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mmu_circArfgef1_647

Basic information of circular RNA
PanCircBase ID:

mmu_circArfgef1_647

mm39_Chr. Position ID:

chr1|10264481|10275134|-

Gene name:

Arfgef1

Transcript:

ENSMUST00000088615.11

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

10,9,8,7

Exon/intron offsets:

0,4586,5472,10551

Genomic length:

10653

Exon/intron sizes in nt:

2,35,13,41,76,102

Flanking exon/introns:

chr1:10259903-10264481|chr1:10275134-10279649

Splice length:

647

Other database IDs:

circAtlas: mmu-Arfgef1_0007

circAtlas: hsa-ARFGEF1_0003, CIRCpedia: HSA_CIRCpedia_69425

Human Ortholog IDs:
Mature spliced Sequence:

CATTATCTAAAAATGATATCTTGTATGATGGAGACTATGAAGAAAAGCCACTTGATATTGTCCAGAGCATTGTAGAAGAAATGGTGAACATCATTGTTGGAGACATGGGAGAAGGGATGGCTATCAGTGCAAGTACAGAAGGCAACACTGGAACTGTAGAAGATGGTAGTGACAGTGAAAACATCCAAGCAAATGGAATCCCAGGAACACCCATTTCTGTTGCATATACACCATCGTTACCTGACGACAGGTTATCTGTCTCCTCCAATGATACTCAGGAATCTGGAAATTCTTCAGGACCTTCACCTGGTGCTAAGTTTTCCCACATTTTACAAAAGGATGCCTTTCTAGTGTTCAGGTCATTGTGTAAGCTGTCAATGAAACCACTGTCAGATGGACCACCAGATCCAAAGTCTCATGAGTTACGGTCCAAGATTCTTTCATTGCAGTTGCTTCTGTCCATTCTGCAGAATGCAGGACCTGTTTTCAGGACAAATGAGATGTTTATTAATGCTATCAAGCAGTATCTATGTGTTGCACTCTCAAAAAACGGAGTCTCATCTGTTCCAGAGGTTTTTGAGCTTTCTCTTTCCATATTTCTTACTTTGTTGTCAAACTTCAAGACACATCTGAAGATGCAAATTGAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ACGGAGTCTCATCTGTTCCAG

59.18

GCTCTGGACAATATCAAGTGGC

59.38

166

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

ACGGAGTCTCATCTGTTCCA

58.08

GCTCTGGACAATATCAAGTGGC

59.38

166

PCR template sequence:

AAACGGAGTCTCATCTGTTCCAGAGGTTTTTGAGCTTTCTCTTTCCATATTTCTTACTTTGTTGTCAAACTTCAAGACACATCTGAAGATGCAAATTGAGCATTATCTAAAAATGATATCTTGTATGATGGAGACTATGAAGAAAAGCCACTTGATATTGTCCAGAGCATTGTAGAAGAAATGGTGAACATCATTGTTGG

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

14

Interacting miRNAs (#binding sites)

mmu-miR-140-5p(2), mmu-miR-199a-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-139-5p(1), mmu-miR-136-5p(1), mmu-miR-363-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-130b-3p(1), mmu-miR-301a-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1), mmu-miR-3065-5p(1)

siRNAs for circular RNA silencing
Junction sequence

GATGCAAATTGAGCATTATCTAAAAA

siRNA sets

TTTTTAGATAATGCTCAAT, TTTTAGATAATGCTCAATT, TTTAGATAATGCTCAATTT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCARFGEF1_647_ORF_1

0.8723

-0.019356714

0.711473035

642

ORF sequence:

ATGGTGAACATCATTGTTGGAGACATGGGAGAAGGGATGGCTATCAGTGCAAGTACAGAAGGCAACACTGGAACTGTAGAAGATGGTAGTGACAGTGAAAACATCCAAGCAAATGGAATCCCAGGAACACCCATTTCTGTTGCATATACACCATCGTTACCTGACGACAGGTTATCTGTCTCCTCCAATGATACTCAGGAATCTGGAAATTCTTCAGGACCTTCACCTGGTGCTAAGTTTTCCCACATTTTACAAAAGGATGCCTTTCTAGTGTTCAGGTCATTGTGTAAGCTGTCAATGAAACCACTGTCAGATGGACCACCAGATCCAAAGTCTCATGAGTTACGGTCCAAGATTCTTTCATTGCAGTTGCTTCTGTCCATTCTGCAGAATGCAGGACCTGTTTTCAGGACAAATGAGATGTTTATTAATGCTATCAAGCAGTATCTATGTGTTGCACTCTCAAAAAACGGAGTCTCATCTGTTCCAGAGGTTTTTGAGCTTTCTCTTTCCATATTTCTTACTTTGTTGTCAAACTTCAAGACACATCTGAAGATGCAAATTGAGCATTATCTAAAAATGATATCTTGTATGATGGAGACTATGAAGAAAAGCCACTTGATATTGTCCAGAGCATTGTAG

Peptide sequence:

MVNIIVGDMGEGMAISASTEGNTGTVEDGSDSENIQANGIPGTPISVAYTPSLPDDRLSVSSNDTQESGNSSGPSPGAKFSHILQKDAFLVFRSLCKLSMKPLSDGPPDPKSHELRSKILSLQLLLSILQNAGPVFRTNEMFINAIKQYLCVALSKNGVSSVPEVFELSLSIFLTLLSNFKTHLKMQIEHYLKMISCMMETMKKSHLILSRAL

IRESfinder result

IRESfinder score

0.74186691

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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