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mmu_circRab4a_414
Basic information of circular RNA
PanCircBase ID:
mmu_circRab4a_414
mm39_Chr. Position ID:
chr8|124550552|124557126|+
Gene name:
Rab4a
Transcript:
ENSMUST00000118535.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,3510,5182,6419
Genomic length:
6574
Exon/intron sizes in nt:
8,11,15,63,155
Flanking exon/introns:
chr8:124532905-124550552|chr8:124557126-124559541
Splice length:
414
Other database IDs:
circAtlas: mmu-Rab4a_0002
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ATTTCTTGTTTAAATTCTTGGTCATCGGAAATGCGGGAACTGGCAAATCTTGCTTGCTTCATCAGTTCATTGAAAAGAAATTCAAAGATGACTCAAATCATACCATAGGAGTGGAATTTGGCTCAAAGATAATAAATGTCGGTGGTAAATATGTAAAGTTACAGATATGGGACACGGCCGGCCAGGAGCGGTTCAGGTCTGTGACGAGAAGCTACTACAGAGGTGCAGCTGGGGCACTCCTTGTCTATGACATCACCAGCCGAGAAACCTACAATGCGCTTACTAATTGGTTAACAGATGCCAGAATGCTGGCGAGCCAGAACATCGTCCTTATCCTCTGCGGGAACAAGAAGGACTTGGATGCCGACCGGGAAGTCACCTTCCTCGAAGCCTCCAGGTTCGCACAAGAGAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATCGTCCTTATCCTCTGCGG
59.04
CAAGATTTGCCAGTTCCCGC
60.11
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGTCCTTATCCTCTGCGGGA
61.11
CAAGATTTGCCAGTTCCCGC
60.11
141
PCR template sequence:
AGCCAGAACATCGTCCTTATCCTCTGCGGGAACAAGAAGGACTTGGATGCCGACCGGGAAGTCACCTTCCTCGAAGCCTCCAGGTTCGCACAAGAGAATGATTTCTTGTTTAAATTCTTGGTCATCGGAAATGCGGGAACTGGCAAATCTTGCTTGCTTCATCAGTTCATTGAAAAGAAATTCAAAGATGACTCAAATCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(1), mmu-miR-138-5p(1), mmu-miR-680(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCACAAGAGAATGATTTCTTGTTTAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAB4A_414_ORF_1
1.1695
0.289031542
0.865417932
522
ORF sequence:
ATGCTGGCGAGCCAGAACATCGTCCTTATCCTCTGCGGGAACAAGAAGGACTTGGATGCCGACCGGGAAGTCACCTTCCTCGAAGCCTCCAGGTTCGCACAAGAGAATGATTTCTTGTTTAAATTCTTGGTCATCGGAAATGCGGGAACTGGCAAATCTTGCTTGCTTCATCAGTTCATTGAAAAGAAATTCAAAGATGACTCAAATCATACCATAGGAGTGGAATTTGGCTCAAAGATAATAAATGTCGGTGGTAAATATGTAAAGTTACAGATATGGGACACGGCCGGCCAGGAGCGGTTCAGGTCTGTGACGAGAAGCTACTACAGAGGTGCAGCTGGGGCACTCCTTGTCTATGACATCACCAGCCGAGAAACCTACAATGCGCTTACTAATTGGTTAACAGATGCCAGAATGCTGGCGAGCCAGAACATCGTCCTTATCCTCTGCGGGAACAAGAAGGACTTGGATGCCGACCGGGAAGTCACCTTCCTCGAAGCCTCCAGGTTCGCACAAGAGAAT
Peptide sequence:
MLASQNIVLILCGNKKDLDADREVTFLEASRFAQENDFLFKFLVIGNAGTGKSCLLHQFIEKKFKDDSNHTIGVEFGSKIINVGGKYVKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVLILCGNKKDLDADREVTFLEASRFAQEN
IRESfinder result
IRESfinder score
0.423381109
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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