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mmu_circRab3gap1_786
Basic information of circular RNA
PanCircBase ID:
mmu_circRab3gap1_786
mm39_Chr. Position ID:
chr1|127862153|127866885|+
Gene name:
Rab3gap1
Transcript:
ENSMUST00000037649.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
18,19,20,21,22,23
Exon/intron offsets:
0,2921,3572,3781,4158,4629
Genomic length:
4732
Exon/intron sizes in nt:
13,82,28,97,10,41,16,100
Flanking exon/introns:
chr1:127858815-127862153|chr1:127866885-127870110
Splice length:
786
Other database IDs:
circAtlas: mmu-Rab3gap1_0016
circAtlas: hsa-RAB3GAP1_0029
Human Ortholog IDs:
Mature spliced Sequence:
GAACCAGCACCCATGACAGAAGATCTGCTGGAAGAGCAGTCTGAGGTCTTAGCAAAATTAGGGACATCTGCTGAGGGGGCGCACCTCCGCGCACGCATGCAGAGTGCCTGTCTCCTCTCCGATATGGAGTCTTTTAAGGCAGCTAATCCAGGCTGCTTTCTGGAAGATTTCGTGAGGTGGTACTCACCAAGGGACTACATTGAGGAGGAGGTGACTGACGAGAAGGGCAATGTGGTCCTGAAGGGGGAGCTGAGTGCCCGTATGAAGATCCCCAGCAACATGTGGGTAGAAGCCTGGGAGACTGCTAAGCCTGTGCCAGCACGACGTCAGAGGAGACTGTTTGATGACACCCGAGAGGCTGAAAAGGTCCTGCACTACCTGGCCATGCAGAAGCCTGCAGACCTAGCCAGGCACCTCCTGCCTTGTGTGATTCATGCAGCTGTTCTCAAGGTAAAGGAAGAAGAAAGTCTGGAAAACATTCCTTCTGTTAAGAAGATTATAAAGCAGATCATAGCCCATTCCAGCAAAGTTCTGCATTTCCCCAATCCTGAGGACAAGAAACTGGAAGAAATCATCCTTCAGATTACTACTGTGGAAGCTATAATAGCCCGAGCCCGGTCCCTGAAGGCCAAATTTGGAACTGAGAAGTGTGAGCACGAGGAGGAAAAGGAAGGTCTGGAAAGGTTTGTCAGCTGCCTGCTGGAGCAGCCTGAGGTATCAGTCACTGGGGCAGGAAGAGGACATGCTGGCCGCATCATCCACAAGCTGTTTGTGAATGCTCAGCGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TATCAGTCACTGGGGCAGGA
59.96
CCCCTCAGCAGATGTCCCTA
60.4
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTATCAGTCACTGGGGCAGG
59.82
CCCCTCAGCAGATGTCCCTA
60.4
150
PCR template sequence:
TGTCAGCTGCCTGCTGGAGCAGCCTGAGGTATCAGTCACTGGGGCAGGAAGAGGACATGCTGGCCGCATCATCCACAAGCTGTTTGTGAATGCTCAGCGGGAACCAGCACCCATGACAGAAGATCTGCTGGAAGAGCAGTCTGAGGTCTTAGCAAAATTAGGGACATCTGCTGAGGGGGCGCACCTCCGCGCACGCATGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-214-3p(1), mmu-miR-382-3p(1), mmu-miR-22-3p(1), mmu-miR-212-3p(1), mmu-miR-377-3p(1), mmu-miR-1187(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAATGCTCAGCGGGAACCAGCACCCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAB3GAP1_786_ORF_1
1.1741
0.343721098
0.999929959
1560
ORF sequence:
ATGACAGAAGATCTGCTGGAAGAGCAGTCTGAGGTCTTAGCAAAATTAGGGACATCTGCTGAGGGGGCGCACCTCCGCGCACGCATGCAGAGTGCCTGTCTCCTCTCCGATATGGAGTCTTTTAAGGCAGCTAATCCAGGCTGCTTTCTGGAAGATTTCGTGAGGTGGTACTCACCAAGGGACTACATTGAGGAGGAGGTGACTGACGAGAAGGGCAATGTGGTCCTGAAGGGGGAGCTGAGTGCCCGTATGAAGATCCCCAGCAACATGTGGGTAGAAGCCTGGGAGACTGCTAAGCCTGTGCCAGCACGACGTCAGAGGAGACTGTTTGATGACACCCGAGAGGCTGAAAAGGTCCTGCACTACCTGGCCATGCAGAAGCCTGCAGACCTAGCCAGGCACCTCCTGCCTTGTGTGATTCATGCAGCTGTTCTCAAGGTAAAGGAAGAAGAAAGTCTGGAAAACATTCCTTCTGTTAAGAAGATTATAAAGCAGATCATAGCCCATTCCAGCAAAGTTCTGCATTTCCCCAATCCTGAGGACAAGAAACTGGAAGAAATCATCCTTCAGATTACTACTGTGGAAGCTATAATAGCCCGAGCCCGGTCCCTGAAGGCCAAATTTGGAACTGAGAAGTGTGAGCACGAGGAGGAAAAGGAAGGTCTGGAAAGGTTTGTCAGCTGCCTGCTGGAGCAGCCTGAGGTATCAGTCACTGGGGCAGGAAGAGGACATGCTGGCCGCATCATCCACAAGCTGTTTGTGAATGCTCAGCGGGAACCAGCACCCATGACAGAAGATCTGCTGGAAGAGCAGTCTGAGGTCTTAGCAAAATTAGGGACATCTGCTGAGGGGGCGCACCTCCGCGCACGCATGCAGAGTGCCTGTCTCCTCTCCGATATGGAGTCTTTTAAGGCAGCTAATCCAGGCTGCTTTCTGGAAGATTTCGTGAGGTGGTACTCACCAAGGGACTACATTGAGGAGGAGGTGACTGACGAGAAGGGCAATGTGGTCCTGAAGGGGGAGCTGAGTGCCCGTATGAAGATCCCCAGCAACATGTGGGTAGAAGCCTGGGAGACTGCTAAGCCTGTGCCAGCACGACGTCAGAGGAGACTGTTTGATGACACCCGAGAGGCTGAAAAGGTCCTGCACTACCTGGCCATGCAGAAGCCTGCAGACCTAGCCAGGCACCTCCTGCCTTGTGTGATTCATGCAGCTGTTCTCAAGGTAAAGGAAGAAGAAAGTCTGGAAAACATTCCTTCTGTTAAGAAGATTATAAAGCAGATCATAGCCCATTCCAGCAAAGTTCTGCATTTCCCCAATCCTGAGGACAAGAAACTGGAAGAAATCATCCTTCAGATTACTACTGTGGAAGCTATAATAGCCCGAGCCCGGTCCCTGAAGGCCAAATTTGGAACTGAGAAGTGTGAGCACGAGGAGGAAAAGGAAGGTCTGGAAAGGTTTGTCAGCTGCCTGCTGGAGCAGCCTGAGGTATCAGTCACTGGGGCAGGAAGAGGACATGCTGGCCGCATCATCCACAAGCTGTTTGTGAATGCTCAGCGG
Peptide sequence:
MTEDLLEEQSEVLAKLGTSAEGAHLRARMQSACLLSDMESFKAANPGCFLEDFVRWYSPRDYIEEEVTDEKGNVVLKGELSARMKIPSNMWVEAWETAKPVPARRQRRLFDDTREAEKVLHYLAMQKPADLARHLLPCVIHAAVLKVKEEESLENIPSVKKIIKQIIAHSSKVLHFPNPEDKKLEEIILQITTVEAIIARARSLKAKFGTEKCEHEEEKEGLERFVSCLLEQPEVSVTGAGRGHAGRIIHKLFVNAQREPAPMTEDLLEEQSEVLAKLGTSAEGAHLRARMQSACLLSDMESFKAANPGCFLEDFVRWYSPRDYIEEEVTDEKGNVVLKGELSARMKIPSNMWVEAWETAKPVPARRQRRLFDDTREAEKVLHYLAMQKPADLARHLLPCVIHAAVLKVKEEESLENIPSVKKIIKQIIAHSSKVLHFPNPEDKKLEEIILQITTVEAIIARARSLKAKFGTEKCEHEEEKEGLERFVSCLLEQPEVSVTGAGRGHAGRIIHKLFVNAQR
IRESfinder result
IRESfinder score
0.455442184
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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