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mmu_circRab3gap1_1346
Basic information of circular RNA
PanCircBase ID:
mmu_circRab3gap1_1346
mm39_Chr. Position ID:
chr1|127816892|127855858|+
Gene name:
Rab3gap1
Transcript:
ENSMUST00000037649.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
4,5,6,7,8,9,10,11,12,13,14,15
Exon/intron offsets:
0,1862,12423,14516,20695,26483,29065,30412,35572,36119,38304,38793
Genomic length:
38966
Exon/intron sizes in nt:
1,33,79,12,01,66,10,08,00,00,00,00,00,00,000
Flanking exon/introns:
chr1:127801892-127816892|chr1:127855858-127858126
Splice length:
1346
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGTATATTTACTTCTGGCACATGGGAAGAGCGATCAGATGAAATTTCCTTTGCTGACTTCAGGTTTTCAGTCACACATCACTATCTTGTACAAGAGTCTCCTGATAAAGAAAGAAAGGATGAAGAATTGGAGGACGCTATTCCACAGTCAATGCAAGATTTGCTATGTATGAATAACGACTTTCCTCCAAGAGCACATTGCCTGGTAAGATGGTATGGCCTGCGTGAGTTTGTGGTGATTGCTCCTGCTGCACACAGTGATGCAGTTCTCAGTGAATCCAAGTGTAACCTCCTCCTTAGTTCCATTTCTATTGCTTTGGGAAACACTGGCTGCCAGGTACCACTGTTTGTCCAAATACATCACAAATGGCGACGAATGTACATGGGAGAATGTCAAGGTCCTGGTGTTCGTACTGACTTTGAAATGGTTCATCTTCGAAAAGTGCCAAGTCAGTACACTCATTTGTCAGGCCTGCTGGACATCTTCAAATCCAAAATTGGCTGTCCTTTAACTCCATTGCCTCCAGTTAGCATTGCGATTCGGCTCACATACGTGCTTCAGGATTGGCAGCAATACTTTTGGCCTCAGCAGCCTCCAGATATAGATGCCCTTGTGGGAGGAGAAGTTGGGGGCCTGGAGTTCGGCAAGTTGCCATTTGGTGCCTGTGAAGATCCTATCAGTGAACTCCATTTAGCAACAACGTGGCCTCATTTGACAGAAGGGATCATTGTAGATAATGATGTTTATTCTGATTTGGATCCTGTTCAAGCTCCCCATTGGTCGGTTAGAGTTCGGAAAGCTGATAATCCCCAGTGCTTACTAGGTGATTTTGTTACTGAATTTTTAAAAATTTGCCGTCGAAAGGAATCAACGGATGAAATTCTTGGACGATCCACATTTGAAGAAGAGGGAAGAGAAGTTGCTGATATAACTCATGCTTTGTCAAAGCTGACTGAGCCAGCGCCAGTTCCAATTCATAAATTATCAGTTTCAAATATGGTACACACTGCAAAGAAGAAGATACGGAAGCACAGAGGGGAAGAGTCGCCGCTGAACAGTGATGTTCTCAATACTATTCTCTTGTTCTTGTTCCCAGATGCTGTCTCTGAGAAGCCGTTAGATGGAACTACTTCAATAGACAATAGCATTCCTGCACCAGAGGCTGGAGACTATACTCTCTACAATCAGTTCAAGTCTGCGCCTTCCGACAGTCTAACATACAAACTGGCCTTGTGTCTTTGTATGATCAACTTCTACCATGGAGGGCTGAAGGGAGTGGCACATCTCTGGCAGGAATTTGTTCTTGAAATGCGTTTCAGATGGGAAAACAACTTTCTGATTCCAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCACATCTCTGGCAGGAAT
60.11
GACTGAAAACCTGAAGTCAGCA
58.79
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCACATCTCTGGCAGGAAT
60.11
TGACTGAAAACCTGAAGTCAGC
58.79
142
PCR template sequence:
TCAACTTCTACCATGGAGGGCTGAAGGGAGTGGCACATCTCTGGCAGGAATTTGTTCTTGAAATGCGTTTCAGATGGGAAAACAACTTTCTGATTCCAGGGGTATATTTACTTCTGGCACATGGGAAGAGCGATCAGATGAAATTTCCTTTGCTGACTTCAGGTTTTCAGTCACACATCACTATCTTGTACAAGAGTCTC
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-214-3p(2), mmu-miR-134-5p(1), mmu-miR-34c-5p(1), mmu-miR-30e-5p(1), mmu-miR-146a-5p(1), mmu-miR-33-5p(1), mmu-miR-217-5p(1), mmu-miR-24-3p(1), mmu-miR-149-5p(1), mmu-miR-22-3p(1), mmu-miR-802-5p(1), mmu-miR-1187(1), mmu-miR-3087-3p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCTGATTCCAGGGGTATATTTACTT
siRNA sets
AAGTAAATATACCCCTGGA, AATATACCCCTGGAATCAG, AAATATACCCCTGGAATCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAB3GAP1_1346_ORF_1
0.9062
0.055679776
0.998499451
1371
ORF sequence:
ATGGGAAAACAACTTTCTGATTCCAGGGGTATATTTACTTCTGGCACATGGGAAGAGCGATCAGATGAAATTTCCTTTGCTGACTTCAGGTTTTCAGTCACACATCACTATCTTGTACAAGAGTCTCCTGATAAAGAAAGAAAGGATGAAGAATTGGAGGACGCTATTCCACAGTCAATGCAAGATTTGCTATGTATGAATAACGACTTTCCTCCAAGAGCACATTGCCTGGTAAGATGGTATGGCCTGCGTGAGTTTGTGGTGATTGCTCCTGCTGCACACAGTGATGCAGTTCTCAGTGAATCCAAGTGTAACCTCCTCCTTAGTTCCATTTCTATTGCTTTGGGAAACACTGGCTGCCAGGTACCACTGTTTGTCCAAATACATCACAAATGGCGACGAATGTACATGGGAGAATGTCAAGGTCCTGGTGTTCGTACTGACTTTGAAATGGTTCATCTTCGAAAAGTGCCAAGTCAGTACACTCATTTGTCAGGCCTGCTGGACATCTTCAAATCCAAAATTGGCTGTCCTTTAACTCCATTGCCTCCAGTTAGCATTGCGATTCGGCTCACATACGTGCTTCAGGATTGGCAGCAATACTTTTGGCCTCAGCAGCCTCCAGATATAGATGCCCTTGTGGGAGGAGAAGTTGGGGGCCTGGAGTTCGGCAAGTTGCCATTTGGTGCCTGTGAAGATCCTATCAGTGAACTCCATTTAGCAACAACGTGGCCTCATTTGACAGAAGGGATCATTGTAGATAATGATGTTTATTCTGATTTGGATCCTGTTCAAGCTCCCCATTGGTCGGTTAGAGTTCGGAAAGCTGATAATCCCCAGTGCTTACTAGGTGATTTTGTTACTGAATTTTTAAAAATTTGCCGTCGAAAGGAATCAACGGATGAAATTCTTGGACGATCCACATTTGAAGAAGAGGGAAGAGAAGTTGCTGATATAACTCATGCTTTGTCAAAGCTGACTGAGCCAGCGCCAGTTCCAATTCATAAATTATCAGTTTCAAATATGGTACACACTGCAAAGAAGAAGATACGGAAGCACAGAGGGGAAGAGTCGCCGCTGAACAGTGATGTTCTCAATACTATTCTCTTGTTCTTGTTCCCAGATGCTGTCTCTGAGAAGCCGTTAGATGGAACTACTTCAATAGACAATAGCATTCCTGCACCAGAGGCTGGAGACTATACTCTCTACAATCAGTTCAAGTCTGCGCCTTCCGACAGTCTAACATACAAACTGGCCTTGTGTCTTTGTATGATCAACTTCTACCATGGAGGGCTGAAGGGAGTGGCACATCTCTGGCAGGAATTTGTTCTTGAAATGCGTTTCAGATGGGAAAACAACTTTCTGATTCCA
Peptide sequence:
MGKQLSDSRGIFTSGTWEERSDEISFADFRFSVTHHYLVQESPDKERKDEELEDAIPQSMQDLLCMNNDFPPRAHCLVRWYGLREFVVIAPAAHSDAVLSESKCNLLLSSISIALGNTGCQVPLFVQIHHKWRRMYMGECQGPGVRTDFEMVHLRKVPSQYTHLSGLLDIFKSKIGCPLTPLPPVSIAIRLTYVLQDWQQYFWPQQPPDIDALVGGEVGGLEFGKLPFGACEDPISELHLATTWPHLTEGIIVDNDVYSDLDPVQAPHWSVRVRKADNPQCLLGDFVTEFLKICRRKESTDEILGRSTFEEEGREVADITHALSKLTEPAPVPIHKLSVSNMVHTAKKKIRKHRGEESPLNSDVLNTILLFLFPDAVSEKPLDGTTSIDNSIPAPEAGDYTLYNQFKSAPSDSLTYKLALCLCMINFYHGGLKGVAHLWQEFVLEMRFRWENNFLIP
IRESfinder result
IRESfinder score
0.642822219
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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