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mmu_circKhdrbs3_523

Basic information of circular RNA
PanCircBase ID:

mmu_circKhdrbs3_523

mm39_Chr. Position ID:

chr15|68866900|68896688|+

Gene name:

Khdrbs3

Transcript:

ENSMUST00000022954.7

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

2,3,4,5

Exon/intron offsets:

0,18306,22276,29648

Genomic length:

29788

Exon/intron sizes in nt:

1,19,11,71,47,140

Flanking exon/introns:

chr15:68800682-68866900|chr15:68896688-68901563

Splice length:

523

Other database IDs:

circBase: mmu_circ_0005746, CIRCpedia: MMU_CIRCpedia_27080, circAtlas: mmu-Khdrbs3_0005

circBase: hsa_circ_0135838, circAtlas: hsa-KHDRBS3_0004, CIRCpedia: HSA_CIRCpedia_69486

Human Ortholog IDs:
Mature spliced Sequence:

AAATAGAAAAGTTTCAAAAGGGAGAAGGCAAGGAGGAAGAGAAGTACATTGACGTGGTGATAAACAAGAACATGAAGCTGGGACAGAAGGTGCTGATTCCCGTGAAGCAGTTTCCCAAGTTCAACTTTGTGGGGAAGCTTTTGGGTCCGCGTGGCAATTCCCTGAAGCGCTTACAAGAAGAAACGTTGACAAAAATGTCCATCCTTGGCAAAGGTTCCATGAGAGACAAGGCAAAGGAGGAAGAGCTGAGGAAAAGTGGAGAAGCGAAGTACTTTCACCTCAATGACGACCTGCACGTGCTCATTGAAGTGTTCGCACCCCCAGCAGAAGCATATGCCCGGATGGGGCACGCCTTGGAAGAGATCAAGAAATTCCTGATCCCTGACTATAATGATGAAATCAGGCAAGCACAACTCCAGGAGTTAACATATTTGAATGGAGGTTCAGAAAATGCAGATGTCCCAGTGGTTCGAGGGAAATCTACTTTGCGTACGAGAGGTGTAACTACACCAGCAATAACCAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TGCAGATGTCCCAGTGGTTC

59.96

CACCTTCTGTCCCAGCTTCA

59.6

164

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GATGTCCCAGTGGTTCGAGG

60.11

CACCTTCTGTCCCAGCTTCA

59.6

160

PCR template sequence:

TAACATATTTGAATGGAGGTTCAGAAAATGCAGATGTCCCAGTGGTTCGAGGGAAATCTACTTTGCGTACGAGAGGTGTAACTACACCAGCAATAACCAGAAATAGAAAAGTTTCAAAAGGGAGAAGGCAAGGAGGAAGAGAAGTACATTGACGTGGTGATAAACAAGAACATGAAGCTGGGACAGAAGGTGCTGATTCC

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

7

Interacting miRNAs (#binding sites)

mmu-miR-211-5p(1), mmu-miR-138-5p(1), mmu-miR-136-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-218-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1)

siRNAs for circular RNA silencing
Junction sequence

CAGCAATAACCAGAAATAGAAAAGTT

siRNA sets

TTTCTATTTCTGGTTATTG, TTCTATTTCTGGTTATTGC, TTTTCTATTTCTGGTTATT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCKHDRBS3_523_ORF_1

0.9474

0.203127877

0.723479281

504

ORF sequence:

ATGAAGCTGGGACAGAAGGTGCTGATTCCCGTGAAGCAGTTTCCCAAGTTCAACTTTGTGGGGAAGCTTTTGGGTCCGCGTGGCAATTCCCTGAAGCGCTTACAAGAAGAAACGTTGACAAAAATGTCCATCCTTGGCAAAGGTTCCATGAGAGACAAGGCAAAGGAGGAAGAGCTGAGGAAAAGTGGAGAAGCGAAGTACTTTCACCTCAATGACGACCTGCACGTGCTCATTGAAGTGTTCGCACCCCCAGCAGAAGCATATGCCCGGATGGGGCACGCCTTGGAAGAGATCAAGAAATTCCTGATCCCTGACTATAATGATGAAATCAGGCAAGCACAACTCCAGGAGTTAACATATTTGAATGGAGGTTCAGAAAATGCAGATGTCCCAGTGGTTCGAGGGAAATCTACTTTGCGTACGAGAGGTGTAACTACACCAGCAATAACCAGAAATAGAAAAGTTTCAAAAGGGAGAAGGCAAGGAGGAAGAGAAGTACATTGA

Peptide sequence:

MKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVLIEVFAPPAEAYARMGHALEEIKKFLIPDYNDEIRQAQLQELTYLNGGSENADVPVVRGKSTLRTRGVTTPAITRNRKVSKGRRQGGREVH

IRESfinder result

IRESfinder score

0.373115613

IRES/non IRES

non-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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