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mmu_circRalgapb_1726
Basic information of circular RNA
PanCircBase ID:
mmu_circRalgapb_1726
mm39_Chr. Position ID:
chr2|158272336|158288113|+
Gene name:
Ralgapb
Transcript:
ENSMUST00000109486.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
4,5,6,7,8,9,10,11,12,13,14
Exon/intron offsets:
0,2317,5041,6073,6586,6843,10353,12821,13410,14156,15712
Genomic length:
15777
Exon/intron sizes in nt:
164,187,132,179,149,217,202,168,115,148,65
Flanking exon/introns:
chr2:158268287-158272336|chr2:158288113-158290239
Splice length:
1726
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_95863
Human Ortholog IDs:
Mature spliced Sequence:
ACAGGAACAGGGCTCCAGTCAAATCCGACTATGCTTACAAGTTCTGAGAGCCATTCAGAAACTGGCCCGGGAGTCATCCATCATGGCTCGAGAAACCTGGGAAGTCTTACTGTTGTTTCTTCTGCAAATTAATGACATACTTCTGGCCCCACCAACTGTTCAAGGTGGCATTGCTGAGAATCTAGCAGAGAAGCTGATTGGTGTTCTCTTTGAAGTTTGGTTACTAGCTTGCACCCGGTGCTTCCCAACACCTCCTTATTGGAAGACAGCCAAGGAGATGGTGGCTAACTGGAGGCACCACCCTGCAGTGGTGGAGCAGTGGAGCAAGGTTATCTGTGCACTGACCTCCAGATTGCTCCGCTTTACATACGGTCCTTCATTTCCTCCATTTAAAGTTCCTGATGAAGATGCCAATCTCATCCCTCCAGAAATGGACAATGAGTGTATTGCACAAACATGGTTTCGATTTTTACACATGCTAAGTAACCCCGTGGATCTGAGTAACCCAGCTGTTATAAGCTCAACTCCCAAGTTTCAAGAACAGTTCCTGAATGTGAGCGGGATGCCACAGGAGCTGAGCCAGTACCCCTGCCTTAAACATCTGCCTCAGATATTCTTTCGTGCCATGCGTGGAATCAGCTGTCTGGTGGATGCATTCTTAGGCATTTCTCGACCTCGATCAGACAGTGCTCCCCCAACACCCGTGAATAGATTAAGTATGCCCCAGAGTGCTGCTGTGAATACCACACCACCACATAACCGGAGGCACCGGGCTGTTACTGTGAACAAGGCCACAATGAAGACGAGTACAGTTACTACTGCTCACACCTCAAAAGTCCAGCACCAGGCATCCTCCACCTCTCCTCTGTCCAGTCCAAATCAGACTAGTTCAGAACCCAGGCCGCTGCCTGCCCCCCGAAGACCAAAGGTTAACAGCATCTTGAATCTCTTTGGATCGTGGTTATTCGATGCAGCATTTGTTCACTGTAAACTCCATAATGGAATAAACAGAGACAACAGCATGACTGCCATTGCAACCCAAGCTAGCATGGAGTTTCGACGGAAAGGGTCCCAAATGTCAACAGACACCATGGTTTCCAACCCTGTGTTTGATGCCAGTGAATTTCCTGATAACTATGAAGCAGGAAGAGCTGAGGCTTGTGGGACATTATGTAGGATTTTTTGTAGCAAGAAGACTGGAGAAGAGATTCTGCCAGCTTATTTATCCAGATTTTACATGCTTTTAATTCAAGGTTTGCAGATAAATGATTATGTATGCCATCCTGTCTTGGCCAGCGTTATTCTAAACTCCCCTCCTTTGTTCTGCTGTGACTTGAAAGGGATTGATGTTGTGGTTCCTTACTTTATTTCAGCTCTTGAAACCATTTTGCCTGACAGAGAACTCTCAAAATTCAAAAGCTATGTAAATCCAACAGAATTGAGAAGGTCATCCATTAATATCCTGCTTTCTTTGTTGCCCCTCCCTCATCATTTTGGCACAGTCAGATCTGAGGTGGTCCTAGAAGGAAAGTTTAGTAATGATGACAGCTCTTCTTATGATAAACCAATAACTTTTCTGTCCCTGAAGCTGAGACTTGTGAATATACTAATAGGTGCCTTGCAAACAGAAACGGACCCTAACAACACCCAAATGATACTAGGGGCAATGTTAAATATTGTTCAAGATTCTGCACTTTTAGAAGCCATTGGTTGCCAAATGGAAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGGACCCTAACAACACCCAA
59.89
CATGATGGATGACTCCCGGG
59.96
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGGACCCTAACAACACCCAA
59.89
CCCGGGCCAGTTTCTGAAT
60
166
PCR template sequence:
AGAAACGGACCCTAACAACACCCAAATGATACTAGGGGCAATGTTAAATATTGTTCAAGATTCTGCACTTTTAGAAGCCATTGGTTGCCAAATGGAAATGACAGGAACAGGGCTCCAGTCAAATCCGACTATGCTTACAAGTTCTGAGAGCCATTCAGAAACTGGCCCGGGAGTCATCCATCATGGCTCGAGAAACCTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
22
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-23b-3p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-181a-5p(1), mmu-miR-15b-5p(1), mmu-miR-335-5p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-23a-3p(1), mmu-miR-143-3p(1), mmu-miR-24-3p(1), mmu-miR-149-5p(1), mmu-miR-382-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-511-3p(1), mmu-miR-183-5p(1), mmu-miR-541-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CCAAATGGAAATGACAGGAACAGGGC
siRNA sets
TTCCTGTCATTTCCATTTG, TCCTGTCATTTCCATTTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRALGAPB_1726_ORF_1
0.7853
0.022741051
0.999882125
1776
ORF sequence:
ATGGCTCGAGAAACCTGGGAAGTCTTACTGTTGTTTCTTCTGCAAATTAATGACATACTTCTGGCCCCACCAACTGTTCAAGGTGGCATTGCTGAGAATCTAGCAGAGAAGCTGATTGGTGTTCTCTTTGAAGTTTGGTTACTAGCTTGCACCCGGTGCTTCCCAACACCTCCTTATTGGAAGACAGCCAAGGAGATGGTGGCTAACTGGAGGCACCACCCTGCAGTGGTGGAGCAGTGGAGCAAGGTTATCTGTGCACTGACCTCCAGATTGCTCCGCTTTACATACGGTCCTTCATTTCCTCCATTTAAAGTTCCTGATGAAGATGCCAATCTCATCCCTCCAGAAATGGACAATGAGTGTATTGCACAAACATGGTTTCGATTTTTACACATGCTAAGTAACCCCGTGGATCTGAGTAACCCAGCTGTTATAAGCTCAACTCCCAAGTTTCAAGAACAGTTCCTGAATGTGAGCGGGATGCCACAGGAGCTGAGCCAGTACCCCTGCCTTAAACATCTGCCTCAGATATTCTTTCGTGCCATGCGTGGAATCAGCTGTCTGGTGGATGCATTCTTAGGCATTTCTCGACCTCGATCAGACAGTGCTCCCCCAACACCCGTGAATAGATTAAGTATGCCCCAGAGTGCTGCTGTGAATACCACACCACCACATAACCGGAGGCACCGGGCTGTTACTGTGAACAAGGCCACAATGAAGACGAGTACAGTTACTACTGCTCACACCTCAAAAGTCCAGCACCAGGCATCCTCCACCTCTCCTCTGTCCAGTCCAAATCAGACTAGTTCAGAACCCAGGCCGCTGCCTGCCCCCCGAAGACCAAAGGTTAACAGCATCTTGAATCTCTTTGGATCGTGGTTATTCGATGCAGCATTTGTTCACTGTAAACTCCATAATGGAATAAACAGAGACAACAGCATGACTGCCATTGCAACCCAAGCTAGCATGGAGTTTCGACGGAAAGGGTCCCAAATGTCAACAGACACCATGGTTTCCAACCCTGTGTTTGATGCCAGTGAATTTCCTGATAACTATGAAGCAGGAAGAGCTGAGGCTTGTGGGACATTATGTAGGATTTTTTGTAGCAAGAAGACTGGAGAAGAGATTCTGCCAGCTTATTTATCCAGATTTTACATGCTTTTAATTCAAGGTTTGCAGATAAATGATTATGTATGCCATCCTGTCTTGGCCAGCGTTATTCTAAACTCCCCTCCTTTGTTCTGCTGTGACTTGAAAGGGATTGATGTTGTGGTTCCTTACTTTATTTCAGCTCTTGAAACCATTTTGCCTGACAGAGAACTCTCAAAATTCAAAAGCTATGTAAATCCAACAGAATTGAGAAGGTCATCCATTAATATCCTGCTTTCTTTGTTGCCCCTCCCTCATCATTTTGGCACAGTCAGATCTGAGGTGGTCCTAGAAGGAAAGTTTAGTAATGATGACAGCTCTTCTTATGATAAACCAATAACTTTTCTGTCCCTGAAGCTGAGACTTGTGAATATACTAATAGGTGCCTTGCAAACAGAAACGGACCCTAACAACACCCAAATGATACTAGGGGCAATGTTAAATATTGTTCAAGATTCTGCACTTTTAGAAGCCATTGGTTGCCAAATGGAAATGACAGGAACAGGGCTCCAGTCAAATCCGACTATGCTTACAAGTTCTGAGAGCCATTCAGAAACTGGCCCGGGAGTCATCCATCATGGCTCGAGAAACCTGGGAAGTCTTACTGTTGTTTCTTCTGCAAATTAA
Peptide sequence:
MARETWEVLLLFLLQINDILLAPPTVQGGIAENLAEKLIGVLFEVWLLACTRCFPTPPYWKTAKEMVANWRHHPAVVEQWSKVICALTSRLLRFTYGPSFPPFKVPDEDANLIPPEMDNECIAQTWFRFLHMLSNPVDLSNPAVISSTPKFQEQFLNVSGMPQELSQYPCLKHLPQIFFRAMRGISCLVDAFLGISRPRSDSAPPTPVNRLSMPQSAAVNTTPPHNRRHRAVTVNKATMKTSTVTTAHTSKVQHQASSTSPLSSPNQTSSEPRPLPAPRRPKVNSILNLFGSWLFDAAFVHCKLHNGINRDNSMTAIATQASMEFRRKGSQMSTDTMVSNPVFDASEFPDNYEAGRAEACGTLCRIFCSKKTGEEILPAYLSRFYMLLIQGLQINDYVCHPVLASVILNSPPLFCCDLKGIDVVVPYFISALETILPDRELSKFKSYVNPTELRRSSINILLSLLPLPHHFGTVRSEVVLEGKFSNDDSSSYDKPITFLSLKLRLVNILIGALQTETDPNNTQMILGAMLNIVQDSALLEAIGCQMEMTGTGLQSNPTMLTSSESHSETGPGVIHHGSRNLGSLTVVSSAN
IRESfinder result
IRESfinder score
0.696015195
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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