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mmu_circApba1_981
Basic information of circular RNA
PanCircBase ID:
mmu_circApba1_981
mm39_Chr. Position ID:
chr19|23889818|23914997|+
Gene name:
Apba1
Transcript:
ENSMUST00000025830.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
3,4,5,6,7,8,9,10
Exon/intron offsets:
0,3496,5098,20229,21245,22320,23963,24966
Genomic length:
25179
Exon/intron sizes in nt:
9,64,01,46,33,87,18,61,00,000
Flanking exon/introns:
chr19:23871384-23889818|chr19:23914997-23921374
Splice length:
981
Other database IDs:
circAtlas: mmu-Apba1_0003
circBase: hsa_circ_0138907, circAtlas: hsa-APBA1_0003, CIRCpedia: HSA_CIRCpedia_111430
Human Ortholog IDs:
Mature spliced Sequence:
TCTCCGTCTCCTGGCAGTTCCTCACCCCTGGGTGCTGAGTCATCAAGCATACCCCTTCATCCCGGCGACCCCACGGAAGCCTCCACAAATAAAGAGTCAAGAAAAAGCTTGGCTTCATTCCCAACCTACGTTGAAGTTCCTGGACCGTGCGACCCTGAAGACTTGATCGATGGAATTATTTTTGCTGCCAATTACCTTGGTTCCACTCAGCTACTCTCAGACAAAACTCCCTCCAAAAATGTACGCATGATGCAGGCCCAGGAAGCAGTAAGCCGGATCAAGACGGCCCAGAAATTAGCCAAAAGCAGGAAGAAGGCTCCTGAAGGCGAATCTCAGCCAATGACTGAGGTGGACCTGTTCATCTCTACCCAGAGGATCAAAGTACTGAATGCGGATACACAGGAACCTATGATGGACCACCCTCTGAGGACCATTTCCTACATCGCAGACATTGGCAACATCGTCGTGCTGATGGCCCGCAGGCGGATGCCCCGTTCTAACTCCCAGGAAAATGTGGAGGCCTCTCACCCTTCCCAGGATGGAAAAAGACAGTACAAGATGATCTGCCATGTCTTTGAGTCTGAGGACGCCCAGCTGATCGCGCAGTCCATAGGACAGGCATTCAGTGTTGCGTACCAGGAATTCCTCAGGGCCAATGGCATCAACCCAGAAGACCTCAGCCAGAAGGAATACAGTGACCTGCTCAACACCCAGGACATGTACAACGATGACCTGATCCACTTCTCCAAGTCGGAAAACTGCAAAGATGTCTTCATAGAGAAGCAGAAAGGTGAGATCCTGGGAGTTGTGATTGTGGAGTCTGGCTGGGGATCCATTCTGCCAACCGTGATCATTGCCAACATGATGCACGGGGGCCCTGCAGAGAAGTCGGGGAAGCTGAATATCGGGGACCAGATCATGTCCATCAACGGCACCAGCCTGGTGGGCCTGCCTCTCTCTACCTGCCAGAGCATCATTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGGAAGCTGAATATCGGGG
59.96
TGCTTGATGACTCAGCACCC
60.32
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGGAAGCTGAATATCGGGG
59.96
CGGGATGAAGGGGTATGCTT
59.53
155
PCR template sequence:
AGAGAAGTCGGGGAAGCTGAATATCGGGGACCAGATCATGTCCATCAACGGCACCAGCCTGGTGGGCCTGCCTCTCTCTACCTGCCAGAGCATCATTAAGTCTCCGTCTCCTGGCAGTTCCTCACCCCTGGGTGCTGAGTCATCAAGCATACCCCTTCATCCCGGCGACCCCACGGAAGCCTCCACAAATAAAGAGTCAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-138-5p(1), mmu-miR-351-5p(1), mmu-miR-182-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GAGCATCATTAAGTCTCCGTCTCCTG
siRNA sets
GACGGAGACTTAATGATGC, ACGGAGACTTAATGATGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAPBA1_981_ORF_1
1.3192
0.441468634
0.99998826
1716
ORF sequence:
ATGATGCAGGCCCAGGAAGCAGTAAGCCGGATCAAGACGGCCCAGAAATTAGCCAAAAGCAGGAAGAAGGCTCCTGAAGGCGAATCTCAGCCAATGACTGAGGTGGACCTGTTCATCTCTACCCAGAGGATCAAAGTACTGAATGCGGATACACAGGAACCTATGATGGACCACCCTCTGAGGACCATTTCCTACATCGCAGACATTGGCAACATCGTCGTGCTGATGGCCCGCAGGCGGATGCCCCGTTCTAACTCCCAGGAAAATGTGGAGGCCTCTCACCCTTCCCAGGATGGAAAAAGACAGTACAAGATGATCTGCCATGTCTTTGAGTCTGAGGACGCCCAGCTGATCGCGCAGTCCATAGGACAGGCATTCAGTGTTGCGTACCAGGAATTCCTCAGGGCCAATGGCATCAACCCAGAAGACCTCAGCCAGAAGGAATACAGTGACCTGCTCAACACCCAGGACATGTACAACGATGACCTGATCCACTTCTCCAAGTCGGAAAACTGCAAAGATGTCTTCATAGAGAAGCAGAAAGGTGAGATCCTGGGAGTTGTGATTGTGGAGTCTGGCTGGGGATCCATTCTGCCAACCGTGATCATTGCCAACATGATGCACGGGGGCCCTGCAGAGAAGTCGGGGAAGCTGAATATCGGGGACCAGATCATGTCCATCAACGGCACCAGCCTGGTGGGCCTGCCTCTCTCTACCTGCCAGAGCATCATTAAGTCTCCGTCTCCTGGCAGTTCCTCACCCCTGGGTGCTGAGTCATCAAGCATACCCCTTCATCCCGGCGACCCCACGGAAGCCTCCACAAATAAAGAGTCAAGAAAAAGCTTGGCTTCATTCCCAACCTACGTTGAAGTTCCTGGACCGTGCGACCCTGAAGACTTGATCGATGGAATTATTTTTGCTGCCAATTACCTTGGTTCCACTCAGCTACTCTCAGACAAAACTCCCTCCAAAAATGTACGCATGATGCAGGCCCAGGAAGCAGTAAGCCGGATCAAGACGGCCCAGAAATTAGCCAAAAGCAGGAAGAAGGCTCCTGAAGGCGAATCTCAGCCAATGACTGAGGTGGACCTGTTCATCTCTACCCAGAGGATCAAAGTACTGAATGCGGATACACAGGAACCTATGATGGACCACCCTCTGAGGACCATTTCCTACATCGCAGACATTGGCAACATCGTCGTGCTGATGGCCCGCAGGCGGATGCCCCGTTCTAACTCCCAGGAAAATGTGGAGGCCTCTCACCCTTCCCAGGATGGAAAAAGACAGTACAAGATGATCTGCCATGTCTTTGAGTCTGAGGACGCCCAGCTGATCGCGCAGTCCATAGGACAGGCATTCAGTGTTGCGTACCAGGAATTCCTCAGGGCCAATGGCATCAACCCAGAAGACCTCAGCCAGAAGGAATACAGTGACCTGCTCAACACCCAGGACATGTACAACGATGACCTGATCCACTTCTCCAAGTCGGAAAACTGCAAAGATGTCTTCATAGAGAAGCAGAAAGGTGAGATCCTGGGAGTTGTGATTGTGGAGTCTGGCTGGGGATCCATTCTGCCAACCGTGATCATTGCCAACATGATGCACGGGGGCCCTGCAGAGAAGTCGGGGAAGCTGAATATCGGGGACCAGATCATGTCCATCAACGGCACCAGCCTGGTGGGCCTGCCTCTCTCTACCTGCCAGAGCATCATTAAG
Peptide sequence:
MMQAQEAVSRIKTAQKLAKSRKKAPEGESQPMTEVDLFISTQRIKVLNADTQEPMMDHPLRTISYIADIGNIVVLMARRRMPRSNSQENVEASHPSQDGKRQYKMICHVFESEDAQLIAQSIGQAFSVAYQEFLRANGINPEDLSQKEYSDLLNTQDMYNDDLIHFSKSENCKDVFIEKQKGEILGVVIVESGWGSILPTVIIANMMHGGPAEKSGKLNIGDQIMSINGTSLVGLPLSTCQSIIKSPSPGSSSPLGAESSSIPLHPGDPTEASTNKESRKSLASFPTYVEVPGPCDPEDLIDGIIFAANYLGSTQLLSDKTPSKNVRMMQAQEAVSRIKTAQKLAKSRKKAPEGESQPMTEVDLFISTQRIKVLNADTQEPMMDHPLRTISYIADIGNIVVLMARRRMPRSNSQENVEASHPSQDGKRQYKMICHVFESEDAQLIAQSIGQAFSVAYQEFLRANGINPEDLSQKEYSDLLNTQDMYNDDLIHFSKSENCKDVFIEKQKGEILGVVIVESGWGSILPTVIIANMMHGGPAEKSGKLNIGDQIMSINGTSLVGLPLSTCQSIIK
IRESfinder result
IRESfinder score
0.336425857
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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