAGTCCCCAGGCCTCCATCATTGCAATGGAGCAGCAACAGCTAAGGGCAGAGCTTCGTTTGGAGGCACTTCACCAGATCCTCACTCTATTGTCTGGCATGGAAGAAAAGGGTAACGTCTTGCTGACAGGAAGCAGATCAAGTTCAGGCTTTCAGTCATCCACCCTGCTCACATCTGTGAGATTGCAGTTTCTAGCAGGGTGTTTCGGTTTAGGTACTGTTGGACACACGGGAACCAAAGGAGAGAGTGGCCGACTGCATCACTATCAAATCACAGATAACCAAGACTCTGCAGATGTTGATCCTCAAGAACATTCCTTTACCCGGACCATTGATGAAGAAGCTGAAATGGAAGAGCTGGCTGAGAGAGACAGGGAGGATGGCCACCCAGAGCCAGAAGATGAGGAAGAAGAGCGGGAACATGAAGTAATGACAGCTGGCAAAATCTTTCAGTGTTTCCTCTCAGCCCGAGAAGTAGCTCGTAGCCGAGACCGAGATAGAATGAACAGTGGGGCAGGGTCTGGGGTCCGAGCTGATGACCCACCTCCACAGTCTCAGCAGGAACGACGGGTCAGCACAGACCTTCCTGAGGGGCAGGATGTGTACACTGCTGCCTGCAACTCTGTGATCCACCGCTGTGCGCTCCTAATATTAGGAGTAAGTCCTGTGATTGATGAGCTTCAGAAGCGAAGGGAAGAAGGGCAGTTACAGCAGCCTTCTGTGAGTGCCTCTGAAGGCACCGGACTTATGACCAGGAGTGAAAGTCTCACTGCTGAGAGCCGCCTAGTTCATGCAAGTCCAAGTTACAGACTGATCAAATCAAGGAGTGAATCTGATCTGTCTCAGCCTGAATCAGATGAAGAGGGTTATGCACTGAGTGGCCGACGAAATGTTGACTTTGATTTGGCATCATCTCATAGGAAGAGAGGTCCTATGCATAGTCAATTAGAATCTCTGAGTGACTCTTGGACTCGCCTGAAACATACCAGAGATTGGTTCTACAACTCCTCTTACTCCTTTGAGTCTGATTTTGACCTTACCAAGTCTTTGGGAGTTCACACATTGATTGAAAATGTTGTAAGTTTTGTGAGTGGAGATGTGGGGAATGCTCCAGGTTTCAAGGAGCCGGAAGAAAGTATGTCTACAAGTCCCCAGGCCTCCATCATTGCAATGGAGCAGCAACAGCTAAGGGCAGAGCTTCGTTTGGAGGCACTTCACCAGATCCTCACTCTATTGTCTGGCATGGAAGAAAAGGGTAACGTCTTGCTGACAGGAAGCAGATCAAGTTCAGGCTTTCAGTCATCCACCCTGCTCACATCTGTGAGATTGCAGTTTCTAGCAGGGTGTTTCGGTTTAGGTACTGTTGGACACACGGGAACCAAAGGAGAGAGTGGCCGACTGCATCACTATCAA
Peptide sequence:
MEELAERDREDGHPEPEDEEEEREHEVMTAGKIFQCFLSAREVARSRDRDRMNSGAGSGVRADDPPPQSQQERRVSTDLPEGQDVYTAACNSVIHRCALLILGVSPVIDELQKRREEGQLQQPSVSASEGTGLMTRSESLTAESRLVHASPSYRLIKSRSESDLSQPESDEEGYALSGRRNVDFDLASSHRKRGPMHSQLESLSDSWTRLKHTRDWFYNSSYSFESDFDLTKSLGVHTLIENVVSFVSGDVGNAPGFKEPEESMSTSPQASIIAMEQQQLRAELRLEALHQILTLLSGMEEKGNVLLTGSRSSSGFQSSTLLTSVRLQFLAGCFGLGTVGHTGTKGESGRLHHYQITDNQDSADVDPQEHSFTRTIDEEAEMEELAERDREDGHPEPEDEEEEREHEVMTAGKIFQCFLSAREVARSRDRDRMNSGAGSGVRADDPPPQSQQERRVSTDLPEGQDVYTAACNSVIHRCALLILGVSPVIDELQKRREEGQLQQPSVSASEGTGLMTRSESLTAESRLVHASPSYRLIKSRSESDLSQPESDEEGYALSGRRNVDFDLASSHRKRGPMHSQLESLSDSWTRLKHTRDWFYNSSYSFESDFDLTKSLGVHTLIENVVSFVSGDVGNAPGFKEPEESMSTSPQASIIAMEQQQLRAELRLEALHQILTLLSGMEEKGNVLLTGSRSSSGFQSSTLLTSVRLQFLAGCFGLGTVGHTGTKGESGRLHHYQ
IRESfinder result
IRESfinder score
0.571879389
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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