top of page

mmu_circAhctf1_410

Basic information of circular RNA
PanCircBase ID:

mmu_circAhctf1_410

mm39_Chr. Position ID:

chr1|179617213|179620118|-

Gene name:

Ahctf1

Transcript:

ENSMUST00000027768.14

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

3

Exon/intron indexes:

7,6,5

Exon/intron offsets:

0,650,2697

Genomic length:

2905

Exon/intron sizes in nt:

8,51,17,208

Flanking exon/introns:

chr1:179615904-179617213|chr1:179620118-179621207

Splice length:

410

Other database IDs:

circAtlas: mmu-Ahctf1_0016

CIRCpedia: HSA_CIRCpedia_116991

Human Ortholog IDs:
Mature spliced Sequence:

ACCTTGAAGTTATCACTGGTATCCCAGCTGAAGTACCACACATCAGAGAGAGAGTGATGAGAGAGGGGCGCCACCTGTGCTTCCAGTTAGTAAGCCCATTGGGAGTAGCCATTTCTACTCTGAGTTACATCAACAGGACAAATCAGCTTGCTGTGGGTTTTTCTGATGGCTACTTAGCACTTTGGAACATGAAAAGCATGAAAAGAGAATACTATACACAGTTGGAAGGTGGAAGGGTTCCTGTCCATGCAGTTGCCTTTCAAGAGCCTGAGAATGATCCTCGTAACTGCTGTTATTTATGGGCTGTTCAGTCCACACAAGATAGTGAAGGGGATGTTTTGAGTTTGCATCTGCTTCAGCTGGCTTTTGGTGATAGAAAATGTTTGGCATCAGGGCAAATTTTATATGAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CTGCTTCAGCTGGCTTTTGG

60.04

TAACTGGAAGCACAGGTGGC

60.25

149

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GCTTCAGCTGGCTTTTGGTG

60.32

TAACTGGAAGCACAGGTGGC

60.25

147

PCR template sequence:

GTCCACACAAGATAGTGAAGGGGATGTTTTGAGTTTGCATCTGCTTCAGCTGGCTTTTGGTGATAGAAAATGTTTGGCATCAGGGCAAATTTTATATGAGACCTTGAAGTTATCACTGGTATCCCAGCTGAAGTACCACACATCAGAGAGAGAGTGATGAGAGAGGGGCGCCACCTGTGCTTCCAGTTAGTAAGCCCATT

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

9

Interacting miRNAs (#binding sites)

mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-20a-5p(1), mmu-miR-106b-5p(1), mmu-miR-217-5p(1), mmu-miR-27a-5p(1), mmu-miR-466a-5p(1), mmu-miR-466p-5p(1), mmu-miR-669d-5p(1)

siRNAs for circular RNA silencing
Junction sequence

AATTTTATATGAGACCTTGAAGTTAT

siRNA sets

TAACTTCAAGGTCTCATAT,ATAACTTCAAGGTCTCATA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAHCTF1_410_ORF_1

0.5211

-0.066017719

0.168364792

411

ORF sequence:

ATGAGAGAGGGGCGCCACCTGTGCTTCCAGTTAGTAAGCCCATTGGGAGTAGCCATTTCTACTCTGAGTTACATCAACAGGACAAATCAGCTTGCTGTGGGTTTTTCTGATGGCTACTTAGCACTTTGGAACATGAAAAGCATGAAAAGAGAATACTATACACAGTTGGAAGGTGGAAGGGTTCCTGTCCATGCAGTTGCCTTTCAAGAGCCTGAGAATGATCCTCGTAACTGCTGTTATTTATGGGCTGTTCAGTCCACACAAGATAGTGAAGGGGATGTTTTGAGTTTGCATCTGCTTCAGCTGGCTTTTGGTGATAGAAAATGTTTGGCATCAGGGCAAATTTTATATGAGACCTTGAAGTTATCACTGGTATCCCAGCTGAAGTACCACACATCAGAGAGAGAGTGA

Peptide sequence:

MREGRHLCFQLVSPLGVAISTLSYINRTNQLAVGFSDGYLALWNMKSMKREYYTQLEGGRVPVHAVAFQEPENDPRNCCYLWAVQSTQDSEGDVLSLHLLQLAFGDRKCLASGQILYETLKLSLVSQLKYHTSERE

IRESfinder result

IRESfinder score

0.670492825

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

logo.png

Institute of Life sciences, Bhubaneswar, India

bottom of page