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mmu_circAlms1_540

Basic information of circular RNA
PanCircBase ID:

mmu_circAlms1_540

mm39_Chr. Position ID:

chr6|85584453|85592389|+

Gene name:

Alms1

Transcript:

ENSMUST00000072018.6

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

4,5,6,7

Exon/intron offsets:

0,1514,3346,7776

Genomic length:

7936

Exon/intron sizes in nt:

121,140,119,160

Flanking exon/introns:

chr6:85578373-85584453|chr6:85592389-85596415

Splice length:

540

Other database IDs:

circBase: mmu_circ_0013565, CIRCpedia: MMU_CIRCpedia_32106, circAtlas: mmu-Alms1_0012

circAtlas: hsa-ALMS1_0055, CIRCpedia: HSA_CIRCpedia_42312

Human Ortholog IDs:
Mature spliced Sequence:

TGATACAGGATAACTTTGCTGCTCCTGATTTGCCTTTGCTGACATGTTTGATACAAGACCAAGAAGAGGTTGAGCCTGATTCCTTGTTTCAACAAAGTGAACTAGAATTTGCACCTTTGAGAGGAATTCCTGATAAGTCTGAAGATTCTGAATGGCTTGCTCGACCATCAGAAGTTAGTGAAGCTTTAATCCAAGCCACCTCAGAAACATCTTCAGACTTAGCTAACAGTTGCTTTAGTATATCTCAGCATCCACTTACAGAGGGCCTGCAGGGGAAGGCTGAATCTGGTGTCCTTACTAGGTGTGGTGATGCTAAGTACTCCAGCCTTTATGAAAACCTTGGTGCACAGAGTGAAAGAATTGCTGTATTGCAGAGAGAGGTAGGTTGTTCTAATCTGGGCATTAGCCAGGCTTCTCCATCTTCATTGCCTTCATTTGTTCCTCAAGAACCAACCAGTGAGCCGGAATACCATTCCTCCAATCTCAGAATGTTGAGGGTATCTCCCGACACTCTGCTAACAACGCATACACATTCAGCAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CCAACCAGTGAGCCGGAATA

59.75

GGCTCAACCTCTTCTTGGTCT

59.65

167

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

AACCAGTGAGCCGGAATACC

59.75

GGCTCAACCTCTTCTTGGTCT

59.65

165

PCR template sequence:

CCTCAAGAACCAACCAGTGAGCCGGAATACCATTCCTCCAATCTCAGAATGTTGAGGGTATCTCCCGACACTCTGCTAACAACGCATACACATTCAGCAGTGATACAGGATAACTTTGCTGCTCCTGATTTGCCTTTGCTGACATGTTTGATACAAGACCAAGAAGAGGTTGAGCCTGATTCCTTGTTTCAACAAAGTGA

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

9

Interacting miRNAs (#binding sites)

mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-19a-3p(1), mmu-miR-18a-5p(1), mmu-miR-1187(1), mmu-miR-335-3p(1), mmu-miR-484(1), mmu-miR-3470b(1), mmu-miR-574-5p(1)

siRNAs for circular RNA silencing
Junction sequence

ACACATTCAGCAGTGATACAGGATAA

siRNA sets

TTATCCTGTATCACTGCTG, TGTATCACTGCTGAATGTG, TATCCTGTATCACTGCTGA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCALMS1_540_ORF_1

0.9879

-0.048793574

0.653429512

591

ORF sequence:

ATGTTGAGGGTATCTCCCGACACTCTGCTAACAACGCATACACATTCAGCAGTGATACAGGATAACTTTGCTGCTCCTGATTTGCCTTTGCTGACATGTTTGATACAAGACCAAGAAGAGGTTGAGCCTGATTCCTTGTTTCAACAAAGTGAACTAGAATTTGCACCTTTGAGAGGAATTCCTGATAAGTCTGAAGATTCTGAATGGCTTGCTCGACCATCAGAAGTTAGTGAAGCTTTAATCCAAGCCACCTCAGAAACATCTTCAGACTTAGCTAACAGTTGCTTTAGTATATCTCAGCATCCACTTACAGAGGGCCTGCAGGGGAAGGCTGAATCTGGTGTCCTTACTAGGTGTGGTGATGCTAAGTACTCCAGCCTTTATGAAAACCTTGGTGCACAGAGTGAAAGAATTGCTGTATTGCAGAGAGAGGTAGGTTGTTCTAATCTGGGCATTAGCCAGGCTTCTCCATCTTCATTGCCTTCATTTGTTCCTCAAGAACCAACCAGTGAGCCGGAATACCATTCCTCCAATCTCAGAATGTTGAGGGTATCTCCCGACACTCTGCTAACAACGCATACACATTCAGCA

Peptide sequence:

MLRVSPDTLLTTHTHSAVIQDNFAAPDLPLLTCLIQDQEEVEPDSLFQQSELEFAPLRGIPDKSEDSEWLARPSEVSEALIQATSETSSDLANSCFSISQHPLTEGLQGKAESGVLTRCGDAKYSSLYENLGAQSERIAVLQREVGCSNLGISQASPSSLPSFVPQEPTSEPEYHSSNLRMLRVSPDTLLTTHTHSA

IRESfinder result

IRESfinder score

0.740393836

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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