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mmu_circSergef_562

Basic information of circular RNA
PanCircBase ID:

mmu_circSergef_562

mm39_Chr. Position ID:

chr7|46270984|46284980|-

Gene name:

Sergef

Transcript:

ENSMUST00000033127.12

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

5

Exon/intron indexes:

6,5,4,3,2

Exon/intron offsets:

0,4648,11099,12194,13860

Genomic length:

13996

Exon/intron sizes in nt:

11,46,19,51,56,136

Flanking exon/introns:

chr7:46268182-46270984|chr7:46284980-46289136

Splice length:

562

Other database IDs:

circBase: mmu_circ_0014226, CIRCpedia: MMU_CIRCpedia_20910, circAtlas: mmu-Sergef_0004

circAtlas: hsa-SERGEF_0005

Human Ortholog IDs:
Mature spliced Sequence:

GGTGCAAACAGCTATGGGCAACTTGGCCTTGGCCATAAGGAAGATGTGTTTCTGCCCCAGCAACTGAGTGACTTCTGTCAAGCTGGGTGTATCAAGAGTGTCACAGGAGGAGGAGGGCATTCTGCAGTTGTCACAGATGGAGGAGATCTTTTTGTTTGTGGCCTGAATAAAGATGGGCAGTTGGGGCTTGGTCACACAGAGGAAGTTCTGCGTTTTACCATCTGCAAGCCTCTCCGTGGTTGTCCCATCCGACAGGTGGCCTGTGGCTGGGACTTCACCATCATGCTTACAGAAAAAGGTCAAGTTCTGTCCTGTGGATCCAATGCCTTTGGCCAGTTAGGTGTGCCTCACGGCCCTCGCAAATGCGTGGTCCCCCAGGCCATTGAGTGCCTGAGAGAGAAGGTTGTTTGTGTCGCTGCTGGACTGAGGCATGCCTTAGCCACTACAGCGACTGGCAGTGTGTTCCAGTGGGGGACTGGCTTGGCATCTTCTGGTCGACGCCTGTGCCCTGGGCAGAATCTCCCACTGTTTTTGACAGCAAAGGAACCCAGCAGAGTGACAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GGACTGGCTTGGCATCTTCT

60.03

AAGTCACTCAGTTGCTGGGG

59.89

164

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TGGCTTGGCATCTTCTGGTC

60.32

AAGTCACTCAGTTGCTGGGG

59.89

160

PCR template sequence:

TTCCAGTGGGGGACTGGCTTGGCATCTTCTGGTCGACGCCTGTGCCCTGGGCAGAATCTCCCACTGTTTTTGACAGCAAAGGAACCCAGCAGAGTGACAGGGTGCAAACAGCTATGGGCAACTTGGCCTTGGCCATAAGGAAGATGTGTTTCTGCCCCAGCAACTGAGTGACTTCTGTCAAGCTGGGTGTATCAAGAGTG

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

4

Interacting miRNAs (#binding sites)

mmu-miR-503-5p(1), mmu-miR-382-5p(1), mmu-miR-324-3p(1), mmu-miR-224-5p(1)

siRNAs for circular RNA silencing
Junction sequence

AGCAGAGTGACAGGGTGCAAACAGCT

siRNA sets

TTTGCACCCTGTCACTCTG,TGTTTGCACCCTGTCACTC,TTGCACCCTGTCACTCTGC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCSERGEF_562_ORF_1

0.52

-0.020224355

0.110043034

318

ORF sequence:

ATGCTTACAGAAAAAGGTCAAGTTCTGTCCTGTGGATCCAATGCCTTTGGCCAGTTAGGTGTGCCTCACGGCCCTCGCAAATGCGTGGTCCCCCAGGCCATTGAGTGCCTGAGAGAGAAGGTTGTTTGTGTCGCTGCTGGACTGAGGCATGCCTTAGCCACTACAGCGACTGGCAGTGTGTTCCAGTGGGGGACTGGCTTGGCATCTTCTGGTCGACGCCTGTGCCCTGGGCAGAATCTCCCACTGTTTTTGACAGCAAAGGAACCCAGCAGAGTGACAGGGTGCAAACAGCTATGGGCAACTTGGCCTTGGCCATAA

Peptide sequence:

MLTEKGQVLSCGSNAFGQLGVPHGPRKCVVPQAIECLREKVVCVAAGLRHALATTATGSVFQWGTGLASSGRRLCPGQNLPLFLTAKEPSRVTGCKQLWATWPWP

IRESfinder result

IRESfinder score

0.588767654

IRES/non IRES

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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