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mmu_circCntln_1464
Basic information of circular RNA
PanCircBase ID:
mmu_circCntln_1464
mm39_Chr. Position ID:
chr4|84923159|84986117|+
Gene name:
Cntln
Transcript:
ENSMUST00000047023.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
11,12,13,14,15,16,17,18
Exon/intron offsets:
0,1482,28865,41380,44681,58255,62557,62734
Genomic length:
62958
Exon/intron sizes in nt:
122,120,101,92,533,178,94,224
Flanking exon/introns:
chr4:84914817-84923159|chr4:84986117-85010873
Splice length:
1464
Other database IDs:
CIRCpedia: MMU_CIRCpedia_31907, circAtlas: mmu-Cntln_0007
circBase: hsa_circ_0138349, circAtlas: hsa-CNTLN_0016, CIRCpedia: HSA_CIRCpedia_165990
Human Ortholog IDs:
Mature spliced Sequence:
AGCCAAGAAAATGATGAGCTAAGAGATGCCCATGAAAAACGCAAGGAGAGACTACAGATGTTACACACCAACTACAGGGCAGTAAAAGAGCAATTAAAACAGTGGGAAGAAGACAGTGGCATGGCTGAATCCAGACAAATGAAGCGAGCAGAGCCTCACCAGCTCCGACAAGAAGACTCTGATGCTGTGTGGAACGAACTGGCATATTTCAAAAGAGAAAACCAGGAGTTGATGGTTCAAAAGATGACTCTTCAAGATGAATTGGATGAGCTTAAAATGCATATGTCCATTGATAAAACAACAATACAGGAATTGAATAGGTGCATGGCAGAGAAAAGAGAAGAACAACTCTTTAGACAGCATGAAGACGCTGAGGTCAAGAAGAGTACTCCAGAGAAGAATGAGAAAGCAATATCGGAAGAGACATTACAGAAGGTCATTGAGTTGGAAAATCGGCTAAAATCTTTTGAGAAAAACTCAAGAAAATTAAAAGAAGAGAGTAAGAGATTAAAGAAAGAGAATGATTTCCTTAAATCCCACTTAAAACACTATCAAGAAGACTCGGAGGCGAGAGAGAAGGAGCTAGAACAACTACTGAGGGTGAGCAAAGATGTAGAACATGACAAAAGTGAGCTTCAAACAAAAATCACTGCTCTGGAGACAGAAGTCACTACCCTGAGGAGACAAGTGACAGAAGCTAAGGCTTTGAGAGGCAAAGATGAAGAGGTGGTGTGCCCAGAGGAAAGAGCACACCGCCCAACAGACAAAGCTAAATCTGAGATGGCCACCACAGATGTGAGAGCCCGGCGCTGTGACTGCAAGACAGCCACTACCAAGGTGAAATTTAAAGCTGCCAAGAGAAAGTGCTCAGTGGGTCGCCACCACACAGTTCTCAATCACTCCATCAAGGTTATGAGCCACGTGGAGAACCTCAGCAAGGACGGCTGGGAGGATGTGAGTGAAGGCAGCAGTGATTCTGAAACACAAACCTTTCAAAATTTGGGAACAATTATTGTGGAAACATCCCAGAATATAAGCCCTATCGAAGATGGTAGAAACCAGAAAGAAATTGACCAAACAGAAGGCAGCTGTGCTCAACAAAGAGCTATGCAGACGTACTCATGTGAGGACATCAAGGCCCCGCAGAGTATTTCTCATAATAAGAACACCAAGAAAATGACATTTCAAAAGAAGAGTGGAAGCCTGCAGAAGAGCTTGCACAGTGCCCTTCCTGCCAGAGTTAACAGAGAAAAGTGCAAAAATCTACCTGCCCAGAAATCCAGTAGCAGCACCATTTCATTACGAGAACGGATCGTATCCTTGCAGCAACAGAACAGTTTGCTTCAGAACGCCAGGAGAGCAGCAGAGGCGTCTGCTAAGGAGTATAAAGAAGCGAACGAGAAGCTCCTCCATCAACAGCAGGTCAGCGATCACCGATTCCAGACCAGCAGACAGACAATAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCGAACGAGAAGCTCCTC
60.11
CTGCCCTGTAGTTGGTGTGT
59.89
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCGAACGAGAAGCTCCTC
60.11
ACTGCCCTGTAGTTGGTGTG
59.89
157
PCR template sequence:
AGAGGCGTCTGCTAAGGAGTATAAAGAAGCGAACGAGAAGCTCCTCCATCAACAGCAGGTCAGCGATCACCGATTCCAGACCAGCAGACAGACAATAAAGAGCCAAGAAAATGATGAGCTAAGAGATGCCCATGAAAAACGCAAGGAGAGACTACAGATGTTACACACCAACTACAGGGCAGTAAAAGAGCAATTAAAAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-326-3p(1), mmu-miR-25-3p(1), mmu-miR-434-3p(1), mmu-miR-431-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-370-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-673-5p(1), mmu-miR-539-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACAGACAATAAAGAGCCAAGAAAATG
siRNA sets
TTTTCTTGGCTCTTTATTG, TTTCTTGGCTCTTTATTGT, TTCTTGGCTCTTTATTGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCNTLN_1464_ORF_1
1.0177
0.2311012
0.999999988
2871
ORF sequence:
ATGTTACACACCAACTACAGGGCAGTAAAAGAGCAATTAAAACAGTGGGAAGAAGACAGTGGCATGGCTGAATCCAGACAAATGAAGCGAGCAGAGCCTCACCAGCTCCGACAAGAAGACTCTGATGCTGTGTGGAACGAACTGGCATATTTCAAAAGAGAAAACCAGGAGTTGATGGTTCAAAAGATGACTCTTCAAGATGAATTGGATGAGCTTAAAATGCATATGTCCATTGATAAAACAACAATACAGGAATTGAATAGGTGCATGGCAGAGAAAAGAGAAGAACAACTCTTTAGACAGCATGAAGACGCTGAGGTCAAGAAGAGTACTCCAGAGAAGAATGAGAAAGCAATATCGGAAGAGACATTACAGAAGGTCATTGAGTTGGAAAATCGGCTAAAATCTTTTGAGAAAAACTCAAGAAAATTAAAAGAAGAGAGTAAGAGATTAAAGAAAGAGAATGATTTCCTTAAATCCCACTTAAAACACTATCAAGAAGACTCGGAGGCGAGAGAGAAGGAGCTAGAACAACTACTGAGGGTGAGCAAAGATGTAGAACATGACAAAAGTGAGCTTCAAACAAAAATCACTGCTCTGGAGACAGAAGTCACTACCCTGAGGAGACAAGTGACAGAAGCTAAGGCTTTGAGAGGCAAAGATGAAGAGGTGGTGTGCCCAGAGGAAAGAGCACACCGCCCAACAGACAAAGCTAAATCTGAGATGGCCACCACAGATGTGAGAGCCCGGCGCTGTGACTGCAAGACAGCCACTACCAAGGTGAAATTTAAAGCTGCCAAGAGAAAGTGCTCAGTGGGTCGCCACCACACAGTTCTCAATCACTCCATCAAGGTTATGAGCCACGTGGAGAACCTCAGCAAGGACGGCTGGGAGGATGTGAGTGAAGGCAGCAGTGATTCTGAAACACAAACCTTTCAAAATTTGGGAACAATTATTGTGGAAACATCCCAGAATATAAGCCCTATCGAAGATGGTAGAAACCAGAAAGAAATTGACCAAACAGAAGGCAGCTGTGCTCAACAAAGAGCTATGCAGACGTACTCATGTGAGGACATCAAGGCCCCGCAGAGTATTTCTCATAATAAGAACACCAAGAAAATGACATTTCAAAAGAAGAGTGGAAGCCTGCAGAAGAGCTTGCACAGTGCCCTTCCTGCCAGAGTTAACAGAGAAAAGTGCAAAAATCTACCTGCCCAGAAATCCAGTAGCAGCACCATTTCATTACGAGAACGGATCGTATCCTTGCAGCAACAGAACAGTTTGCTTCAGAACGCCAGGAGAGCAGCAGAGGCGTCTGCTAAGGAGTATAAAGAAGCGAACGAGAAGCTCCTCCATCAACAGCAGGTCAGCGATCACCGATTCCAGACCAGCAGACAGACAATAAAGAGCCAAGAAAATGATGAGCTAAGAGATGCCCATGAAAAACGCAAGGAGAGACTACAGATGTTACACACCAACTACAGGGCAGTAAAAGAGCAATTAAAACAGTGGGAAGAAGACAGTGGCATGGCTGAATCCAGACAAATGAAGCGAGCAGAGCCTCACCAGCTCCGACAAGAAGACTCTGATGCTGTGTGGAACGAACTGGCATATTTCAAAAGAGAAAACCAGGAGTTGATGGTTCAAAAGATGACTCTTCAAGATGAATTGGATGAGCTTAAAATGCATATGTCCATTGATAAAACAACAATACAGGAATTGAATAGGTGCATGGCAGAGAAAAGAGAAGAACAACTCTTTAGACAGCATGAAGACGCTGAGGTCAAGAAGAGTACTCCAGAGAAGAATGAGAAAGCAATATCGGAAGAGACATTACAGAAGGTCATTGAGTTGGAAAATCGGCTAAAATCTTTTGAGAAAAACTCAAGAAAATTAAAAGAAGAGAGTAAGAGATTAAAGAAAGAGAATGATTTCCTTAAATCCCACTTAAAACACTATCAAGAAGACTCGGAGGCGAGAGAGAAGGAGCTAGAACAACTACTGAGGGTGAGCAAAGATGTAGAACATGACAAAAGTGAGCTTCAAACAAAAATCACTGCTCTGGAGACAGAAGTCACTACCCTGAGGAGACAAGTGACAGAAGCTAAGGCTTTGAGAGGCAAAGATGAAGAGGTGGTGTGCCCAGAGGAAAGAGCACACCGCCCAACAGACAAAGCTAAATCTGAGATGGCCACCACAGATGTGAGAGCCCGGCGCTGTGACTGCAAGACAGCCACTACCAAGGTGAAATTTAAAGCTGCCAAGAGAAAGTGCTCAGTGGGTCGCCACCACACAGTTCTCAATCACTCCATCAAGGTTATGAGCCACGTGGAGAACCTCAGCAAGGACGGCTGGGAGGATGTGAGTGAAGGCAGCAGTGATTCTGAAACACAAACCTTTCAAAATTTGGGAACAATTATTGTGGAAACATCCCAGAATATAAGCCCTATCGAAGATGGTAGAAACCAGAAAGAAATTGACCAAACAGAAGGCAGCTGTGCTCAACAAAGAGCTATGCAGACGTACTCATGTGAGGACATCAAGGCCCCGCAGAGTATTTCTCATAATAAGAACACCAAGAAAATGACATTTCAAAAGAAGAGTGGAAGCCTGCAGAAGAGCTTGCACAGTGCCCTTCCTGCCAGAGTTAACAGAGAAAAGTGCAAAAATCTACCTGCCCAGAAATCCAGTAGCAGCACCATTTCATTACGAGAACGGATCGTATCCTTGCAGCAACAGAACAGTTTGCTTCAGAACGCCAGGAGAGCAGCAGAGGCGTCTGCTAAGGAGTATAAAGAAGCGAACGAGAAGCTCCTCCATCAACAGCAGGTCAGCGATCACCGATTCCAGACCAGCAGACAGACAATAAAG
Peptide sequence:
MLHTNYRAVKEQLKQWEEDSGMAESRQMKRAEPHQLRQEDSDAVWNELAYFKRENQELMVQKMTLQDELDELKMHMSIDKTTIQELNRCMAEKREEQLFRQHEDAEVKKSTPEKNEKAISEETLQKVIELENRLKSFEKNSRKLKEESKRLKKENDFLKSHLKHYQEDSEAREKELEQLLRVSKDVEHDKSELQTKITALETEVTTLRRQVTEAKALRGKDEEVVCPEERAHRPTDKAKSEMATTDVRARRCDCKTATTKVKFKAAKRKCSVGRHHTVLNHSIKVMSHVENLSKDGWEDVSEGSSDSETQTFQNLGTIIVETSQNISPIEDGRNQKEIDQTEGSCAQQRAMQTYSCEDIKAPQSISHNKNTKKMTFQKKSGSLQKSLHSALPARVNREKCKNLPAQKSSSSTISLRERIVSLQQQNSLLQNARRAAEASAKEYKEANEKLLHQQQVSDHRFQTSRQTIKSQENDELRDAHEKRKERLQMLHTNYRAVKEQLKQWEEDSGMAESRQMKRAEPHQLRQEDSDAVWNELAYFKRENQELMVQKMTLQDELDELKMHMSIDKTTIQELNRCMAEKREEQLFRQHEDAEVKKSTPEKNEKAISEETLQKVIELENRLKSFEKNSRKLKEESKRLKKENDFLKSHLKHYQEDSEAREKELEQLLRVSKDVEHDKSELQTKITALETEVTTLRRQVTEAKALRGKDEEVVCPEERAHRPTDKAKSEMATTDVRARRCDCKTATTKVKFKAAKRKCSVGRHHTVLNHSIKVMSHVENLSKDGWEDVSEGSSDSETQTFQNLGTIIVETSQNISPIEDGRNQKEIDQTEGSCAQQRAMQTYSCEDIKAPQSISHNKNTKKMTFQKKSGSLQKSLHSALPARVNREKCKNLPAQKSSSSTISLRERIVSLQQQNSLLQNARRAAEASAKEYKEANEKLLHQQQVSDHRFQTSRQTIK
IRESfinder result
IRESfinder score
0.391635402
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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