top of page
mmu_circNcl_1561
Basic information of circular RNA
PanCircBase ID:
mmu_circNcl_1561
mm39_Chr. Position ID:
chr1|86279919|86285174|-
Gene name:
Ncl
Transcript:
ENSMUST00000027438.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
11,10,9,8,7,6,5,4,3
Exon/intron offsets:
0,312,928,1534,2822,3854,4173,4358,4759
Genomic length:
5255
Exon/intron sizes in nt:
1,22,12,41,55,12,41,25,00,00,00,00,000
Flanking exon/introns:
chr1:86279215-86279919|chr1:86285174-86285828
Splice length:
1561
Other database IDs:
circAtlas: mmu-Ncl_0005
circBase: hsa_circ_0058671
Human Ortholog IDs:
Mature spliced Sequence:
GTTGTCATCCCTCAGAAAAAAGGCAAAAAGGCTACCACAACCCCAGCAAAGAAGGTGGTTGTTTCACAAACAAAAAAGGCTGCAGTTCCCACACCAGCTAAGAAAGCAGCTGTGACCCCAGGCAAAAAGGCAGTAGCCACACCAGCTAAGAAAAACATTACACCAGCCAAAGTCATTCCAACACCGGGTAAGAAGGGAGCTGCACAAGCAAAAGCGTTGGTACCAACTCCTGGTAAAAAGGGAGCTGCCACTCCAGCTAAGGGGGCTAAGAACGGTAAGAATGCCAAGAAGGAAGACAGTGATGAGGATGAAGATGAAGAGGATGAAGATGATAGCGATGAGGATGAAGATGATGAGGAAGAGGATGAGTTTGAGCCACCAATAGTAAAAGGAGTGAAGCCAGCAAAAGCAGCTCCTGCTGCTCCTGCCTCAGAGGATGAGGAAGATGATGAGGATGAAGATGATGAGGAAGATGATGATGAAGAGGAGGAAGATGACTCTGAGGAAGAAGTTATGGAGATCACAACAGCCAAAGGAAAGAAAACTCCTGCAAAAGTTGTTCCTATGAAAGCCAAGAGTGTGGCTGAGGAGGAGGATGATGAGGAAGAGGATGAAGATGACGAGGATGAGGATGATGAGGAAGAGGATGACGAAGATGATGATGAGGAAGAAGAGGAGGAAGAACCTGTTAAAGCAGCACCTGGAAAACGGAAGAAGGAGATGACCAAGCAGAAAGAAGCCCCTGAAGCCAAGAAACAGAAAGTAGAAGGCTCAGAACCAACTACACCTTTCAATCTGTTCATTGGAAACCTTAATCCAAACAAGTCTGTTAATGAATTAAAATTTGCCATCAGTGAACTTTTTGCTAAAAATGATCTTGCTGTTGTGGATGTCAGAACTGGTACAAATAGGAAATTTGGTTATGTGGACTTTGAGTCTGCTGAAGACCTAGAAAAGGCCTTGGAGCTCACTGGTTTAAAAGTGTTTGGCAATGAAATTAAACTAGAAAAACCAAAAGGAAGAGATAGTAAGAAAGTTCGAGCTGCAAGAACACTTCTAGCCAAAAACCTCTCTTTCAACATCACTGAGGATGAATTAAAGGAAGTGTTTGAAGACGCCATGGAGATCAGATTAGTCAGCCAGGATGGGAAAAGTAAAGGGATTGCTTATATTGAATTTAAGTCTGAAGCTGATGCAGAGAAAAATTTGGAAGAAAAGCAGGGGGCAGAAATTGATGGACGATCTGTTTCACTCTACTATACTGGAGAGAAAGGTCAAAGGCAAGAGAGAACTGGAAAGACCAGCACTTGGAGTGGTGAATCAAAGACTTTGGTTTTAAGTAACCTTTCCTACAGTGCAACAAAAGAAACTCTTGAGGAAGTATTTGAGAAAGCAACTTTTATCAAAGTGCCCCAGAACCCACATGGCAAACCTAAAGGGTATGCATTTATAGAATTTGCTTCATTTGAAGATGCTAAAGAAGCTTTAAATTCCTGTAATAAAATGGAAATTGAGGGCAGAACAATCAGGCTGGAGTTGCAAGGATCCAATTCGAGAAGTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGGCAGAACAATCAGGCT
60.03
TGTGGGAACTGCAGCCTTTT
60.4
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGAGGGCAGAACAATCAGGC
60.32
TGTGGGAACTGCAGCCTTTT
60.4
143
PCR template sequence:
TCATTTGAAGATGCTAAAGAAGCTTTAAATTCCTGTAATAAAATGGAAATTGAGGGCAGAACAATCAGGCTGGAGTTGCAAGGATCCAATTCGAGAAGTCGTTGTCATCCCTCAGAAAAAAGGCAAAAAGGCTACCACAACCCCAGCAAAGAAGGTGGTTGTTTCACAAACAAAAAAGGCTGCAGTTCCCACACCAGCTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-138-5p(3), mmu-miR-322-5p(2), mmu-miR-129-5p(2), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-709(1), mmu-miR-362-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AATTCGAGAAGTCGTTGTCATCCCTC
siRNA sets
GATGACAACGACTTCTCGA, ATGACAACGACTTCTCGAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNCL_1561_ORF_1
1.1274
0.225758889
0.997515245
1149
ORF sequence:
ATGGAGATCACAACAGCCAAAGGAAAGAAAACTCCTGCAAAAGTTGTTCCTATGAAAGCCAAGAGTGTGGCTGAGGAGGAGGATGATGAGGAAGAGGATGAAGATGACGAGGATGAGGATGATGAGGAAGAGGATGACGAAGATGATGATGAGGAAGAAGAGGAGGAAGAACCTGTTAAAGCAGCACCTGGAAAACGGAAGAAGGAGATGACCAAGCAGAAAGAAGCCCCTGAAGCCAAGAAACAGAAAGTAGAAGGCTCAGAACCAACTACACCTTTCAATCTGTTCATTGGAAACCTTAATCCAAACAAGTCTGTTAATGAATTAAAATTTGCCATCAGTGAACTTTTTGCTAAAAATGATCTTGCTGTTGTGGATGTCAGAACTGGTACAAATAGGAAATTTGGTTATGTGGACTTTGAGTCTGCTGAAGACCTAGAAAAGGCCTTGGAGCTCACTGGTTTAAAAGTGTTTGGCAATGAAATTAAACTAGAAAAACCAAAAGGAAGAGATAGTAAGAAAGTTCGAGCTGCAAGAACACTTCTAGCCAAAAACCTCTCTTTCAACATCACTGAGGATGAATTAAAGGAAGTGTTTGAAGACGCCATGGAGATCAGATTAGTCAGCCAGGATGGGAAAAGTAAAGGGATTGCTTATATTGAATTTAAGTCTGAAGCTGATGCAGAGAAAAATTTGGAAGAAAAGCAGGGGGCAGAAATTGATGGACGATCTGTTTCACTCTACTATACTGGAGAGAAAGGTCAAAGGCAAGAGAGAACTGGAAAGACCAGCACTTGGAGTGGTGAATCAAAGACTTTGGTTTTAAGTAACCTTTCCTACAGTGCAACAAAAGAAACTCTTGAGGAAGTATTTGAGAAAGCAACTTTTATCAAAGTGCCCCAGAACCCACATGGCAAACCTAAAGGGTATGCATTTATAGAATTTGCTTCATTTGAAGATGCTAAAGAAGCTTTAAATTCCTGTAATAAAATGGAAATTGAGGGCAGAACAATCAGGCTGGAGTTGCAAGGATCCAATTCGAGAAGTCGTTGTCATCCCTCAGAAAAAAGGCAAAAAGGCTACCACAACCCCAGCAAAGAAGGTGGTTGTTTCACAAACAAAAAAGGCTGCAGTTCCCACACCAGCTAA
Peptide sequence:
MEITTAKGKKTPAKVVPMKAKSVAEEEDDEEEDEDDEDEDDEEEDDEDDDEEEEEEEPVKAAPGKRKKEMTKQKEAPEAKKQKVEGSEPTTPFNLFIGNLNPNKSVNELKFAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAMEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGQRQERTGKTSTWSGESKTLVLSNLSYSATKETLEEVFEKATFIKVPQNPHGKPKGYAFIEFASFEDAKEALNSCNKMEIEGRTIRLELQGSNSRSRCHPSEKRQKGYHNPSKEGGCFTNKKGCSSHTS
IRESfinder result
IRESfinder score
0.328302455
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page