top of page
mmu_circKcnma1_621
Basic information of circular RNA
PanCircBase ID:
mmu_circKcnma1_621
mm39_Chr. Position ID:
chr14|23576792|23641749|-
Gene name:
Kcnma1
Transcript:
ENSMUST00000172099.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
8,7,6,5,4,3
Exon/intron offsets:
0,1625,3494,16306,63916,64863
Genomic length:
64957
Exon/intron sizes in nt:
92,171,76,76,112,94
Flanking exon/introns:
chr14:23559968-23576792|chr14:23641749-23700192
Splice length:
621
Other database IDs:
circBase: mmu_circ_0005122, CIRCpedia: MMU_CIRCpedia_13918, circAtlas: mmu-Kcnma1_0005
circBase: hsa_circ_0094232, circAtlas: hsa-KCNMA1_0008, CIRCpedia: HSA_CIRCpedia_129103
Human Ortholog IDs:
Mature spliced Sequence:
CCCAATAGAATCCTGCCAGAATTTCTACAAAGATTTCACATTACAGATCGACATGGCTTTCAACGTGTTCTTCCTCCTCTACTTTGGCTTGCGGTTTATTGCAGCCAACGATAAGCTGTGGTTCTGGCTGGAAGTGAATTCAGTAGTAGATTTCTTCACAGTCCCTCCTGTGTTTGTGTCTGTGTACTTAAACAGAAGTTGGCTTGGCTTGAGATTTTTAAGAGCTCTCAGACTGATACAGTTTTCAGAGATTTTGCAGTTTCTGAATATCCTTAAAACAAGTAACTCCATCAAGCTGGTGAATCTGCTCTCCATATTTATCAGCACGTGGCTGACTGCAGCTGGATTCATCCACTTGGTGGAGAATTCAGGGGACCCATGGGAAAATTTCCAAAACAACCAGGCACTTACGTACTGGGAATGTGTCTACTTACTCATGGTCACAATGTCTACAGTGGGTTATGGGGACGTTTATGCAAAAACCACACTTGGACGCCTCTTCATGGTCTTCTTCATCCTCGGGGGACTGGCCATGTTTGCCAGCTACGTCCCTGAAATCATAGAGTTAATAGGAAACCGCAAGAAATACGGGGGCTCCTATAGCGCGGTTAGTGGAAGAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAGCTACGTCCCTGAAAT
60.11
CCGCAAGCCAAAGTAGAGGA
60.04
177
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAGCTACGTCCCTGAAAT
60.11
ACCGCAAGCCAAAGTAGAGG
60.32
178
PCR template sequence:
GGGGACTGGCCATGTTTGCCAGCTACGTCCCTGAAATCATAGAGTTAATAGGAAACCGCAAGAAATACGGGGGCTCCTATAGCGCGGTTAGTGGAAGAAACCCAATAGAATCCTGCCAGAATTTCTACAAAGATTTCACATTACAGATCGACATGGCTTTCAACGTGTTCTTCCTCCTCTACTTTGGCTTGCGGTTTATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-19a-3p(1), mmu-miR-216a-5p(1), mmu-miR-467b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTAGTGGAAGAAACCCAATAGAATCC
siRNA sets
ATTCTATTGGGTTTCTTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKCNMA1_621_ORF_1
1.0293
0.145326434
0.997009046
1188
ORF sequence:
ATGGCTTTCAACGTGTTCTTCCTCCTCTACTTTGGCTTGCGGTTTATTGCAGCCAACGATAAGCTGTGGTTCTGGCTGGAAGTGAATTCAGTAGTAGATTTCTTCACAGTCCCTCCTGTGTTTGTGTCTGTGTACTTAAACAGAAGTTGGCTTGGCTTGAGATTTTTAAGAGCTCTCAGACTGATACAGTTTTCAGAGATTTTGCAGTTTCTGAATATCCTTAAAACAAGTAACTCCATCAAGCTGGTGAATCTGCTCTCCATATTTATCAGCACGTGGCTGACTGCAGCTGGATTCATCCACTTGGTGGAGAATTCAGGGGACCCATGGGAAAATTTCCAAAACAACCAGGCACTTACGTACTGGGAATGTGTCTACTTACTCATGGTCACAATGTCTACAGTGGGTTATGGGGACGTTTATGCAAAAACCACACTTGGACGCCTCTTCATGGTCTTCTTCATCCTCGGGGGACTGGCCATGTTTGCCAGCTACGTCCCTGAAATCATAGAGTTAATAGGAAACCGCAAGAAATACGGGGGCTCCTATAGCGCGGTTAGTGGAAGAAACCCAATAGAATCCTGCCAGAATTTCTACAAAGATTTCACATTACAGATCGACATGGCTTTCAACGTGTTCTTCCTCCTCTACTTTGGCTTGCGGTTTATTGCAGCCAACGATAAGCTGTGGTTCTGGCTGGAAGTGAATTCAGTAGTAGATTTCTTCACAGTCCCTCCTGTGTTTGTGTCTGTGTACTTAAACAGAAGTTGGCTTGGCTTGAGATTTTTAAGAGCTCTCAGACTGATACAGTTTTCAGAGATTTTGCAGTTTCTGAATATCCTTAAAACAAGTAACTCCATCAAGCTGGTGAATCTGCTCTCCATATTTATCAGCACGTGGCTGACTGCAGCTGGATTCATCCACTTGGTGGAGAATTCAGGGGACCCATGGGAAAATTTCCAAAACAACCAGGCACTTACGTACTGGGAATGTGTCTACTTACTCATGGTCACAATGTCTACAGTGGGTTATGGGGACGTTTATGCAAAAACCACACTTGGACGCCTCTTCATGGTCTTCTTCATCCTCGGGGGACTGGCCATGTTTGCCAGCTACGTCCCTGAAATCATAGAGTTAATAGGAAACCGCAAGAAATACGGGGGCTCCTATAGCGCGGTTAGTGGAAGA
Peptide sequence:
MAFNVFFLLYFGLRFIAANDKLWFWLEVNSVVDFFTVPPVFVSVYLNRSWLGLRFLRALRLIQFSEILQFLNILKTSNSIKLVNLLSIFISTWLTAAGFIHLVENSGDPWENFQNNQALTYWECVYLLMVTMSTVGYGDVYAKTTLGRLFMVFFILGGLAMFASYVPEIIELIGNRKKYGGSYSAVSGRNPIESCQNFYKDFTLQIDMAFNVFFLLYFGLRFIAANDKLWFWLEVNSVVDFFTVPPVFVSVYLNRSWLGLRFLRALRLIQFSEILQFLNILKTSNSIKLVNLLSIFISTWLTAAGFIHLVENSGDPWENFQNNQALTYWECVYLLMVTMSTVGYGDVYAKTTLGRLFMVFFILGGLAMFASYVPEIIELIGNRKKYGGSYSAVSGR
IRESfinder result
IRESfinder score
0.74476166
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page