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mmu_circRfx3_2035

Basic information of circular RNA
PanCircBase ID:

mmu_circRfx3_2035

mm39_Chr. Position ID:

chr19|27764013|27900666|-

Gene name:

Rfx3

Transcript:

ENSMUST00000165566.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

15

Exon/intron indexes:

16,15,14,13,12,11,10,9,8,7,6,5,4,3,2

Exon/intron offsets:

0,6997,13503,15768,19574,20179,26964,28871,39419,43997,50793,63097,80899,114165,136594

Genomic length:

136653

Exon/intron sizes in nt:

154,209,150,98,155,116,113,122,120,182,75,259,98,125,59

Flanking exon/introns:

chr19:27748071-27764013|chr19:27900666-27960253

Splice length:

2035

Other database IDs:

circAtlas: mmu-Rfx3_0061

Human Ortholog IDs:
Mature spliced Sequence:

AGATTTTTATCAGAGGAATGTAGACTGGAATCTGCAATGGTTCTCAAAATCCCAAAGTGAGACCATCATGCAGACTTCAGAGACGGGTTCAGACACAGGTTCGACAGTGACTCTGCAGACGTCTGTGGCTAGCCAAGCAGCAGTGCCTACACAGGTGGTACAGCAAGTGCCAGTGCAGCAGCAGGTGCAGCAGGTACAGACAGTTCAGCAGGTCCAACATGTCTACCCAGCTCAGGTGCAGTATGTGGAAGGAAGTGATACTGTCTATACCAATGGAGCAATCCGAACAACAACTTATCCCTACACAGAAACACAGATGTACAGCCAAAACACTGGAGGAAATTACTTTGATACTCAAGGAAGTTCTGCCCAGGTGACAACTGTGGTGTCCTCCCACAGTATGGTGGGTACTGGTGGGATTCAGATGGGCGTCACAGGAGGACAACTCATCAGCAGCTCGGGAGGAACCTATTTGATCGGCAATTCAATGGAGAACTCTGGTCACTCAGTGACACACACAACTCGGGCCTCCCCAGCAACAATTGAAATGGCGATTGAGACGCTGCAAAAGTCTGACGGTCTGTCCACTCACAGAAGCTCTCTTCTCAACAGCCATCTGCAATGGCTGCTGGACAATTATGAGACAGCGGAGGGAGTGAGCCTGCCGAGGAGCACGCTGTACAACCACTACCTTCGACACTGCCAGGAGCACAAGCTGGACCCGGTCAATGCCGCCTCTTTCGGAAAACTAATAAGGTCCATTTTTATGGGGCTACGAACTAGGAGATTAGGCACTAGAGGAAACTCCAAATACCATTACTATGGGATTCGTGTGAAGCCAGATTCTCCTCTTAACCGTCTACAAGAAGATATGCAGTACATGGCTATGAGGCAGCAGCCCATGCAACAGAAGCAAAGGTACAAGCCTATGCAGAAAGTGGATGGGGTTGCAGATGGTTTCACAGGAAGTGGCCAACAGACAGGCACATCTGTTGAGCAAACTGTAATTGCCCAAAGTCAACATCATCAACAGTTTTTAGATGCATCTCGAGCACTTCCAGAGTTTGGAGAAGTTGAAATCTCTTCTCTGCCAGATGGTACTACCTTTGAGGATATCAAGTCACTGCAGAGTCTTTATCGAGAGCACTGTGAGGCAATACTGGACGTTGTTGTGAATCTTCAGTTTAGCCTGATAGAAAAACTGTGGCAAACATTCTGGCGCTATTCCCCATCTACTCCAGCCGACGGCACTACCATCACGGAATCAAGCAATCTGAGTGAAATAGAAAGTCGACTTCCGAAAGCAAAGCTGATAACTCTGTGCAAACATGAGTCTATCCTGAAATGGATGTGTAACTGTGACCATGGGATGTACCAGGCTTTGGTGGAGATTCTCATCCCCGACGTCCTTAGACCCATTCCTAGTGCCTTGACCCAAGCCATTCGAAATTTCGCAAAAAGCCTAGAAGGTTGGCTTTCAAATGCCATGAACAATATTCCACAGAGAATGATTCAAACCAAGGTTGCCGCTGTAAGTGCCTTTGCTCAGACTCTGCGAAGATACACATCGCTCAATCACCTGGCCCAGGCAGCCCGCGCAGTGCTTCAGAACACTTCCCAGATCAACCAGATGCTCAGTGACCTCAACCGCGTTGACTTTGCCAATGTCCAGGAGCAGGCTTCCTGGGTGTGCCAGTGTGATGACAACATGGTTCAGAGACTAGAAACAGACTTCAAGATGACCCTGCAGCAGCAGAGCACTCTGGAGCAGTGGGCTGCTTGGCTGGACAATGTGATGATGCAAGCGCTGAAGCCCTATGAAGGAAGGCCCAGCTTCCCGAAGGCTGCTCGGCAGTTTCTGCTCAAGTGGTCTTTCTACAGCTCCATGGTTATCCGGGACTTAACCTTGCGCAGTGCTGCTAGCTTTGGCTCCTTTCACCTGATCCGGCTGCTCTATGATGAGTACATGTTCTACTTAGTAGAGCATCGTGTTGCTCAAGTGACAGGAGAGACACCGATAGCAGTGATGGGTGAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CGTGTTGCTCAAGTGACAGG

59.42

CCTGTGTCTGAACCCGTCTC

60.04

147

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GCATCGTGTTGCTCAAGTGA

59.13

CCTGTGTCTGAACCCGTCTC

60.04

151

PCR template sequence:

TCACCTGATCCGGCTGCTCTATGATGAGTACATGTTCTACTTAGTAGAGCATCGTGTTGCTCAAGTGACAGGAGAGACACCGATAGCAGTGATGGGTGAGAGATTTTTATCAGAGGAATGTAGACTGGAATCTGCAATGGTTCTCAAAATCCCAAAGTGAGACCATCATGCAGACTTCAGAGACGGGTTCAGACACAGGT

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

30

Interacting miRNAs (#binding sites)

mmu-miR-136-5p(2), mmu-miR-370-3p(2), mmu-miR-29b-2-5p(2), mmu-miR-124-3p(1), mmu-miR-23b-3p(1), mmu-miR-140-5p(1), mmu-miR-134-5p(1), mmu-let-7a-5p(1), mmu-miR-199a-5p(1), mmu-miR-375-3p(1), mmu-miR-103-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-let-7c-5p(1), mmu-miR-15b-5p(1), mmu-miR-298-5p(1), mmu-miR-196a-5p(1), mmu-miR-23a-3p(1), mmu-let-7d-5p(1), mmu-miR-382-5p(1), mmu-miR-34b-5p(1), mmu-miR-107-3p(1), mmu-miR-98-5p(1), mmu-miR-499-5p(1), mmu-miR-207(1), mmu-miR-5101(1), mmu-miR-484(1), mmu-miR-542-5p(1)

siRNAs for circular RNA silencing
Junction sequence

AGTGATGGGTGAGAGATTTTTATCAG

siRNA sets

AAATCTCTCACCCATCACT, AAAATCTCTCACCCATCAC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCRFX3_2035_ORF_1

0.913

0.233940119

0.999993546

2028

ORF sequence:

ATGCAGACTTCAGAGACGGGTTCAGACACAGGTTCGACAGTGACTCTGCAGACGTCTGTGGCTAGCCAAGCAGCAGTGCCTACACAGGTGGTACAGCAAGTGCCAGTGCAGCAGCAGGTGCAGCAGGTACAGACAGTTCAGCAGGTCCAACATGTCTACCCAGCTCAGGTGCAGTATGTGGAAGGAAGTGATACTGTCTATACCAATGGAGCAATCCGAACAACAACTTATCCCTACACAGAAACACAGATGTACAGCCAAAACACTGGAGGAAATTACTTTGATACTCAAGGAAGTTCTGCCCAGGTGACAACTGTGGTGTCCTCCCACAGTATGGTGGGTACTGGTGGGATTCAGATGGGCGTCACAGGAGGACAACTCATCAGCAGCTCGGGAGGAACCTATTTGATCGGCAATTCAATGGAGAACTCTGGTCACTCAGTGACACACACAACTCGGGCCTCCCCAGCAACAATTGAAATGGCGATTGAGACGCTGCAAAAGTCTGACGGTCTGTCCACTCACAGAAGCTCTCTTCTCAACAGCCATCTGCAATGGCTGCTGGACAATTATGAGACAGCGGAGGGAGTGAGCCTGCCGAGGAGCACGCTGTACAACCACTACCTTCGACACTGCCAGGAGCACAAGCTGGACCCGGTCAATGCCGCCTCTTTCGGAAAACTAATAAGGTCCATTTTTATGGGGCTACGAACTAGGAGATTAGGCACTAGAGGAAACTCCAAATACCATTACTATGGGATTCGTGTGAAGCCAGATTCTCCTCTTAACCGTCTACAAGAAGATATGCAGTACATGGCTATGAGGCAGCAGCCCATGCAACAGAAGCAAAGGTACAAGCCTATGCAGAAAGTGGATGGGGTTGCAGATGGTTTCACAGGAAGTGGCCAACAGACAGGCACATCTGTTGAGCAAACTGTAATTGCCCAAAGTCAACATCATCAACAGTTTTTAGATGCATCTCGAGCACTTCCAGAGTTTGGAGAAGTTGAAATCTCTTCTCTGCCAGATGGTACTACCTTTGAGGATATCAAGTCACTGCAGAGTCTTTATCGAGAGCACTGTGAGGCAATACTGGACGTTGTTGTGAATCTTCAGTTTAGCCTGATAGAAAAACTGTGGCAAACATTCTGGCGCTATTCCCCATCTACTCCAGCCGACGGCACTACCATCACGGAATCAAGCAATCTGAGTGAAATAGAAAGTCGACTTCCGAAAGCAAAGCTGATAACTCTGTGCAAACATGAGTCTATCCTGAAATGGATGTGTAACTGTGACCATGGGATGTACCAGGCTTTGGTGGAGATTCTCATCCCCGACGTCCTTAGACCCATTCCTAGTGCCTTGACCCAAGCCATTCGAAATTTCGCAAAAAGCCTAGAAGGTTGGCTTTCAAATGCCATGAACAATATTCCACAGAGAATGATTCAAACCAAGGTTGCCGCTGTAAGTGCCTTTGCTCAGACTCTGCGAAGATACACATCGCTCAATCACCTGGCCCAGGCAGCCCGCGCAGTGCTTCAGAACACTTCCCAGATCAACCAGATGCTCAGTGACCTCAACCGCGTTGACTTTGCCAATGTCCAGGAGCAGGCTTCCTGGGTGTGCCAGTGTGATGACAACATGGTTCAGAGACTAGAAACAGACTTCAAGATGACCCTGCAGCAGCAGAGCACTCTGGAGCAGTGGGCTGCTTGGCTGGACAATGTGATGATGCAAGCGCTGAAGCCCTATGAAGGAAGGCCCAGCTTCCCGAAGGCTGCTCGGCAGTTTCTGCTCAAGTGGTCTTTCTACAGCTCCATGGTTATCCGGGACTTAACCTTGCGCAGTGCTGCTAGCTTTGGCTCCTTTCACCTGATCCGGCTGCTCTATGATGAGTACATGTTCTACTTAGTAGAGCATCGTGTTGCTCAAGTGACAGGAGAGACACCGATAGCAGTGATGGGTGAGAGATTTTTATCAGAGGAATGTAGACTGGAATCTGCAATGGTTCTCAAAATCCCAAAGTGA

Peptide sequence:

MQTSETGSDTGSTVTLQTSVASQAAVPTQVVQQVPVQQQVQQVQTVQQVQHVYPAQVQYVEGSDTVYTNGAIRTTTYPYTETQMYSQNTGGNYFDTQGSSAQVTTVVSSHSMVGTGGIQMGVTGGQLISSSGGTYLIGNSMENSGHSVTHTTRASPATIEMAIETLQKSDGLSTHRSSLLNSHLQWLLDNYETAEGVSLPRSTLYNHYLRHCQEHKLDPVNAASFGKLIRSIFMGLRTRRLGTRGNSKYHYYGIRVKPDSPLNRLQEDMQYMAMRQQPMQQKQRYKPMQKVDGVADGFTGSGQQTGTSVEQTVIAQSQHHQQFLDASRALPEFGEVEISSLPDGTTFEDIKSLQSLYREHCEAILDVVVNLQFSLIEKLWQTFWRYSPSTPADGTTITESSNLSEIESRLPKAKLITLCKHESILKWMCNCDHGMYQALVEILIPDVLRPIPSALTQAIRNFAKSLEGWLSNAMNNIPQRMIQTKVAAVSAFAQTLRRYTSLNHLAQAARAVLQNTSQINQMLSDLNRVDFANVQEQASWVCQCDDNMVQRLETDFKMTLQQQSTLEQWAAWLDNVMMQALKPYEGRPSFPKAARQFLLKWSFYSSMVIRDLTLRSAASFGSFHLIRLLYDEYMFYLVEHRVAQVTGETPIAVMGERFLSEECRLESAMVLKIPK

IRESfinder result

IRESfinder score

0.506411806

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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