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mmu_circFam126b_560
Basic information of circular RNA
PanCircBase ID:
mmu_circFam126b_560
mm39_Chr. Position ID:
chr1|58585265|58597216|-
Gene name:
Fam126b
Transcript:
ENSMUST00000161600.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,6,5,4,3
Exon/intron offsets:
0,2532,6043,11165,11870
Genomic length:
11951
Exon/intron sizes in nt:
116,81,180,102,81
Flanking exon/introns:
chr1:58583921-58585265|chr1:58597216-58605015
Splice length:
560
Other database IDs:
CIRCpedia: MMU_CIRCpedia_217940, circAtlas: mmu-Fam126b_0004
circBase: hsa_circ_0118629, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_39140
Human Ortholog IDs:
Mature spliced Sequence:
AGATAAAAGAAGAATAGAAGGTAAAGGAAGATGCTGGGATCGGAACGAGCTGTTGTGGAAGAATGGTTATCAGAATTCAAGGCATTACCTGACACTCAGATTACCAGTTATGCAGCAACCTTGCACCGGAAAAAAGCCCTTGTACCAGCTCTCTATAAAGTTATTCAGGATTCAAACAATGAGCTCCTGGAGCCTGTCTGCCACCAACTGTTTGAGCTCTATCGTAGCTCTGAAGTTCGACTTAAGAGGTTCACACTGCAGTTCCTGCCCGAATTGATTTGGGTTTATTTGCGACTTACAGTTAGTAGAGACAGGCAGAGCAATGGCTGCATTGAAGCACTTCTCCTAGGAATTTATAATTTGGAAATTGCTGATAAAGATGGAAACAATAAAGTGCTGTCTTTCACTATCCCTTCCTTGTCTAAGCCTTCAATATACCATGAACCCTCAACAATTGGATCCATGGCTTTGACAGAAGGGGCATTATGTCAGCATGATCTCATCAGGGTTGTTTACAGTGATCTTCATCCTCAGAGAGAAACATTCACTGCACAGAACCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTTTGACAGAAGGGGCAT
60.61
CGTTCCGATCCCAGCATCTT
60.18
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGCTTTGACAGAAGGGGC
60.61
CGTTCCGATCCCAGCATCTT
60.18
145
PCR template sequence:
CCATGGCTTTGACAGAAGGGGCATTATGTCAGCATGATCTCATCAGGGTTGTTTACAGTGATCTTCATCCTCAGAGAGAAACATTCACTGCACAGAACCGAGATAAAAGAAGAATAGAAGGTAAAGGAAGATGCTGGGATCGGAACGAGCTGTTGTGGAAGAATGGTTATCAGAATTCAAGGCATTACCTGACACTCAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-155-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-30d-5p(1), mmu-miR-30b-5p(1), mmu-miR-384-3p(1), mmu-miR-5101(1), mmu-miR-532-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGCACAGAACCGAGATAAAAGAAGA
siRNA sets
TTTTATCTCGGTTCTGTGC, TTCTTTTATCTCGGTTCTG, TTTATCTCGGTTCTGTGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFAM126B_560_ORF_1
0.3864
0.012208176
0.789633543
807
ORF sequence:
ATGCTGGGATCGGAACGAGCTGTTGTGGAAGAATGGTTATCAGAATTCAAGGCATTACCTGACACTCAGATTACCAGTTATGCAGCAACCTTGCACCGGAAAAAAGCCCTTGTACCAGCTCTCTATAAAGTTATTCAGGATTCAAACAATGAGCTCCTGGAGCCTGTCTGCCACCAACTGTTTGAGCTCTATCGTAGCTCTGAAGTTCGACTTAAGAGGTTCACACTGCAGTTCCTGCCCGAATTGATTTGGGTTTATTTGCGACTTACAGTTAGTAGAGACAGGCAGAGCAATGGCTGCATTGAAGCACTTCTCCTAGGAATTTATAATTTGGAAATTGCTGATAAAGATGGAAACAATAAAGTGCTGTCTTTCACTATCCCTTCCTTGTCTAAGCCTTCAATATACCATGAACCCTCAACAATTGGATCCATGGCTTTGACAGAAGGGGCATTATGTCAGCATGATCTCATCAGGGTTGTTTACAGTGATCTTCATCCTCAGAGAGAAACATTCACTGCACAGAACCGAGATAAAAGAAGAATAGAAGGTAAAGGAAGATGCTGGGATCGGAACGAGCTGTTGTGGAAGAATGGTTATCAGAATTCAAGGCATTACCTGACACTCAGATTACCAGTTATGCAGCAACCTTGCACCGGAAAAAAGCCCTTGTACCAGCTCTCTATAAAGTTATTCAGGATTCAAACAATGAGCTCCTGGAGCCTGTCTGCCACCAACTGTTTGAGCTCTATCGTAGCTCTGAAGTTCGACTTAAGAGGTTCACACTGCAGTTCCTGCCCGAATTGA
Peptide sequence:
MLGSERAVVEEWLSEFKALPDTQITSYAATLHRKKALVPALYKVIQDSNNELLEPVCHQLFELYRSSEVRLKRFTLQFLPELIWVYLRLTVSRDRQSNGCIEALLLGIYNLEIADKDGNNKVLSFTIPSLSKPSIYHEPSTIGSMALTEGALCQHDLIRVVYSDLHPQRETFTAQNRDKRRIEGKGRCWDRNELLWKNGYQNSRHYLTLRLPVMQQPCTGKKPLYQLSIKLFRIQTMSSWSLSATNCLSSIVALKFDLRGSHCSSCPN
IRESfinder result
IRESfinder score
0.756260065
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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