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mmu_circRab3gap1_1083
Basic information of circular RNA
PanCircBase ID:
mmu_circRab3gap1_1083
mm39_Chr. Position ID:
chr1|127816892|127853178|+
Gene name:
Rab3gap1
Transcript:
ENSMUST00000037649.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
4,5,6,7,8,9,10,11,12,13
Exon/intron offsets:
0,1862,12423,14516,20695,26483,29065,30412,35572,36119
Genomic length:
36286
Exon/intron sizes in nt:
133,79,120,166,100,82,69,74,93,167
Flanking exon/introns:
chr1:127801892-127816892|chr1:127853178-127855196
Splice length:
1083
Other database IDs:
CIRCpedia: MMU_CIRCpedia_40040, circAtlas: mmu-Rab3gap1_0025
Human Ortholog IDs:
Mature spliced Sequence:
GGTATATTTACTTCTGGCACATGGGAAGAGCGATCAGATGAAATTTCCTTTGCTGACTTCAGGTTTTCAGTCACACATCACTATCTTGTACAAGAGTCTCCTGATAAAGAAAGAAAGGATGAAGAATTGGAGGACGCTATTCCACAGTCAATGCAAGATTTGCTATGTATGAATAACGACTTTCCTCCAAGAGCACATTGCCTGGTAAGATGGTATGGCCTGCGTGAGTTTGTGGTGATTGCTCCTGCTGCACACAGTGATGCAGTTCTCAGTGAATCCAAGTGTAACCTCCTCCTTAGTTCCATTTCTATTGCTTTGGGAAACACTGGCTGCCAGGTACCACTGTTTGTCCAAATACATCACAAATGGCGACGAATGTACATGGGAGAATGTCAAGGTCCTGGTGTTCGTACTGACTTTGAAATGGTTCATCTTCGAAAAGTGCCAAGTCAGTACACTCATTTGTCAGGCCTGCTGGACATCTTCAAATCCAAAATTGGCTGTCCTTTAACTCCATTGCCTCCAGTTAGCATTGCGATTCGGCTCACATACGTGCTTCAGGATTGGCAGCAATACTTTTGGCCTCAGCAGCCTCCAGATATAGATGCCCTTGTGGGAGGAGAAGTTGGGGGCCTGGAGTTCGGCAAGTTGCCATTTGGTGCCTGTGAAGATCCTATCAGTGAACTCCATTTAGCAACAACGTGGCCTCATTTGACAGAAGGGATCATTGTAGATAATGATGTTTATTCTGATTTGGATCCTGTTCAAGCTCCCCATTGGTCGGTTAGAGTTCGGAAAGCTGATAATCCCCAGTGCTTACTAGGTGATTTTGTTACTGAATTTTTAAAAATTTGCCGTCGAAAGGAATCAACGGATGAAATTCTTGGACGATCCACATTTGAAGAAGAGGGAAGAGAAGTTGCTGATATAACTCATGCTTTGTCAAAGCTGACTGAGCCAGCGCCAGTTCCAATTCATAAATTATCAGTTTCAAATATGGTACACACTGCAAAGAAGAAGATACGGAAGCACAGAGGGGAAGAGTCGCCGCTGAACAGTGATGTTCTCAATACTATTCTCTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GATACGGAAGCACAGAGGGG
59.89
GTGATGTGTGACTGAAAACCTGA
59.12
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATACGGAAGCACAGAGGGG
59.89
AGTGATGTGTGACTGAAAACCTG
59.12
146
PCR template sequence:
ATCAGTTTCAAATATGGTACACACTGCAAAGAAGAAGATACGGAAGCACAGAGGGGAAGAGTCGCCGCTGAACAGTGATGTTCTCAATACTATTCTCTTGGGTATATTTACTTCTGGCACATGGGAAGAGCGATCAGATGAAATTTCCTTTGCTGACTTCAGGTTTTCAGTCACACATCACTATCTTGTACAAGAGTCTC
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
TACTATTCTCTTGGGTATATTTACTT
siRNA sets
AAGTAAATATACCCAAGAG, AATATACCCAAGAGAATAG, AAATATACCCAAGAGAATA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAB3GAP1_1083_ORF_1
1.0702
0.059940894
0.999989765
2016
ORF sequence:
ATGCAAGATTTGCTATGTATGAATAACGACTTTCCTCCAAGAGCACATTGCCTGGTAAGATGGTATGGCCTGCGTGAGTTTGTGGTGATTGCTCCTGCTGCACACAGTGATGCAGTTCTCAGTGAATCCAAGTGTAACCTCCTCCTTAGTTCCATTTCTATTGCTTTGGGAAACACTGGCTGCCAGGTACCACTGTTTGTCCAAATACATCACAAATGGCGACGAATGTACATGGGAGAATGTCAAGGTCCTGGTGTTCGTACTGACTTTGAAATGGTTCATCTTCGAAAAGTGCCAAGTCAGTACACTCATTTGTCAGGCCTGCTGGACATCTTCAAATCCAAAATTGGCTGTCCTTTAACTCCATTGCCTCCAGTTAGCATTGCGATTCGGCTCACATACGTGCTTCAGGATTGGCAGCAATACTTTTGGCCTCAGCAGCCTCCAGATATAGATGCCCTTGTGGGAGGAGAAGTTGGGGGCCTGGAGTTCGGCAAGTTGCCATTTGGTGCCTGTGAAGATCCTATCAGTGAACTCCATTTAGCAACAACGTGGCCTCATTTGACAGAAGGGATCATTGTAGATAATGATGTTTATTCTGATTTGGATCCTGTTCAAGCTCCCCATTGGTCGGTTAGAGTTCGGAAAGCTGATAATCCCCAGTGCTTACTAGGTGATTTTGTTACTGAATTTTTAAAAATTTGCCGTCGAAAGGAATCAACGGATGAAATTCTTGGACGATCCACATTTGAAGAAGAGGGAAGAGAAGTTGCTGATATAACTCATGCTTTGTCAAAGCTGACTGAGCCAGCGCCAGTTCCAATTCATAAATTATCAGTTTCAAATATGGTACACACTGCAAAGAAGAAGATACGGAAGCACAGAGGGGAAGAGTCGCCGCTGAACAGTGATGTTCTCAATACTATTCTCTTGGGTATATTTACTTCTGGCACATGGGAAGAGCGATCAGATGAAATTTCCTTTGCTGACTTCAGGTTTTCAGTCACACATCACTATCTTGTACAAGAGTCTCCTGATAAAGAAAGAAAGGATGAAGAATTGGAGGACGCTATTCCACAGTCAATGCAAGATTTGCTATGTATGAATAACGACTTTCCTCCAAGAGCACATTGCCTGGTAAGATGGTATGGCCTGCGTGAGTTTGTGGTGATTGCTCCTGCTGCACACAGTGATGCAGTTCTCAGTGAATCCAAGTGTAACCTCCTCCTTAGTTCCATTTCTATTGCTTTGGGAAACACTGGCTGCCAGGTACCACTGTTTGTCCAAATACATCACAAATGGCGACGAATGTACATGGGAGAATGTCAAGGTCCTGGTGTTCGTACTGACTTTGAAATGGTTCATCTTCGAAAAGTGCCAAGTCAGTACACTCATTTGTCAGGCCTGCTGGACATCTTCAAATCCAAAATTGGCTGTCCTTTAACTCCATTGCCTCCAGTTAGCATTGCGATTCGGCTCACATACGTGCTTCAGGATTGGCAGCAATACTTTTGGCCTCAGCAGCCTCCAGATATAGATGCCCTTGTGGGAGGAGAAGTTGGGGGCCTGGAGTTCGGCAAGTTGCCATTTGGTGCCTGTGAAGATCCTATCAGTGAACTCCATTTAGCAACAACGTGGCCTCATTTGACAGAAGGGATCATTGTAGATAATGATGTTTATTCTGATTTGGATCCTGTTCAAGCTCCCCATTGGTCGGTTAGAGTTCGGAAAGCTGATAATCCCCAGTGCTTACTAGGTGATTTTGTTACTGAATTTTTAAAAATTTGCCGTCGAAAGGAATCAACGGATGAAATTCTTGGACGATCCACATTTGAAGAAGAGGGAAGAGAAGTTGCTGATATAACTCATGCTTTGTCAAAGCTGACTGAGCCAGCGCCAGTTCCAATTCATAAATTATCAGTTTCAAATATGGTACACACTGCAAAGAAGAAGATACGGAAGCACAGAGGGGAAGAGTCGCCGCTGAACAGTGATGTTCTCAATACTATTCTCTTG
Peptide sequence:
MQDLLCMNNDFPPRAHCLVRWYGLREFVVIAPAAHSDAVLSESKCNLLLSSISIALGNTGCQVPLFVQIHHKWRRMYMGECQGPGVRTDFEMVHLRKVPSQYTHLSGLLDIFKSKIGCPLTPLPPVSIAIRLTYVLQDWQQYFWPQQPPDIDALVGGEVGGLEFGKLPFGACEDPISELHLATTWPHLTEGIIVDNDVYSDLDPVQAPHWSVRVRKADNPQCLLGDFVTEFLKICRRKESTDEILGRSTFEEEGREVADITHALSKLTEPAPVPIHKLSVSNMVHTAKKKIRKHRGEESPLNSDVLNTILLGIFTSGTWEERSDEISFADFRFSVTHHYLVQESPDKERKDEELEDAIPQSMQDLLCMNNDFPPRAHCLVRWYGLREFVVIAPAAHSDAVLSESKCNLLLSSISIALGNTGCQVPLFVQIHHKWRRMYMGECQGPGVRTDFEMVHLRKVPSQYTHLSGLLDIFKSKIGCPLTPLPPVSIAIRLTYVLQDWQQYFWPQQPPDIDALVGGEVGGLEFGKLPFGACEDPISELHLATTWPHLTEGIIVDNDVYSDLDPVQAPHWSVRVRKADNPQCLLGDFVTEFLKICRRKESTDEILGRSTFEEEGREVADITHALSKLTEPAPVPIHKLSVSNMVHTAKKKIRKHRGEESPLNSDVLNTILL
IRESfinder result
IRESfinder score
0.580365223
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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