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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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Institute of Life sciences, Bhubaneswar, India

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