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mmu_circRanbp9_842

Basic information of circular RNA
PanCircBase ID:

mmu_circRanbp9_842

mm39_Chr. Position ID:

chr13|43573051|43589618|-

Gene name:

Ranbp9

Transcript:

ENSMUST00000144326.4

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

7

Exon/intron indexes:

9,8,7,6,5,4,3

Exon/intron offsets:

0,1635,2975,5454,10872,15238,16514

Genomic length:

16567

Exon/intron sizes in nt:

191,109,113,185,23,168,53

Flanking exon/introns:

chr13:43569945-43573051|chr13:43589618-43615187

Splice length:

842

Other database IDs:

circAtlas: mmu-Ranbp9_0017

circBase: hsa_circ_0075658, circAtlas: hsa-RANBP9_0013, CIRCpedia: HSA_CIRCpedia_99103

Human Ortholog IDs:
Mature spliced Sequence:

CTACATGGGAATTGGTCTTTCTGCTCAAGGTGTGAACATGAATAGACTACCAGGTTGGGATAAACATTCATATGGTTACCATGGGGATGATGGACATTCATTTTGTTCTTCTGGAACTGGACAACCGTATGGACCAACTTTTACAACTGGTGATGTCATTGGCTGTTGTGTTAATCTTATCAACAATACCTGCTTTTACACGAAGAATGGACATAGTTTAGGTATTGCTTTCACCGACTTACCGCCAAATTTGTATCCTACTGTGGGGCTTCAGACACCAGGAGAAGTGGTTGATGCCAACTTTGGGCAACATCCTTTTGTGTTTGATATAGAAGACTACATGCGAGAATGGAGAACCAAAATACAGGCCCAGATAGACCGCTTTCCTATCGGGGATCGAGAAGGAGAATGGCAGACCATGATCCAAAAAATGGTTTCATCTTATTTAGTCCACCATGGGTACTGTGCCACAGCAGAGGCCTTTGCCAGATCTACAGACCAGACTGTTCTAGAAGAATTAGCTTCCATTAAGAATAGACAAAGAATTCAGAAGTTGGTGTTAGCAGGACGAATGGGAGAAGCCATTGAAACAACACAACAGTTATACCCAAGTTTACTTGAAAGAAATCCCAATCTCCTTTTCACATTAAAAGTACGTCAGTTTATAGAAATGGTGAATGGTACAGACAGTGAAGTGCGGTGTTTGGGAGGCCGAAGTCCAAAATCTCAAGACAGTTATCCCGTCAGTCCTCGACCCTTTAGTAGTCCAAGCATGAGCCCCAGTCATGGAATGAGTATCCACAGCTTAGCACCAGGCAAAAGCAGCACTGCACATTTTTCTG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ATCCACAGCTTAGCACCAGG

59.75

ATGTCCATCATCCCCATGGT

58.46

143

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CAAGCATGAGCCCCAGTCAT

60.4

CCATCATCCCCATGGTAACCA

59.5

168

PCR template sequence:

GTCAGTCCTCGACCCTTTAGTAGTCCAAGCATGAGCCCCAGTCATGGAATGAGTATCCACAGCTTAGCACCAGGCAAAAGCAGCACTGCACATTTTTCTGCTACATGGGAATTGGTCTTTCTGCTCAAGGTGTGAACATGAATAGACTACCAGGTTGGGATAAACATTCATATGGTTACCATGGGGATGATGGACATTCA

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

6

Interacting miRNAs (#binding sites)

mmu-miR-207(2), mmu-miR-150-5p(1), mmu-miR-135a-5p(1), mmu-miR-26a-5p(1), mmu-miR-26b-5p(1), mmu-miR-490-3p(1)

siRNAs for circular RNA silencing
Junction sequence

GCACATTTTTCTGCTACATGGGAATT

siRNA sets

AATTCCCATGTAGCAGAAA, CATGTAGCAGAAAAATGTG, ATTCCCATGTAGCAGAAAA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCRANBP9_842_ORF_1

0.7837

0.004137481

0.923557413

873

ORF sequence:

ATGGGAATTGGTCTTTCTGCTCAAGGTGTGAACATGAATAGACTACCAGGTTGGGATAAACATTCATATGGTTACCATGGGGATGATGGACATTCATTTTGTTCTTCTGGAACTGGACAACCGTATGGACCAACTTTTACAACTGGTGATGTCATTGGCTGTTGTGTTAATCTTATCAACAATACCTGCTTTTACACGAAGAATGGACATAGTTTAGGTATTGCTTTCACCGACTTACCGCCAAATTTGTATCCTACTGTGGGGCTTCAGACACCAGGAGAAGTGGTTGATGCCAACTTTGGGCAACATCCTTTTGTGTTTGATATAGAAGACTACATGCGAGAATGGAGAACCAAAATACAGGCCCAGATAGACCGCTTTCCTATCGGGGATCGAGAAGGAGAATGGCAGACCATGATCCAAAAAATGGTTTCATCTTATTTAGTCCACCATGGGTACTGTGCCACAGCAGAGGCCTTTGCCAGATCTACAGACCAGACTGTTCTAGAAGAATTAGCTTCCATTAAGAATAGACAAAGAATTCAGAAGTTGGTGTTAGCAGGACGAATGGGAGAAGCCATTGAAACAACACAACAGTTATACCCAAGTTTACTTGAAAGAAATCCCAATCTCCTTTTCACATTAAAAGTACGTCAGTTTATAGAAATGGTGAATGGTACAGACAGTGAAGTGCGGTGTTTGGGAGGCCGAAGTCCAAAATCTCAAGACAGTTATCCCGTCAGTCCTCGACCCTTTAGTAGTCCAAGCATGAGCCCCAGTCATGGAATGAGTATCCACAGCTTAGCACCAGGCAAAAGCAGCACTGCACATTTTTCTGCTACATGGGAATTGGTCTTTCTGCTCAAGGTGTGA

Peptide sequence:

MGIGLSAQGVNMNRLPGWDKHSYGYHGDDGHSFCSSGTGQPYGPTFTTGDVIGCCVNLINNTCFYTKNGHSLGIAFTDLPPNLYPTVGLQTPGEVVDANFGQHPFVFDIEDYMREWRTKIQAQIDRFPIGDREGEWQTMIQKMVSSYLVHHGYCATAEAFARSTDQTVLEELASIKNRQRIQKLVLAGRMGEAIETTQQLYPSLLERNPNLLFTLKVRQFIEMVNGTDSEVRCLGGRSPKSQDSYPVSPRPFSSPSMSPSHGMSIHSLAPGKSSTAHFSATWELVFLLKV

IRESfinder result

IRESfinder score

0.683152632

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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