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mmu_circEp400_1901
Basic information of circular RNA
PanCircBase ID:
mmu_circEp400_1901
mm39_Chr. Position ID:
chr5|110858896|110887547|-
Gene name:
Ep400
Transcript:
ENSMUST00000041558.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
16,15,14,13,12,11,10,9,8,7,6,5
Exon/intron offsets:
0,8056,8402,9705,13391,15860,16498,18203,18792,22688,24319,28265
Genomic length:
28651
Exon/intron sizes in nt:
1,37,17,81,91,10,89,05,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr5:110856809-110858896|chr5:110887547-110888047
Splice length:
1901
Other database IDs:
circAtlas: mmu-Ep400_0034
Human Ortholog IDs:
Mature spliced Sequence:
GAGGGATGCCCCCAACTCCTCAGGCCACACAGCTCACTGGACAGAAGCAGAGTCAGCAGCAGTACGACCCTTCCACAGGGCCTCCTGTGCAGAACGCCGCCAGCTTGCATACCCCACCACCACAGCTTCCTGCGAGGCTGCCTCCGGCCAGTGTCCCAGCCACAGCCCTCCCTTCCACCTTACAGTTTTCACAGCAGTCACAGATGGTGGAGGCTTCAACTCAGCTCCAAATCCCTGTGAAGACTCAACAGCTAAATGCCCCCATCCCTGCCCCCCTGCCCAGCCAGCTCCCTGCTCCTTCTTCACAGCCCGCCCAGCCGGCCCTACATGTTCCGATGCCCGGGAAGGCGCAGATGCAGACATCTCAGCTTTCCTCCCAGACCCAGACAGTGGCATCGACCAGGCCCCCCTTGGACTCTGCCCAGCCCTGCCAGCGGTCTCTGCCCACTTCCTCCTCTTCCTCATCCCTTGTACCTGTGAGTGGCTCAGGTCCTGGACCCTCACCTGCTCGTTCTTCACCAGTGAACAGACCCTCTTCTGCTACCAACAAGGCTCTGTCTCCCATCACTTCTCGGTCTCCAGGGGTGGCAGTATCAGCTCCTCCTAAGCCACAGAGTCCTGCTCAGAATGCAGCCTCATCCCAGGACGGTTCTCAGGATAAACTGGCAGAACAAATAACACTGGAAAACCAGATCCATCAGCGAATAGCAGATTTAAGGAAGGAAGGCTTGTGGTCCCTAAGGCGGTTGCCAAAGCTTCAAGAGGCCCCACGCCCGAAATCTCACTGGGACTATTTGCTGGAAGAGATGCAGTGGATGGCCACAGACTTTGCTCAAGAGCGGAGGTGGAAGTTGGCTGCTGCTAAGAAGCTTGTCAGAACTGTAGCCCGGCATCATGAGGAAAAGAAACTTCGTGAGGAAAGAGGGAAGAAGGAAGAACAGAGCAGACTGAGGCGCATTGCTGCCACTACTGCCAGAGAAATAGAATATTTTTGGTCAAATATTGAACAGGTTGTGGAAATAAAATTACAAGTAGAATTAGAAGAGAAAAGAAAAAAAGCCTTAAATTTACAGAAAGTTTCCAGAAGAGGTAAAGAGTCCAGATTAAAGGGATTTGATACATCACCAGAACACTCTCTGGATCTAGGAATATCTGGAAGGAAAAGAAAAGCTAGCACATCTTTGACTGATGATGAAGTGGAAGATGAAGAAGAGACCATTGAAGAGGAGGAAGCACACGAAGGGCTTGTAGACCACCACACAGAACTTACTAATCTGGCCAAAGAAGCTGAGTTGCCCTTAATCGATTTGATGAAGTTGTATGAAGGTGCCTTTCTGCCAAATTTTCAGTGGCCACAGCCTGAACCTGATCATGAAGAGTCAAGTGGGGAAGAAGATGTAGAAGACTGTCCTAGTGACAGGGAGAGCCGGAGGGACTCCGTTCTCATTGACTCACTCTTCATCATGGATCAGTTTAAAGCTGCAGAGAGAATGAGCATTGGAAAATCCAACACCAAGGACATCACAGAAGTTACTGCTGTGGCTGAAGCCATCCTCCCTAAGGGCAGTGCCCGAGTCACAACTGCGGTGAAGTTTAGTGCTCCATCTTTGTTGTATGGTGCTCTCCGAGACTATCAGAAGATAGGCCTGGACTGGTTGGCCAAGCTATACCGGAAGAATCTCAATGGCATATTGGCTGATGAAGCAGGGCTTGGGAAAACTGTGCAGATCATTGCTTTTTTTGCTCACCTTGCCTGTAATGAAGGTAACTGGGGCCCTCATCTTGTTGTCATGAGGAGTTGTAACATACTCAAGTGGGAACTCGAGTTGAAACGCTGGTGTCCTGGCCTCAAAACTCTTTCTTATGTTGGCAGCCACAGAGAACTCAAAGCAAAGAGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTCGAGTTGAAACGCTGGT
59.9
CTGCTGCTGACTCTGCTTCT
60.04
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCGAGTTGAAACGCTGGTGT
60.18
CTGCTGCTGACTCTGCTTCT
60.04
142
PCR template sequence:
TAACATACTCAAGTGGGAACTCGAGTTGAAACGCTGGTGTCCTGGCCTCAAAACTCTTTCTTATGTTGGCAGCCACAGAGAACTCAAAGCAAAGAGACAGGAGGGATGCCCCCAACTCCTCAGGCCACACAGCTCACTGGACAGAAGCAGAGTCAGCAGCAGTACGACCCTTCCACAGGGCCTCCTGTGCAGAACGCCGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
23
Interacting miRNAs (#binding sites)
mmu-miR-205-5p(1), mmu-miR-211-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-298-5p(1), mmu-miR-709(1), mmu-miR-320-3p(1), mmu-miR-339-5p(1), mmu-miR-139-5p(1), mmu-miR-495-3p(1), mmu-miR-433-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-199b-3p(1), mmu-miR-182-5p(1), mmu-miR-199a-3p(1), mmu-miR-758-3p(1), mmu-miR-541-5p(1), mmu-miR-410-3p(1), mmu-miR-5101(1), mmu-miR-3061-5p(1), mmu-miR-296-3p(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCAAAGAGACAGGAGGGATGCCCCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCEP400_1901_ORF_1
0.7825
0.143732591
0.999994577
2136
ORF sequence:
ATGCCCCCAACTCCTCAGGCCACACAGCTCACTGGACAGAAGCAGAGTCAGCAGCAGTACGACCCTTCCACAGGGCCTCCTGTGCAGAACGCCGCCAGCTTGCATACCCCACCACCACAGCTTCCTGCGAGGCTGCCTCCGGCCAGTGTCCCAGCCACAGCCCTCCCTTCCACCTTACAGTTTTCACAGCAGTCACAGATGGTGGAGGCTTCAACTCAGCTCCAAATCCCTGTGAAGACTCAACAGCTAAATGCCCCCATCCCTGCCCCCCTGCCCAGCCAGCTCCCTGCTCCTTCTTCACAGCCCGCCCAGCCGGCCCTACATGTTCCGATGCCCGGGAAGGCGCAGATGCAGACATCTCAGCTTTCCTCCCAGACCCAGACAGTGGCATCGACCAGGCCCCCCTTGGACTCTGCCCAGCCCTGCCAGCGGTCTCTGCCCACTTCCTCCTCTTCCTCATCCCTTGTACCTGTGAGTGGCTCAGGTCCTGGACCCTCACCTGCTCGTTCTTCACCAGTGAACAGACCCTCTTCTGCTACCAACAAGGCTCTGTCTCCCATCACTTCTCGGTCTCCAGGGGTGGCAGTATCAGCTCCTCCTAAGCCACAGAGTCCTGCTCAGAATGCAGCCTCATCCCAGGACGGTTCTCAGGATAAACTGGCAGAACAAATAACACTGGAAAACCAGATCCATCAGCGAATAGCAGATTTAAGGAAGGAAGGCTTGTGGTCCCTAAGGCGGTTGCCAAAGCTTCAAGAGGCCCCACGCCCGAAATCTCACTGGGACTATTTGCTGGAAGAGATGCAGTGGATGGCCACAGACTTTGCTCAAGAGCGGAGGTGGAAGTTGGCTGCTGCTAAGAAGCTTGTCAGAACTGTAGCCCGGCATCATGAGGAAAAGAAACTTCGTGAGGAAAGAGGGAAGAAGGAAGAACAGAGCAGACTGAGGCGCATTGCTGCCACTACTGCCAGAGAAATAGAATATTTTTGGTCAAATATTGAACAGGTTGTGGAAATAAAATTACAAGTAGAATTAGAAGAGAAAAGAAAAAAAGCCTTAAATTTACAGAAAGTTTCCAGAAGAGGTAAAGAGTCCAGATTAAAGGGATTTGATACATCACCAGAACACTCTCTGGATCTAGGAATATCTGGAAGGAAAAGAAAAGCTAGCACATCTTTGACTGATGATGAAGTGGAAGATGAAGAAGAGACCATTGAAGAGGAGGAAGCACACGAAGGGCTTGTAGACCACCACACAGAACTTACTAATCTGGCCAAAGAAGCTGAGTTGCCCTTAATCGATTTGATGAAGTTGTATGAAGGTGCCTTTCTGCCAAATTTTCAGTGGCCACAGCCTGAACCTGATCATGAAGAGTCAAGTGGGGAAGAAGATGTAGAAGACTGTCCTAGTGACAGGGAGAGCCGGAGGGACTCCGTTCTCATTGACTCACTCTTCATCATGGATCAGTTTAAAGCTGCAGAGAGAATGAGCATTGGAAAATCCAACACCAAGGACATCACAGAAGTTACTGCTGTGGCTGAAGCCATCCTCCCTAAGGGCAGTGCCCGAGTCACAACTGCGGTGAAGTTTAGTGCTCCATCTTTGTTGTATGGTGCTCTCCGAGACTATCAGAAGATAGGCCTGGACTGGTTGGCCAAGCTATACCGGAAGAATCTCAATGGCATATTGGCTGATGAAGCAGGGCTTGGGAAAACTGTGCAGATCATTGCTTTTTTTGCTCACCTTGCCTGTAATGAAGGTAACTGGGGCCCTCATCTTGTTGTCATGAGGAGTTGTAACATACTCAAGTGGGAACTCGAGTTGAAACGCTGGTGTCCTGGCCTCAAAACTCTTTCTTATGTTGGCAGCCACAGAGAACTCAAAGCAAAGAGACAGGAGGGATGCCCCCAACTCCTCAGGCCACACAGCTCACTGGACAGAAGCAGAGTCAGCAGCAGTACGACCCTTCCACAGGGCCTCCTGTGCAGAACGCCGCCAGCTTGCATACCCCACCACCACAGCTTCCTGCGAGGCTGCCTCCGGCCAGTGTCCCAGCCACAGCCCTCCCTTCCACCTTACAGTTTTCACAGCAGTCACAGATGGTGGAGGCTTCAACTCAGCTCCAAATCCCTGTGA
Peptide sequence:
MPPTPQATQLTGQKQSQQQYDPSTGPPVQNAASLHTPPPQLPARLPPASVPATALPSTLQFSQQSQMVEASTQLQIPVKTQQLNAPIPAPLPSQLPAPSSQPAQPALHVPMPGKAQMQTSQLSSQTQTVASTRPPLDSAQPCQRSLPTSSSSSSLVPVSGSGPGPSPARSSPVNRPSSATNKALSPITSRSPGVAVSAPPKPQSPAQNAASSQDGSQDKLAEQITLENQIHQRIADLRKEGLWSLRRLPKLQEAPRPKSHWDYLLEEMQWMATDFAQERRWKLAAAKKLVRTVARHHEEKKLREERGKKEEQSRLRRIAATTAREIEYFWSNIEQVVEIKLQVELEEKRKKALNLQKVSRRGKESRLKGFDTSPEHSLDLGISGRKRKASTSLTDDEVEDEEETIEEEEAHEGLVDHHTELTNLAKEAELPLIDLMKLYEGAFLPNFQWPQPEPDHEESSGEEDVEDCPSDRESRRDSVLIDSLFIMDQFKAAERMSIGKSNTKDITEVTAVAEAILPKGSARVTTAVKFSAPSLLYGALRDYQKIGLDWLAKLYRKNLNGILADEAGLGKTVQIIAFFAHLACNEGNWGPHLVVMRSCNILKWELELKRWCPGLKTLSYVGSHRELKAKRQEGCPQLLRPHSSLDRSRVSSSTTLPQGLLCRTPPACIPHHHSFLRGCLRPVSQPQPSLPPYSFHSSHRWWRLQLSSKSL
IRESfinder result
IRESfinder score
0.549503457
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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