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mmu_circSrpk2_1302
Basic information of circular RNA
PanCircBase ID:
mmu_circSrpk2_1302
mm39_Chr. Position ID:
chr5|23729145|23753561|-
Gene name:
Srpk2
Transcript:
ENSMUST00000088392.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
10,9,8,7,6,5,4,3
Exon/intron offsets:
0,1348,2642,3749,16227,21375,22832,24307
Genomic length:
24416
Exon/intron sizes in nt:
46,82,50,26,16,61,07,80,00,000
Flanking exon/introns:
chr5:23723717-23729145|chr5:23753561-23770111
Splice length:
1302
Other database IDs:
CIRCpedia: MMU_CIRCpedia_13917, circAtlas: mmu-Srpk2_0009
circBase: hsa_circ_0081831, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_56165
Human Ortholog IDs:
Mature spliced Sequence:
GTGGCTATCATCCAGTGAAAATTGGAGATCTCTTCAATGGTCGATATCATGTCATTAGAAAGCTAGGATGGGGGCACTTTTCTACTGTATGGCTGTGCTGGGATATGCAAGGGAAAAGATTTGTTGCAATGAAAGTTGTAAAAAGTGCCCAGCATTATACAGAGACAGCCTTGGATGAAATTAAACTACTCAAATGCGTTCGAGAAAGTGACCCCAGTGACCCAAACAAAGACATGGTAGTTCAGCTAATTGATGACTTCAAGATCTCAGGCATGAATGGGATACATGTCTGCATGGTCTTTGAAGTACTTGGTCACCATCTCCTCAAATGGATCATCAAATCCAACTATCAAGGCCTCCCAGTACGTTGTGTGAAGAGTATCATTCGACAGGTCCTTCAAGGGTTAGATTATCTACACAGTAAGTGCAAGATAATTCACACCGACATAAAGCCGGAAAACATCTTGATGTGTGTGGATGACGCTTACGTGAGAAGAATGGCAGCCGAAGCCACGGAGTGGCAGAAAGCAGGTGCTCCTCCTCCCTCTGGGTCTGCAGTGAGTACGGCTCCACAGCAAAAACCTATAGGAAAAATATCTAAAAACAAAAAGAAAAAGCTGAAAAAGAAACAGAAGAGACAGGCTGAGTTGCTGGAGAAACGCCTACAGGAGATTGAGGAATTGGAGCGAGAAGCCGAAAGGAAAATCCTAGAGGAGAACATCACCTCTGCAGAAGCTTCCGGGGAGCAGCAGGATGGAGAGTACCAGCCGGAGGTGACACTGAAAGCAGCCGACTTAGAGGACACAACTGAGGAAGAGACAGCAAAGGATAATGGTGAAGTTGAAGACCAGGAAGAGAAAGAAGATGCAGAGAAGGAGAACGCGGAGAAGGATGAAGATGATGTTGAACAGGAACTTGCAAACTTAGACCCTACCTGGGTGGAGTCCCCGAAAGCCAATGGCCATATTGAAAATGGCCCGTTCTCACTGGAGCAGCAGCTGGAGGATGAAGAGGACGATGAAGATGACTGTGCAAATCCCGAGGAGTATAACCTCGATGAGCCAAATGCAGAGAGTGATTACACGTATAGCAGCTCCTATGAACAATTCAATGGTGAATTGCCAAATGGACAACATAAGACTTCAGAGTTTCCCACACCGTTGTTTTCTGGGCCCTTAGAACCTGTGGCCTGTGGCTCTGTGATTTCAGAGGGATCGCCACTTACCGAGCAGGAGGAAAGCAGTCCCTCCCATGACAGAAGCAGGACAGTTTCAGCCTCTAGTACTGGAGATTTGCCAAAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGAGGGATCGCCACTTACC
59.89
AAAAGTGCCCCCATCCTAGC
60.03
177
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCCTCCCATGACAGAAGC
60.11
AAAAGTGCCCCCATCCTAGC
60.03
141
PCR template sequence:
ATTTCAGAGGGATCGCCACTTACCGAGCAGGAGGAAAGCAGTCCCTCCCATGACAGAAGCAGGACAGTTTCAGCCTCTAGTACTGGAGATTTGCCAAAAAGTGGCTATCATCCAGTGAAAATTGGAGATCTCTTCAATGGTCGATATCATGTCATTAGAAAGCTAGGATGGGGGCACTTTTCTACTGTATGGCTGTGCTG
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-20b-5p(1), mmu-miR-93-5p(1), mmu-miR-17-5p(1), mmu-miR-298-5p(1), mmu-miR-129-5p(1), mmu-miR-207(1), mmu-miR-5101(1)
siRNAs for circular RNA silencing
Junction sequence
GATTTGCCAAAAAGTGGCTATCATCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSRPK2_1302_ORF_1
1.0477
0.286623389
0.999999869
2499
ORF sequence:
ATGCAAGGGAAAAGATTTGTTGCAATGAAAGTTGTAAAAAGTGCCCAGCATTATACAGAGACAGCCTTGGATGAAATTAAACTACTCAAATGCGTTCGAGAAAGTGACCCCAGTGACCCAAACAAAGACATGGTAGTTCAGCTAATTGATGACTTCAAGATCTCAGGCATGAATGGGATACATGTCTGCATGGTCTTTGAAGTACTTGGTCACCATCTCCTCAAATGGATCATCAAATCCAACTATCAAGGCCTCCCAGTACGTTGTGTGAAGAGTATCATTCGACAGGTCCTTCAAGGGTTAGATTATCTACACAGTAAGTGCAAGATAATTCACACCGACATAAAGCCGGAAAACATCTTGATGTGTGTGGATGACGCTTACGTGAGAAGAATGGCAGCCGAAGCCACGGAGTGGCAGAAAGCAGGTGCTCCTCCTCCCTCTGGGTCTGCAGTGAGTACGGCTCCACAGCAAAAACCTATAGGAAAAATATCTAAAAACAAAAAGAAAAAGCTGAAAAAGAAACAGAAGAGACAGGCTGAGTTGCTGGAGAAACGCCTACAGGAGATTGAGGAATTGGAGCGAGAAGCCGAAAGGAAAATCCTAGAGGAGAACATCACCTCTGCAGAAGCTTCCGGGGAGCAGCAGGATGGAGAGTACCAGCCGGAGGTGACACTGAAAGCAGCCGACTTAGAGGACACAACTGAGGAAGAGACAGCAAAGGATAATGGTGAAGTTGAAGACCAGGAAGAGAAAGAAGATGCAGAGAAGGAGAACGCGGAGAAGGATGAAGATGATGTTGAACAGGAACTTGCAAACTTAGACCCTACCTGGGTGGAGTCCCCGAAAGCCAATGGCCATATTGAAAATGGCCCGTTCTCACTGGAGCAGCAGCTGGAGGATGAAGAGGACGATGAAGATGACTGTGCAAATCCCGAGGAGTATAACCTCGATGAGCCAAATGCAGAGAGTGATTACACGTATAGCAGCTCCTATGAACAATTCAATGGTGAATTGCCAAATGGACAACATAAGACTTCAGAGTTTCCCACACCGTTGTTTTCTGGGCCCTTAGAACCTGTGGCCTGTGGCTCTGTGATTTCAGAGGGATCGCCACTTACCGAGCAGGAGGAAAGCAGTCCCTCCCATGACAGAAGCAGGACAGTTTCAGCCTCTAGTACTGGAGATTTGCCAAAAAGTGGCTATCATCCAGTGAAAATTGGAGATCTCTTCAATGGTCGATATCATGTCATTAGAAAGCTAGGATGGGGGCACTTTTCTACTGTATGGCTGTGCTGGGATATGCAAGGGAAAAGATTTGTTGCAATGAAAGTTGTAAAAAGTGCCCAGCATTATACAGAGACAGCCTTGGATGAAATTAAACTACTCAAATGCGTTCGAGAAAGTGACCCCAGTGACCCAAACAAAGACATGGTAGTTCAGCTAATTGATGACTTCAAGATCTCAGGCATGAATGGGATACATGTCTGCATGGTCTTTGAAGTACTTGGTCACCATCTCCTCAAATGGATCATCAAATCCAACTATCAAGGCCTCCCAGTACGTTGTGTGAAGAGTATCATTCGACAGGTCCTTCAAGGGTTAGATTATCTACACAGTAAGTGCAAGATAATTCACACCGACATAAAGCCGGAAAACATCTTGATGTGTGTGGATGACGCTTACGTGAGAAGAATGGCAGCCGAAGCCACGGAGTGGCAGAAAGCAGGTGCTCCTCCTCCCTCTGGGTCTGCAGTGAGTACGGCTCCACAGCAAAAACCTATAGGAAAAATATCTAAAAACAAAAAGAAAAAGCTGAAAAAGAAACAGAAGAGACAGGCTGAGTTGCTGGAGAAACGCCTACAGGAGATTGAGGAATTGGAGCGAGAAGCCGAAAGGAAAATCCTAGAGGAGAACATCACCTCTGCAGAAGCTTCCGGGGAGCAGCAGGATGGAGAGTACCAGCCGGAGGTGACACTGAAAGCAGCCGACTTAGAGGACACAACTGAGGAAGAGACAGCAAAGGATAATGGTGAAGTTGAAGACCAGGAAGAGAAAGAAGATGCAGAGAAGGAGAACGCGGAGAAGGATGAAGATGATGTTGAACAGGAACTTGCAAACTTAGACCCTACCTGGGTGGAGTCCCCGAAAGCCAATGGCCATATTGAAAATGGCCCGTTCTCACTGGAGCAGCAGCTGGAGGATGAAGAGGACGATGAAGATGACTGTGCAAATCCCGAGGAGTATAACCTCGATGAGCCAAATGCAGAGAGTGATTACACGTATAGCAGCTCCTATGAACAATTCAATGGTGAATTGCCAAATGGACAACATAAGACTTCAGAGTTTCCCACACCGTTGTTTTCTGGGCCCTTAGAACCTGTGGCCTGTGGCTCTGTGATTTCAGAGGGATCGCCACTTACCGAGCAGGAGGAAAGCAGTCCCTCCCATGACAGAAGCAGGACAGTTTCAGCCTCTAGTACTGGAGATTTGCCAAAA
Peptide sequence:
MQGKRFVAMKVVKSAQHYTETALDEIKLLKCVRESDPSDPNKDMVVQLIDDFKISGMNGIHVCMVFEVLGHHLLKWIIKSNYQGLPVRCVKSIIRQVLQGLDYLHSKCKIIHTDIKPENILMCVDDAYVRRMAAEATEWQKAGAPPPSGSAVSTAPQQKPIGKISKNKKKKLKKKQKRQAELLEKRLQEIEELEREAERKILEENITSAEASGEQQDGEYQPEVTLKAADLEDTTEEETAKDNGEVEDQEEKEDAEKENAEKDEDDVEQELANLDPTWVESPKANGHIENGPFSLEQQLEDEEDDEDDCANPEEYNLDEPNAESDYTYSSSYEQFNGELPNGQHKTSEFPTPLFSGPLEPVACGSVISEGSPLTEQEESSPSHDRSRTVSASSTGDLPKSGYHPVKIGDLFNGRYHVIRKLGWGHFSTVWLCWDMQGKRFVAMKVVKSAQHYTETALDEIKLLKCVRESDPSDPNKDMVVQLIDDFKISGMNGIHVCMVFEVLGHHLLKWIIKSNYQGLPVRCVKSIIRQVLQGLDYLHSKCKIIHTDIKPENILMCVDDAYVRRMAAEATEWQKAGAPPPSGSAVSTAPQQKPIGKISKNKKKKLKKKQKRQAELLEKRLQEIEELEREAERKILEENITSAEASGEQQDGEYQPEVTLKAADLEDTTEEETAKDNGEVEDQEEKEDAEKENAEKDEDDVEQELANLDPTWVESPKANGHIENGPFSLEQQLEDEEDDEDDCANPEEYNLDEPNAESDYTYSSSYEQFNGELPNGQHKTSEFPTPLFSGPLEPVACGSVISEGSPLTEQEESSPSHDRSRTVSASSTGDLPK
IRESfinder result
IRESfinder score
0.364456746
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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