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mmu_circRab3gap1_611
Basic information of circular RNA
PanCircBase ID:
mmu_circRab3gap1_611
mm39_Chr. Position ID:
chr1|127829315|127847378|+
Gene name:
Rab3gap1
Transcript:
ENSMUST00000037649.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
6,7,8,9,10,11
Exon/intron offsets:
0,2093,8272,14060,16642,17989
Genomic length:
18063
Exon/intron sizes in nt:
120,166,100,82,69,74
Flanking exon/introns:
chr1:127818833-127829315|chr1:127847378-127852464
Splice length:
611
Other database IDs:
circAtlas: mmu-Rab3gap1_0024
circBase: hsa_circ_0056546, CIRCpedia: HSA_CIRCpedia_37934
Human Ortholog IDs:
Mature spliced Sequence:
GTATGGCCTGCGTGAGTTTGTGGTGATTGCTCCTGCTGCACACAGTGATGCAGTTCTCAGTGAATCCAAGTGTAACCTCCTCCTTAGTTCCATTTCTATTGCTTTGGGAAACACTGGCTGCCAGGTACCACTGTTTGTCCAAATACATCACAAATGGCGACGAATGTACATGGGAGAATGTCAAGGTCCTGGTGTTCGTACTGACTTTGAAATGGTTCATCTTCGAAAAGTGCCAAGTCAGTACACTCATTTGTCAGGCCTGCTGGACATCTTCAAATCCAAAATTGGCTGTCCTTTAACTCCATTGCCTCCAGTTAGCATTGCGATTCGGCTCACATACGTGCTTCAGGATTGGCAGCAATACTTTTGGCCTCAGCAGCCTCCAGATATAGATGCCCTTGTGGGAGGAGAAGTTGGGGGCCTGGAGTTCGGCAAGTTGCCATTTGGTGCCTGTGAAGATCCTATCAGTGAACTCCATTTAGCAACAACGTGGCCTCATTTGACAGAAGGGATCATTGTAGATAATGATGTTTATTCTGATTTGGATCCTGTTCAAGCTCCCCATTGGTCGGTTAGAGTTCGGAAAGCTGATAATCCCCAGTGCTTACTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGATCCTGTTCAAGCTCCCC
60.11
AGGAGGAGGTTACACTTGGA
57.28
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCAAGCTCCCCATTGGTCG
60.32
AGGAGGAGGTTACACTTGGA
57.28
144
PCR template sequence:
ATCATTGTAGATAATGATGTTTATTCTGATTTGGATCCTGTTCAAGCTCCCCATTGGTCGGTTAGAGTTCGGAAAGCTGATAATCCCCAGTGCTTACTAGGTATGGCCTGCGTGAGTTTGTGGTGATTGCTCCTGCTGCACACAGTGATGCAGTTCTCAGTGAATCCAAGTGTAACCTCCTCCTTAGTTCCATTTCTATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-214-3p(2), mmu-miR-34c-5p(1), mmu-miR-30e-5p(1), mmu-miR-146a-5p(1), mmu-miR-217-5p(1), mmu-miR-22-3p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGTGCTTACTAGGTATGGCCTGCGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAB3GAP1_611_ORF_1
0.9565
0.075099965
0.558398325
474
ORF sequence:
ATGTACATGGGAGAATGTCAAGGTCCTGGTGTTCGTACTGACTTTGAAATGGTTCATCTTCGAAAAGTGCCAAGTCAGTACACTCATTTGTCAGGCCTGCTGGACATCTTCAAATCCAAAATTGGCTGTCCTTTAACTCCATTGCCTCCAGTTAGCATTGCGATTCGGCTCACATACGTGCTTCAGGATTGGCAGCAATACTTTTGGCCTCAGCAGCCTCCAGATATAGATGCCCTTGTGGGAGGAGAAGTTGGGGGCCTGGAGTTCGGCAAGTTGCCATTTGGTGCCTGTGAAGATCCTATCAGTGAACTCCATTTAGCAACAACGTGGCCTCATTTGACAGAAGGGATCATTGTAGATAATGATGTTTATTCTGATTTGGATCCTGTTCAAGCTCCCCATTGGTCGGTTAGAGTTCGGAAAGCTGATAATCCCCAGTGCTTACTAGGTATGGCCTGCGTGAGTTTGTGGTGA
Peptide sequence:
MYMGECQGPGVRTDFEMVHLRKVPSQYTHLSGLLDIFKSKIGCPLTPLPPVSIAIRLTYVLQDWQQYFWPQQPPDIDALVGGEVGGLEFGKLPFGACEDPISELHLATTWPHLTEGIIVDNDVYSDLDPVQAPHWSVRVRKADNPQCLLGMACVSLW
IRESfinder result
IRESfinder score
0.607678269
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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