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mmu_circStk4_577

Basic information of circular RNA
PanCircBase ID:

mmu_circStk4_577

mm39_Chr. Position ID:

chr2|163925549|163938826|+

Gene name:

Stk4

Transcript:

ENSMUST00000018353.14

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

3,4,5,6

Exon/intron offsets:

0,2865,5211,13109

Genomic length:

13277

Exon/intron sizes in nt:

1,29,11,51,65,168

Flanking exon/introns:

chr2:163921513-163925549|chr2:163938826-163940358

Splice length:

577

Other database IDs:

CIRCpedia: MMU_CIRCpedia_11431, circAtlas: mmu-Stk4_0005

circBase: hsa_circ_0060523, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_133603

Human Ortholog IDs:
Mature spliced Sequence:

GTCTTATGGCAGCGTGTACAAGGCTATTCATAAAGAGACTGGCCAGATTGTTGCAATCAAGCAAGTGCCCGTGGAATCGGACCTGCAGGAGATAATCAAGGAAATCTCCATCATGCAGCAGTGTGACAGCCCTCACGTAGTCAAGTATTATGGCAGCTACTTTAAGAACACAGACCTGTGGATTGTTATGGAGTACTGTGGGGCTGGTTCTGTATCTGATATCATTCGGCTACGGAACAAGACGTTAACAGAAGATGAAATAGCTACAATATTACAATCAACTCTTAAGGGACTAGAATACCTTCATTTTATGAGAAAAATACACCGAGATATCAAGGCGGGAAATATTTTGCTAAACACAGAAGGCCATGCAAAGCTTGCAGACTTTGGAGTCGCAGGTCAACTTACAGATACCATGGCAAAGAGGAATACAGTAATAGGGACCCCGTTTTGGATGGCTCCTGAAGTTATTCAGGAAATTGGGTACAACTGTGTGGCAGACATCTGGTCTCTGGGAATAACTGCCATAGAAATGGCTGAAGGAAAGCCCCCATATGCTGATATCCATCCAATGAGG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TTGGGTACAACTGTGTGGCA

59.74

TGCAACAATCTGGCCAGTCT

59.89

153

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TTGGGTACAACTGTGTGGCA

59.74

CACGGGCACTTGCTTGATTG

60.39

171

PCR template sequence:

AATTGGGTACAACTGTGTGGCAGACATCTGGTCTCTGGGAATAACTGCCATAGAAATGGCTGAAGGAAAGCCCCCATATGCTGATATCCATCCAATGAGGGTCTTATGGCAGCGTGTACAAGGCTATTCATAAAGAGACTGGCCAGATTGTTGCAATCAAGCAAGTGCCCGTGGAATCGGACCTGCAGGAGATAATCAAG

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

3

Interacting miRNAs (#binding sites)

mmu-miR-101a-3p(1), mmu-miR-369-3p(1), mmu-miR-452-3p(1)

siRNAs for circular RNA silencing
Junction sequence

CCATCCAATGAGGGTCTTATGGCAGC

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCSTK4_577_ORF_1

0.8456

0.076474228

0.552015937

498

ORF sequence:

ATGCAGCAGTGTGACAGCCCTCACGTAGTCAAGTATTATGGCAGCTACTTTAAGAACACAGACCTGTGGATTGTTATGGAGTACTGTGGGGCTGGTTCTGTATCTGATATCATTCGGCTACGGAACAAGACGTTAACAGAAGATGAAATAGCTACAATATTACAATCAACTCTTAAGGGACTAGAATACCTTCATTTTATGAGAAAAATACACCGAGATATCAAGGCGGGAAATATTTTGCTAAACACAGAAGGCCATGCAAAGCTTGCAGACTTTGGAGTCGCAGGTCAACTTACAGATACCATGGCAAAGAGGAATACAGTAATAGGGACCCCGTTTTGGATGGCTCCTGAAGTTATTCAGGAAATTGGGTACAACTGTGTGGCAGACATCTGGTCTCTGGGAATAACTGCCATAGAAATGGCTGAAGGAAAGCCCCCATATGCTGATATCCATCCAATGAGGGTCTTATGGCAGCGTGTACAAGGCTATTCATAA

Peptide sequence:

MQQCDSPHVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRLRNKTLTEDEIATILQSTLKGLEYLHFMRKIHRDIKAGNILLNTEGHAKLADFGVAGQLTDTMAKRNTVIGTPFWMAPEVIQEIGYNCVADIWSLGITAIEMAEGKPPYADIHPMRVLWQRVQGYS

IRESfinder result

IRESfinder score

0.461609249

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

RPF, cORF, m6A

mmu_circStk4_001

Evidence
Peptide sequence:

MQQCDSPHVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRLRNKTLTEDEIATILQSTLKGLEYLHFMRKIHRDIKAGNILLNTEGHAKLADFGVAGQLTDTMAKRNTVIGTPFWMAPEVIQEIGYNCVADIWSLGITAIEMAEGKPPYADIHPMRVLWQRVQGYS*

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Institute of Life sciences, Bhubaneswar, India

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