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mmu_circSlmap_1019
Basic information of circular RNA
PanCircBase ID:
mmu_circSlmap_1019
mm39_Chr. Position ID:
chr14|26159833|26191555|-
Gene name:
Slmap
Transcript:
ENSMUST00000102956.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
16,15,14,13,12,11,10,9,8,7,6,5
Exon/intron offsets:
0,269,3896,20731,21225,21363,23582,24897,26522,26889,29804,31685
Genomic length:
31722
Exon/intron sizes in nt:
60,81,60,51,51,169,138,141,72,96,63,37
Flanking exon/introns:
chr14:26151065-26159833|chr14:26191555-26195053
Splice length:
1019
Other database IDs:
circAtlas: mmu-Slmap_0011
circBase: hsa_circ_0066282, circAtlas: hsa-SLMAP_0011, CIRCpedia: HSA_CIRCpedia_165180
Human Ortholog IDs:
Mature spliced Sequence:
TGTCATCCATGCTCCATTACCGAGTCCTGTAGACAAAGTTGCTGCTAACACTCCAAGTATGTACTCTCAGGAACTATTCCAACTTTCTCAGTATCTACAGGAGGCCTTACATCGGGAACAGATGTTGGAACAGAAGTTAGCCACACTTCAGCGGCTACTAGCCATCACCCAAGAGGCTTCAGATACTAGTTGGCAGGCTTTAATAGATGAAGATAGACTCTTATCACGGTTAGAAGTTATGGGAAACCAGTTGCAGGCATGCTCCAAAAATCAAACAGAAGACAGTTTACGGAAGGAGCTGATTGCACTGCAGGAGGATAAACACAGCTATGAAACCACAGCCAAAGAGTCCCTGAGGCGGGTTCTTCAGGAGAAAATCGAAGTGGTTAGAAAACTTTCAGAAGTTGAGCGAAGTCTGAGTAATACTGAAGATGAATGTACCCACCTGAAAGAGATGAATGAGCGCACTCAGGAAGAGTTGAGAGAATTAGCCAATAAATATAATGGAGCAGTTAATGAAATTAAAGATTTATCTGATAAATTAAAGGTAGCAGAGGGAAAACAAGAGGAAATCCAACAGAAGGGACAAGCTGAGAAGAAGGAATTACAGACGAAAATTGATGAAATGGAAGAAAAAGAACAAGAGCTCCAGGCAAAAATCGAAGCTTTGCAAGCTGATAACGACTTCACCAATGAAAGGCTGACAGCTCTGCAAGTACGGTTAGAACACCTGCAGGAGAAAACCCTTAAAGAATGCAGCAGCTTAGGGATACAAGTTGATGACTTCTTACCTAAAATAAATGGGAGCACAGAAAAAGAGAAGCTGATGGTCCAAGGGCATCTAACCAAAGTGGTAGAAGAATCAAAGCTTTCAAAAGAAAATCAGGCAAAAGCAAAGGAATCCGACTTATCAGACACTCTGAGTCCAAGCAAGGAAAAAAGCAGCGACGACACTACAGACGCCCAGATGGATGAGCAAGACCTAAATGAACCCCTTGCTAAGGTGTCTCTATTAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAGCAGCGACGACACTACA
59.97
ACATACTTGGAGTGTTAGCAGCA
59.99
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAGCAGCGACGACACTACA
59.97
TACTTGGAGTGTTAGCAGCAACT
59.93
140
PCR template sequence:
CTGAGTCCAAGCAAGGAAAAAAGCAGCGACGACACTACAGACGCCCAGATGGATGAGCAAGACCTAAATGAACCCCTTGCTAAGGTGTCTCTATTAAAAGTGTCATCCATGCTCCATTACCGAGTCCTGTAGACAAAGTTGCTGCTAACACTCCAAGTATGTACTCTCAGGAACTATTCCAACTTTCTCAGTATCTACAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-181b-5p(2), mmu-miR-29b-1-5p(2), mmu-miR-29b-2-5p(2), mmu-miR-181d-5p(2), mmu-miR-9-5p(1), mmu-miR-34c-5p(1), mmu-miR-122-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-136-5p(1), mmu-miR-721(1), mmu-miR-34b-5p(1), mmu-miR-301a-3p(1), mmu-miR-129-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTCTATTAAAAGTGTCATCCATGCT
siRNA sets
ATGACACTTTTAATAGAGA,GATGACACTTTTAATAGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSLMAP_1019_ORF_1
1.1116
0.219359866
0.992148179
993
ORF sequence:
ATGTACTCTCAGGAACTATTCCAACTTTCTCAGTATCTACAGGAGGCCTTACATCGGGAACAGATGTTGGAACAGAAGTTAGCCACACTTCAGCGGCTACTAGCCATCACCCAAGAGGCTTCAGATACTAGTTGGCAGGCTTTAATAGATGAAGATAGACTCTTATCACGGTTAGAAGTTATGGGAAACCAGTTGCAGGCATGCTCCAAAAATCAAACAGAAGACAGTTTACGGAAGGAGCTGATTGCACTGCAGGAGGATAAACACAGCTATGAAACCACAGCCAAAGAGTCCCTGAGGCGGGTTCTTCAGGAGAAAATCGAAGTGGTTAGAAAACTTTCAGAAGTTGAGCGAAGTCTGAGTAATACTGAAGATGAATGTACCCACCTGAAAGAGATGAATGAGCGCACTCAGGAAGAGTTGAGAGAATTAGCCAATAAATATAATGGAGCAGTTAATGAAATTAAAGATTTATCTGATAAATTAAAGGTAGCAGAGGGAAAACAAGAGGAAATCCAACAGAAGGGACAAGCTGAGAAGAAGGAATTACAGACGAAAATTGATGAAATGGAAGAAAAAGAACAAGAGCTCCAGGCAAAAATCGAAGCTTTGCAAGCTGATAACGACTTCACCAATGAAAGGCTGACAGCTCTGCAAGTACGGTTAGAACACCTGCAGGAGAAAACCCTTAAAGAATGCAGCAGCTTAGGGATACAAGTTGATGACTTCTTACCTAAAATAAATGGGAGCACAGAAAAAGAGAAGCTGATGGTCCAAGGGCATCTAACCAAAGTGGTAGAAGAATCAAAGCTTTCAAAAGAAAATCAGGCAAAAGCAAAGGAATCCGACTTATCAGACACTCTGAGTCCAAGCAAGGAAAAAAGCAGCGACGACACTACAGACGCCCAGATGGATGAGCAAGACCTAAATGAACCCCTTGCTAAGGTGTCTCTATTAAAAGTGTCATCCATGCTCCATTACCGAGTCCTGTAG
Peptide sequence:
MYSQELFQLSQYLQEALHREQMLEQKLATLQRLLAITQEASDTSWQALIDEDRLLSRLEVMGNQLQACSKNQTEDSLRKELIALQEDKHSYETTAKESLRRVLQEKIEVVRKLSEVERSLSNTEDECTHLKEMNERTQEELRELANKYNGAVNEIKDLSDKLKVAEGKQEEIQQKGQAEKKELQTKIDEMEEKEQELQAKIEALQADNDFTNERLTALQVRLEHLQEKTLKECSSLGIQVDDFLPKINGSTEKEKLMVQGHLTKVVEESKLSKENQAKAKESDLSDTLSPSKEKSSDDTTDAQMDEQDLNEPLAKVSLLKVSSMLHYRVL
IRESfinder result
IRESfinder score
0.445926791
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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