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mmu_ciHnrnpk_1119

Basic information of circular RNA
PanCircBase ID:

mmu_ciHnrnpk_1119

mm39_Chr. Position ID:

chr13|58545850|58546969|-

Gene name:

Hnrnpk

Transcript:

ENSMUST00000116403.9

CircRNA type:

Circular intronic (ci)RNA

Exon/Intron count:

1

Exon/intron indexes:

6

Exon/intron offsets:

0

Genomic length:

1119

Exon/intron sizes in nt:

1119

Flanking exon/introns:

chr13:58545610-58546969

Splice length:

1119

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

GTAAGTATTAAACTACTGAACAAGCAAGCACATTCATTGTATGTTTCTAGAATTTTAAAGGTTCACATCTTAGAAATCACTGACTAGCTACAAACCATTTGTAATAATTAATGGTTATGTAAATGACTTCTTTTTTTTTAAAACCCTGATTAAGGTGGAACATAATTAAATCTTTTCATATTTTAATAAAACCCTTCAAATTAATTCATTTCAAATAAGATTAAAACATCTTAATTAGGAATGGAGACAAAGTGTAAAAACCCTTAATTGTATAATTCCTCTTGTATGTGTAAGAGGGATTTAGTCATTTCTGAAAGCCATTGAATATGGCTGATAAAAACTTTATTTCCTTTTTTTTTCTTTTAAATCATCTGTTCCACAGTTTGCAACATGGAGCTCATGCTGACTGATTTCTAAATATGGGTAATGAATAGATTAATCTTGGCAATCAGAACTGTTTGCCTAGGATTTGAGTCTTCATAATTTATAGTGGGTTGACTCTTGTGATTAGACACATTAAATGTTGGCAGCACCAGAAGTGTGTGTGTATTTCTAGAACTGATTACACCAAAATTTATTTTTTTCCCTCATACTATCTACATTTCTTAATGTTTATCTTGGTAAAATTGAGGCAAATAACTTTGAGTACCTAACAGTATTTCATTTCTCTTGGTAACAGATCTTTGTGTTTCTCTTAATAAACTTTAGATTTCGTTGTAATTTTTATAAATCTGCTTATAAGATGTGTTTTATACCTTATGAAACCAAATCAGTCTTAATATTTGGGGGTTTGGTGTGGGAATTTTTGTTTTGTCTTTGAACCTCTTTCCTCTTAATCCAGATGTTCTGTATAATTATCTGGGTTATTTCCCCATTTTCCTCAATTTCAGTAAACTTTTGAGTCATGACAGGTTTTGTGTCTACCCTCACGAGCCAGCCTGCTACTGAAACATTAAAAAACAAAACAAAACCTAGAACCATCATTTAAGGTCCTTAAATGTTAAGAAGCCACGGTCAGGTATAGAGAAGTCCATTATTGTGTTAGTCTTCAGAACAACTTAAGCTTGTTTCATTGAGAGTATGAGTATAGTTTGTATTAAATTAAAATTTATTGCTTTT

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AGTCTTCAGAACAACTTAAGCTTGT

58.88

TGGTTTGTAGCTAGTCAGTGA

56.33

173

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GTCTTCAGAACAACTTAAGCTTGT

57.64

TGGTTTGTAGCTAGTCAGTGA

56.33

172

PCR template sequence:

TATAGAGAAGTCCATTATTGTGTTAGTCTTCAGAACAACTTAAGCTTGTTTCATTGAGAGTATGAGTATAGTTTGTATTAAATTAAAATTTATTGCTTTTGTAAGTATTAAACTACTGAACAAGCAAGCACATTCATTGTATGTTTCTAGAATTTTAAAGGTTCACATCTTAGAAATCACTGACTAGCTACAAACCATTT

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

10

Interacting miRNAs (#binding sites)

mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-143-3p(1), mmu-miR-381-3p(1), mmu-miR-136-5p(1), mmu-miR-494-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-382-5p(1), mmu-miR-29b-2-5p(1)

siRNAs for circular RNA silencing
Junction sequence

ATTTATTGCTTTTGTAAGTATTAAAC

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIHNRNPK_1119_ORF_1

0.7189

-0.450283924

0.007463294

126

ORF sequence:

ATGAGTATAGTTTGTATTAAATTAAAATTTATTGCTTTTGTAAGTATTAAACTACTGAACAAGCAAGCACATTCATTGTATGTTTCTAGAATTTTAAAGGTTCACATCTTAGAAATCACTGACTAG

Peptide sequence:

MSIVCIKLKFIAFVSIKLLNKQAHSLYVSRILKVHILEITD

IRESfinder result

IRESfinder score

0.953360141

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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