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mmu_circ9130401M01Rik_804

Basic information of circular RNA
PanCircBase ID:

mmu_circ9130401M01Rik_804

mm39_Chr. Position ID:

chr15|57888669|57895475|-

Gene name:

9130401M01Rik

Transcript:

ENSMUST00000100655.5

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

5,4,3,2

Exon/intron offsets:

0,3340,5683,6710

Genomic length:

6806

Exon/intron sizes in nt:

133,431,144,96

Flanking exon/introns:

chr15:57885959-57888669|chr15:57895475-57897479

Splice length:

804

Other database IDs:

circAtlas: mmu-9130401M01Rik_0008

circBase: hsa_circ_0002788, circAtlas: hsa-C8orf76_0002, CIRCpedia: HSA_CIRCpedia_59965

Human Ortholog IDs:
Mature spliced Sequence:

TGGTTTTATGAAGAGACAGAATGTAGTGACGATATTGAAGTTCTCACTCTCAAGAAATTCAGAGGGGACCTGGCCTACAGACGACAGGAATACGAGAAAGCCCTGCAGGAATACTCCAGTATCTCCGAACAGTTACCATCTACTAATTTTGCCATGAAAAGGGATGTCCAAGAAGGCCAGGCTCGGTGTCTGGCTCACCTTGGGAGGCATGAGGAGGCGCTGGAGATGGCAGCAGACCTGGAAAGCAAAGCCACCAACACAGACCATCTGACCGTGGTGCTCCACCTCCACCTGGCCGTCTTTTCCAGCCTGCAGAGCCGGGAGCACACGATCCTCTGCCTGCACAAGCTGATTGCTTTGCACCCGCTCAACCCGTGGAGCTGGTGTAAGCTGGCAGAGGCATACCTGAGTCCAGGGCCCGGCCTGCCAGCAGGCGTGTCACCGCAGGGACAGAAGAGTTCTGCCTCAAGTGACAAGGCCGTCGGTCCCTCCTCTGTACACTCGGGAACAGGCTCTCTTTTGTCTTTGCCCACGACCTTGCCTGAGAATGCACTGCTCTCCGTGGAAGCGAGTGGTAGTGCTCAGGAGAATATGCCTTCCCTGGCAAGGCGGAGGGAAGAGGCACAGATGGAGGCTCGGAGGAAAGCATGCGCCTCTCTGCTCCGCGCCAGGCTCCTGCTTCAGCTCGCCCAGTCTCAGCAAACATCATTCGCGTTGGAGAAGAACTTGAGGACTCAGCAGGAAATTGCAGGGAAAGTGAAGGACTTCAACTTTAGGGAAGATACTTTGCTGTTGATGGAGGAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TCAGCAGGAAATTGCAGGGA

59.59

GCCAGGTCCCCTCTGAATTT

59.67

144

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TCAGCAGGAAATTGCAGGGA

59.59

TTCCTGTCGTCTGTAGGCCA

60.54

160

PCR template sequence:

ATCATTCGCGTTGGAGAAGAACTTGAGGACTCAGCAGGAAATTGCAGGGAAAGTGAAGGACTTCAACTTTAGGGAAGATACTTTGCTGTTGATGGAGGAGTGGTTTTATGAAGAGACAGAATGTAGTGACGATATTGAAGTTCTCACTCTCAAGAAATTCAGAGGGGACCTGGCCTACAGACGACAGGAATACGAGAAAG

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

8

Interacting miRNAs (#binding sites)

mmu-miR-19b-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-19a-3p(1), mmu-miR-148b-3p(1), mmu-miR-298-5p(1), mmu-miR-370-3p(1), mmu-miR-540-3p(1)

siRNAs for circular RNA silencing
Junction sequence

GTTGATGGAGGAGTGGTTTTATGAAG

siRNA sets

TTCATAAAACCACTCCTCC, AAACCACTCCTCCATCAAC, CTTCATAAAACCACTCCTC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRC9130401M01RIK_804_ORF_1

1.0227

0.286485218

0.999749608

1455

ORF sequence:

ATGAAAAGGGATGTCCAAGAAGGCCAGGCTCGGTGTCTGGCTCACCTTGGGAGGCATGAGGAGGCGCTGGAGATGGCAGCAGACCTGGAAAGCAAAGCCACCAACACAGACCATCTGACCGTGGTGCTCCACCTCCACCTGGCCGTCTTTTCCAGCCTGCAGAGCCGGGAGCACACGATCCTCTGCCTGCACAAGCTGATTGCTTTGCACCCGCTCAACCCGTGGAGCTGGTGTAAGCTGGCAGAGGCATACCTGAGTCCAGGGCCCGGCCTGCCAGCAGGCGTGTCACCGCAGGGACAGAAGAGTTCTGCCTCAAGTGACAAGGCCGTCGGTCCCTCCTCTGTACACTCGGGAACAGGCTCTCTTTTGTCTTTGCCCACGACCTTGCCTGAGAATGCACTGCTCTCCGTGGAAGCGAGTGGTAGTGCTCAGGAGAATATGCCTTCCCTGGCAAGGCGGAGGGAAGAGGCACAGATGGAGGCTCGGAGGAAAGCATGCGCCTCTCTGCTCCGCGCCAGGCTCCTGCTTCAGCTCGCCCAGTCTCAGCAAACATCATTCGCGTTGGAGAAGAACTTGAGGACTCAGCAGGAAATTGCAGGGAAAGTGAAGGACTTCAACTTTAGGGAAGATACTTTGCTGTTGATGGAGGAGTGGTTTTATGAAGAGACAGAATGTAGTGACGATATTGAAGTTCTCACTCTCAAGAAATTCAGAGGGGACCTGGCCTACAGACGACAGGAATACGAGAAAGCCCTGCAGGAATACTCCAGTATCTCCGAACAGTTACCATCTACTAATTTTGCCATGAAAAGGGATGTCCAAGAAGGCCAGGCTCGGTGTCTGGCTCACCTTGGGAGGCATGAGGAGGCGCTGGAGATGGCAGCAGACCTGGAAAGCAAAGCCACCAACACAGACCATCTGACCGTGGTGCTCCACCTCCACCTGGCCGTCTTTTCCAGCCTGCAGAGCCGGGAGCACACGATCCTCTGCCTGCACAAGCTGATTGCTTTGCACCCGCTCAACCCGTGGAGCTGGTGTAAGCTGGCAGAGGCATACCTGAGTCCAGGGCCCGGCCTGCCAGCAGGCGTGTCACCGCAGGGACAGAAGAGTTCTGCCTCAAGTGACAAGGCCGTCGGTCCCTCCTCTGTACACTCGGGAACAGGCTCTCTTTTGTCTTTGCCCACGACCTTGCCTGAGAATGCACTGCTCTCCGTGGAAGCGAGTGGTAGTGCTCAGGAGAATATGCCTTCCCTGGCAAGGCGGAGGGAAGAGGCACAGATGGAGGCTCGGAGGAAAGCATGCGCCTCTCTGCTCCGCGCCAGGCTCCTGCTTCAGCTCGCCCAGTCTCAGCAAACATCATTCGCGTTGGAGAAGAACTTGAGGACTCAGCAGGAAATTGCAGGGAAAGTGAAGGACTTCAACTTTAGGGAAGATACTTTGCTGTTGATGGAGGAG

Peptide sequence:

MKRDVQEGQARCLAHLGRHEEALEMAADLESKATNTDHLTVVLHLHLAVFSSLQSREHTILCLHKLIALHPLNPWSWCKLAEAYLSPGPGLPAGVSPQGQKSSASSDKAVGPSSVHSGTGSLLSLPTTLPENALLSVEASGSAQENMPSLARRREEAQMEARRKACASLLRARLLLQLAQSQQTSFALEKNLRTQQEIAGKVKDFNFREDTLLLMEEWFYEETECSDDIEVLTLKKFRGDLAYRRQEYEKALQEYSSISEQLPSTNFAMKRDVQEGQARCLAHLGRHEEALEMAADLESKATNTDHLTVVLHLHLAVFSSLQSREHTILCLHKLIALHPLNPWSWCKLAEAYLSPGPGLPAGVSPQGQKSSASSDKAVGPSSVHSGTGSLLSLPTTLPENALLSVEASGSAQENMPSLARRREEAQMEARRKACASLLRARLLLQLAQSQQTSFALEKNLRTQQEIAGKVKDFNFREDTLLLMEE

IRESfinder result

IRESfinder score

0.475379894

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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