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mmu_circFam135a_890
Basic information of circular RNA
PanCircBase ID:
mmu_circFam135a_890
mm39_Chr. Position ID:
chr1|24071743|24096586|-
Gene name:
Fam135a
Transcript:
ENSMUST00000188712.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,11451,13695,16467,20520,21341,23081,24541,24703
Genomic length:
24843
Exon/intron sizes in nt:
7,41,56,50,78,15,41,27,00,00,000
Flanking exon/introns:
chr1:24069977-24071743|chr1:24096586-24106979
Splice length:
890
Other database IDs:
circBase: mmu_circ_0008602, circAtlas: mmu-Fam135a_0009
circAtlas: hsa-FAM135A_0012, CIRCpedia: HSA_CIRCpedia_150755
Human Ortholog IDs:
Mature spliced Sequence:
GCATGACATTAGCCTTTCCAGCTTCCGTTCATGATGCTCTGGTTTGCAGCAAAACATTTCAGATCCTATATAAAAATGAAGAAGTTGTTTTAAATGATGTCATGATCTTCAAAGTTAAAATGCTGTTGGATGAAAGAAAGATTGAAGAAACCCTTGAAGAAATCAGTTTTTTGTTATCGTTGGGTCTACATTTCACAGATGGAGACTATTCTTCACGCGTCATTGGTTGCACTACACCAGCCGCTAATAAGCTTTCCTCGCCCTGTGAAGACCACTTGGTTAAATAGAAATGCGCCAGCACAGAGCAAAGACTCGGCGATTCCGACTCTGGAAAGTGTAGTCTTTGGTATTAACTACACAAAACAGTTATCACCAGATGGCTGTAGCTTCCTCATTGCAGAGTCCTTCCTGCACCATGCCTATCATTTTCATTATACACTTTGTGCTACTTTGCTGCTAGCCTTCAAGGGATTGCACAGCTACTTCATTACGGTAACAGAAGAGATTCCCTCTTGTCAGAAACTAGACCTGGCCAAGGCCAGCATGCAGGTCCTATATGAGCGCCTCCTCAGAAGAACACAGCCAAGAACTCAGAACGACACGTGTCTAGAGGAAATGGATGTAGAAGCTCGTCTTACTGAACTGTGTGAAGAAGTTAAGAAAGTAGAAAACCCTGATGAACTGGCAGAACTCATCAACATGAACCTTGCACAGCTCTGCTCACTTCTCATGGCTTTATGGGGACAGTTTTTGGAAGCTATAACACTGCATGAAGATTTAAGAGTGCTGTTAGCACAGGAACACCATACTTTGAGGGTTCGCAGATTTTCGGAGGCGTTCTTTTGTTTTGAACATCCAAGAGAAGCTGCCATTGCATACCAAGAACTCCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCATACTTTGAGGGTTCGCA
59.65
TTGCTGCAAACCAGAGCATC
59.4
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCATACTTTGAGGGTTCGCA
59.65
TTTTGCTGCAAACCAGAGCA
59.18
142
PCR template sequence:
TAGCACAGGAACACCATACTTTGAGGGTTCGCAGATTTTCGGAGGCGTTCTTTTGTTTTGAACATCCAAGAGAAGCTGCCATTGCATACCAAGAACTCCAGCATGACATTAGCCTTTCCAGCTTCCGTTCATGATGCTCTGGTTTGCAGCAAAACATTTCAGATCCTATATAAAAATGAAGAAGTTGTTTTAAATGATGT
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-203-3p(2), mmu-miR-138-5p(1), mmu-miR-191-5p(1), mmu-miR-130b-3p(1), mmu-miR-721(1), mmu-miR-340-5p(1), mmu-miR-690(1)
siRNAs for circular RNA silencing
Junction sequence
ACCAAGAACTCCAGCATGACATTAGC
siRNA sets
AATGTCATGCTGGAGTTCT, TAATGTCATGCTGGAGTTC, ATGTCATGCTGGAGTTCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFAM135A_890_ORF_1
0.7504
0.025639948
0.875725529
795
ORF sequence:
ATGAAAGAAAGATTGAAGAAACCCTTGAAGAAATCAGTTTTTTGTTATCGTTGGGTCTACATTTCACAGATGGAGACTATTCTTCACGCGTCATTGGTTGCACTACACCAGCCGCTAATAAGCTTTCCTCGCCCTGTGAAGACCACTTGGTTAAATAGAAATGCGCCAGCACAGAGCAAAGACTCGGCGATTCCGACTCTGGAAAGTGTAGTCTTTGGTATTAACTACACAAAACAGTTATCACCAGATGGCTGTAGCTTCCTCATTGCAGAGTCCTTCCTGCACCATGCCTATCATTTTCATTATACACTTTGTGCTACTTTGCTGCTAGCCTTCAAGGGATTGCACAGCTACTTCATTACGGTAACAGAAGAGATTCCCTCTTGTCAGAAACTAGACCTGGCCAAGGCCAGCATGCAGGTCCTATATGAGCGCCTCCTCAGAAGAACACAGCCAAGAACTCAGAACGACACGTGTCTAGAGGAAATGGATGTAGAAGCTCGTCTTACTGAACTGTGTGAAGAAGTTAAGAAAGTAGAAAACCCTGATGAACTGGCAGAACTCATCAACATGAACCTTGCACAGCTCTGCTCACTTCTCATGGCTTTATGGGGACAGTTTTTGGAAGCTATAACACTGCATGAAGATTTAAGAGTGCTGTTAGCACAGGAACACCATACTTTGAGGGTTCGCAGATTTTCGGAGGCGTTCTTTTGTTTTGAACATCCAAGAGAAGCTGCCATTGCATACCAAGAACTCCAGCATGACATTAGCCTTTCCAGCTTCCGTTCATGA
Peptide sequence:
MKERLKKPLKKSVFCYRWVYISQMETILHASLVALHQPLISFPRPVKTTWLNRNAPAQSKDSAIPTLESVVFGINYTKQLSPDGCSFLIAESFLHHAYHFHYTLCATLLLAFKGLHSYFITVTEEIPSCQKLDLAKASMQVLYERLLRRTQPRTQNDTCLEEMDVEARLTELCEEVKKVENPDELAELINMNLAQLCSLLMALWGQFLEAITLHEDLRVLLAQEHHTLRVRRFSEAFFCFEHPREAAIAYQELQHDISLSSFRS
IRESfinder result
IRESfinder score
0.636380977
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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