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mmu_circNdst1_924
Basic information of circular RNA
PanCircBase ID:
mmu_circNdst1_924
mm39_Chr. Position ID:
chr18|60835844|60841167|-
Gene name:
Ndst1
Transcript:
ENSMUST00000237783.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,964,2303,4828
Genomic length:
5323
Exon/intron sizes in nt:
18,61,55,88,495
Flanking exon/introns:
chr18:60833572-60835844|chr18:60841167-60845794
Splice length:
924
Other database IDs:
circAtlas: mmu-Ndst1_0001
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GCCAATGAGAACAGCCTGCTGAGTGCACAGCTCAAAGGCTTCCCTCTCTTCCTGCATTCGAACCTGGGCTTGAAAGACTGCAGCATCAACCCCAAGTCACCACTGCTCTATGTGACACGGCCCAGTGAGGTAGAGAAAGGCGTGCTGCCCGGAGAGGATTGGACTGTGTTCCAGTCCAACCATTCTACCTACGAACCAGTGCTGTTGGCCAAGACACGCTCCTCCGAATCCATCCCACACCTGGGTGCTGATGCTGGCCTGCATGCTGCGCTGCACGCTACTGTGGTCCAGGACCTGGGTCTCCACGATGGCATCCAGCGTGTGCTCTTTGGCAACAACCTCAACTTTTGGCTGCATAAGCTTGTCTTCGTGGATGCTGTGGCCTTCCTCACGGGGAAGCGCCTCTCACTGCCTTTGGACCGATACATCCTGGTGGATATTGATGACATTTTTGTGGGCAAGGAGGGCACACGCATGAAGGTGGAGGATGTGAAGGCCCTGTTTGATACACAGAATGAACTCCGCACACATATTCCAAACTTCACCTTCAACCTGGGCTACTCAGGGAAATTCTTCCACACAGGTACGGATGCTGAGGATGCTGGCGACGATCTGCTGTTGTCCTATGTGAAAGAGTTCTGGTGGTTCCCCCACATGTGGAGCCATATGCAACCCCACCTCTTCCACAACCAATCTGTGCTGGCAGAGCAGATGGCCCTGAACAAGAAGTTCGCTGTCGAGCACGGCATCCCCACAGATATGGGCTATGCGGTGGCGCCCCACCACTCCGGTGTGTACCCTGTGCACGTGCAGCTGTATGAGGCCTGGAAGCAAGTGTGGGGCATCCGTGTGACCAGCACAGAGGAGTACCCACATCTGAAGCCGGCCCGGTACCGCCGTGGCTTTATCCACAATGGCATCATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCACAGAGGAGTACCCACA
60.18
TGCAGTCTTTCAAGCCCAGG
60.54
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCACAGAGGAGTACCCACA
60.18
GCAGTCTTTCAAGCCCAGGT
60.54
150
PCR template sequence:
CTGGAAGCAAGTGTGGGGCATCCGTGTGACCAGCACAGAGGAGTACCCACATCTGAAGCCGGCCCGGTACCGCCGTGGCTTTATCCACAATGGCATCATGGCCAATGAGAACAGCCTGCTGAGTGCACAGCTCAAAGGCTTCCCTCTCTTCCTGCATTCGAACCTGGGCTTGAAAGACTGCAGCATCAACCCCAAGTCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-125b-5p(1), mmu-miR-351-5p(1), mmu-miR-1187(1), mmu-miR-670-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAATGGCATCATGGCCAATGAGAACA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNDST1_924_ORF_1
1.2746
0.456892512
0.999859094
1374
ORF sequence:
ATGAAGGTGGAGGATGTGAAGGCCCTGTTTGATACACAGAATGAACTCCGCACACATATTCCAAACTTCACCTTCAACCTGGGCTACTCAGGGAAATTCTTCCACACAGGTACGGATGCTGAGGATGCTGGCGACGATCTGCTGTTGTCCTATGTGAAAGAGTTCTGGTGGTTCCCCCACATGTGGAGCCATATGCAACCCCACCTCTTCCACAACCAATCTGTGCTGGCAGAGCAGATGGCCCTGAACAAGAAGTTCGCTGTCGAGCACGGCATCCCCACAGATATGGGCTATGCGGTGGCGCCCCACCACTCCGGTGTGTACCCTGTGCACGTGCAGCTGTATGAGGCCTGGAAGCAAGTGTGGGGCATCCGTGTGACCAGCACAGAGGAGTACCCACATCTGAAGCCGGCCCGGTACCGCCGTGGCTTTATCCACAATGGCATCATGGCCAATGAGAACAGCCTGCTGAGTGCACAGCTCAAAGGCTTCCCTCTCTTCCTGCATTCGAACCTGGGCTTGAAAGACTGCAGCATCAACCCCAAGTCACCACTGCTCTATGTGACACGGCCCAGTGAGGTAGAGAAAGGCGTGCTGCCCGGAGAGGATTGGACTGTGTTCCAGTCCAACCATTCTACCTACGAACCAGTGCTGTTGGCCAAGACACGCTCCTCCGAATCCATCCCACACCTGGGTGCTGATGCTGGCCTGCATGCTGCGCTGCACGCTACTGTGGTCCAGGACCTGGGTCTCCACGATGGCATCCAGCGTGTGCTCTTTGGCAACAACCTCAACTTTTGGCTGCATAAGCTTGTCTTCGTGGATGCTGTGGCCTTCCTCACGGGGAAGCGCCTCTCACTGCCTTTGGACCGATACATCCTGGTGGATATTGATGACATTTTTGTGGGCAAGGAGGGCACACGCATGAAGGTGGAGGATGTGAAGGCCCTGTTTGATACACAGAATGAACTCCGCACACATATTCCAAACTTCACCTTCAACCTGGGCTACTCAGGGAAATTCTTCCACACAGGTACGGATGCTGAGGATGCTGGCGACGATCTGCTGTTGTCCTATGTGAAAGAGTTCTGGTGGTTCCCCCACATGTGGAGCCATATGCAACCCCACCTCTTCCACAACCAATCTGTGCTGGCAGAGCAGATGGCCCTGAACAAGAAGTTCGCTGTCGAGCACGGCATCCCCACAGATATGGGCTATGCGGTGGCGCCCCACCACTCCGGTGTGTACCCTGTGCACGTGCAGCTGTATGAGGCCTGGAAGCAAGTGTGGGGCATCCGTGTGACCAGCACAGAGGAGTACCCACATCTGAAGCCGGCCCGGTACCGCCGTGGCTTTATCCACAATGGCATCATG
Peptide sequence:
MKVEDVKALFDTQNELRTHIPNFTFNLGYSGKFFHTGTDAEDAGDDLLLSYVKEFWWFPHMWSHMQPHLFHNQSVLAEQMALNKKFAVEHGIPTDMGYAVAPHHSGVYPVHVQLYEAWKQVWGIRVTSTEEYPHLKPARYRRGFIHNGIMANENSLLSAQLKGFPLFLHSNLGLKDCSINPKSPLLYVTRPSEVEKGVLPGEDWTVFQSNHSTYEPVLLAKTRSSESIPHLGADAGLHAALHATVVQDLGLHDGIQRVLFGNNLNFWLHKLVFVDAVAFLTGKRLSLPLDRYILVDIDDIFVGKEGTRMKVEDVKALFDTQNELRTHIPNFTFNLGYSGKFFHTGTDAEDAGDDLLLSYVKEFWWFPHMWSHMQPHLFHNQSVLAEQMALNKKFAVEHGIPTDMGYAVAPHHSGVYPVHVQLYEAWKQVWGIRVTSTEEYPHLKPARYRRGFIHNGIM
IRESfinder result
IRESfinder score
0.326995961
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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