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mmu_circNipsnap2_339
Basic information of circular RNA
PanCircBase ID:
mmu_circNipsnap2_339
mm39_Chr. Position ID:
chr5|129821768|129825097|+
Gene name:
Nipsnap2
Transcript:
ENSMUST00000086046.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
4,5,6,7
Exon/intron offsets:
0,511,1622,3297
Genomic length:
3329
Exon/intron sizes in nt:
95,71,141,32
Flanking exon/introns:
chr5:129816827-129821768|chr5:129825097-129830289
Splice length:
339
Other database IDs:
circAtlas: mmu-Gbas_0005
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
TCAAGAAGTGTTACCAAAGATCCACGAAGGCAAGCAGTACCCTTGTACCCTGGTGGGGACGTGGAACACGTGGTATGGCGAGCAGGATCAAGCAGTCCACCTCTGGAGGTATGAAGGAGGCTATCCAGCCCTCACGGAGGTCATGAATAAACTCAAAGAAAACCAGGAATTTGTAAATTTCCGAAAGGCCAGAAGTGACATGCTTCTCTCCAGGAAGAACCAGCTGCTGCTGGAGTTCAGTTTCTGGAATGAGCCAGTGCCAAGACCGGGCCCCAATATATACGAACTCAGGTCCTACCAACTCCGACCAGGAACAATGATCGAGTGGGGCAACTACTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGGTCCTACCAACTCCGA
59.59
GTGGACTGCTTGATCCTGCT
60.04
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGGTCCTACCAACTCCGA
59.59
TTGATCCTGCTCGCCATACC
59.89
143
PCR template sequence:
GTTTCTGGAATGAGCCAGTGCCAAGACCGGGCCCCAATATATACGAACTCAGGTCCTACCAACTCCGACCAGGAACAATGATCGAGTGGGGCAACTACTGTCAAGAAGTGTTACCAAAGATCCACGAAGGCAAGCAGTACCCTTGTACCCTGGTGGGGACGTGGAACACGTGGTATGGCGAGCAGGATCAAGCAGTCCAC
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-205-5p(1), mmu-miR-322-5p(1), mmu-miR-185-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-96-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGGGCAACTACTGTCAAGAAGTGTTA
siRNA sets
TAACACTTCTTGACAGTAG, AACACTTCTTGACAGTAGT, TCTTGACAGTAGTTGCCCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNIPSNAP2_339_ORF_1
1.107
0.274764881
0.855273596
534
ORF sequence:
ATGAATAAACTCAAAGAAAACCAGGAATTTGTAAATTTCCGAAAGGCCAGAAGTGACATGCTTCTCTCCAGGAAGAACCAGCTGCTGCTGGAGTTCAGTTTCTGGAATGAGCCAGTGCCAAGACCGGGCCCCAATATATACGAACTCAGGTCCTACCAACTCCGACCAGGAACAATGATCGAGTGGGGCAACTACTGTCAAGAAGTGTTACCAAAGATCCACGAAGGCAAGCAGTACCCTTGTACCCTGGTGGGGACGTGGAACACGTGGTATGGCGAGCAGGATCAAGCAGTCCACCTCTGGAGGTATGAAGGAGGCTATCCAGCCCTCACGGAGGTCATGAATAAACTCAAAGAAAACCAGGAATTTGTAAATTTCCGAAAGGCCAGAAGTGACATGCTTCTCTCCAGGAAGAACCAGCTGCTGCTGGAGTTCAGTTTCTGGAATGAGCCAGTGCCAAGACCGGGCCCCAATATATACGAACTCAGGTCCTACCAACTCCGACCAGGAACAATGATCGAGTGGGGCAACTAC
Peptide sequence:
MNKLKENQEFVNFRKARSDMLLSRKNQLLLEFSFWNEPVPRPGPNIYELRSYQLRPGTMIEWGNYCQEVLPKIHEGKQYPCTLVGTWNTWYGEQDQAVHLWRYEGGYPALTEVMNKLKENQEFVNFRKARSDMLLSRKNQLLLEFSFWNEPVPRPGPNIYELRSYQLRPGTMIEWGNY
IRESfinder result
IRESfinder score
0.390802812
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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