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mmu_circAtg4c_1049
Basic information of circular RNA
PanCircBase ID:
mmu_circAtg4c_1049
mm39_Chr. Position ID:
chr4|99106201|99123423|+
Gene name:
Atg4c
Transcript:
ENSMUST00000030279.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
4,5,6,7,8,9,10
Exon/intron offsets:
0,3227,4908,6449,10591,11523,17102
Genomic length:
17222
Exon/intron sizes in nt:
234,331,71,137,79,77,120
Flanking exon/introns:
chr4:99104198-99106201|chr4:99123423-99146633
Splice length:
1049
Other database IDs:
CIRCpedia: MMU_CIRCpedia_223813, circAtlas: mmu-Atg4c_0003
circBase: hsa_circ_0012827, circAtlas: hsa-ATG4C_0008, CIRCpedia: HSA_CIRCpedia_32688
Human Ortholog IDs:
Mature spliced Sequence:
ATGAAAGCAAGATGTTGCCTGCAAGATCAGGATGTGCCATTGAAGATCATGTAATTGCAGGGAATGTGGAAGAGTTCCGTAAGGATTTCATTTCTAGAATATGGCTGACCTACAGGGAAGAATTTCCTCAAATCGAAGCTTCAGCCTTGACGACAGACTGTGGCTGGGGCTGCACGCTGCGGACCGGCCAGATGCTGCTGGCTCAGGGACTCATACTCCATTTTCTCGGTAGAGCTTGGACCTGGCCTGATGCGCTGCACATTGAGAACGCAGACTCTGACTCATGGACTTCCAACACTGTCAAAAAGTTTACTGCATCGTTTGAAGCTTCACTTTCGGGGGACAGAGAACTCAGAACTCCAGCAGTTTCTCTGAAGGAAACATCTGGGAAGTGTCCCGATGACCACGCAGTGCGGAATGAGGCTTATCACAGGAAGATCATCTCTTGGTTTGGAGATTCCCCCGTGGCCGTCTTTGGCTTACATCGTCTGATAGAGTTTGGGAAGAAGTCTGGGAAAAAAGCTGGCGATTGGTATGGACCAGCGGTGGTTGCTCACATTTTAAGAAAAGCAGTTGAAGAAGCAAGGCATCCGGATTTGCAAGGGCTAACTATTTATGTTGCCCAGGACTGTACAGTTTACAATTCTGACGTGATTGATAAGCAGACTGACTCCGTGACAGCTGGAGATGCACGTGACAAGGCTGTCATTATTTTAGTTCCTGTTAGACTCGGTGGAGAAAGGACCAATACCGACTATCTGGAGTTTGTGAAGGGTGTTTTAAGCCTTGAATACTGTGTAGGTATCATTGGCGGCAAACCTAAACAGTCATATTACTTTGCTGGATTTCAAGATGACAGTTTGATTTACATGGATCCTCATTACTGCCAGTCTTTTGTAGATGTCAGCATAAAGGATTTCCCTCTCGAGACATTCCACTGTCCATCTCCTAAAAAGATGTCATTTCGAAAAATGGATCCTAGTTGTACGATAGGATTTTACTGTCGAAATGTCCAGGACTTTGAACGAGCGTCTGAAGAAATCACTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGATCCTAGTTGTACGATAGGA
57.69
ACTCTTCCACATTCCCTGCA
58.93
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGATCCTAGTTGTACGATAGGA
57.69
ACTCTTCCACATTCCCTGCAA
59.57
152
PCR template sequence:
TAAAAAGATGTCATTTCGAAAAATGGATCCTAGTTGTACGATAGGATTTTACTGTCGAAATGTCCAGGACTTTGAACGAGCGTCTGAAGAAATCACTAAGATGAAAGCAAGATGTTGCCTGCAAGATCAGGATGTGCCATTGAAGATCATGTAATTGCAGGGAATGTGGAAGAGTTCCGTAAGGATTTCATTTCTAGAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-431-5p(1), mmu-miR-351-5p(1), mmu-miR-127-5p(1), mmu-miR-499-5p(1), mmu-miR-532-5p(1), mmu-miR-350-3p(1), mmu-miR-670-5p(1), mmu-miR-697(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAATCACTAAGATGAAAGCAAGAT
siRNA sets
TCTTGCTTTCATCTTAGTG, ATCTTGCTTTCATCTTAGT, TTTCATCTTAGTGATTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATG4C_1049_ORF_1
0.8597
0.104064647
0.990168556
1092
ORF sequence:
ATGTTGCCTGCAAGATCAGGATGTGCCATTGAAGATCATGTAATTGCAGGGAATGTGGAAGAGTTCCGTAAGGATTTCATTTCTAGAATATGGCTGACCTACAGGGAAGAATTTCCTCAAATCGAAGCTTCAGCCTTGACGACAGACTGTGGCTGGGGCTGCACGCTGCGGACCGGCCAGATGCTGCTGGCTCAGGGACTCATACTCCATTTTCTCGGTAGAGCTTGGACCTGGCCTGATGCGCTGCACATTGAGAACGCAGACTCTGACTCATGGACTTCCAACACTGTCAAAAAGTTTACTGCATCGTTTGAAGCTTCACTTTCGGGGGACAGAGAACTCAGAACTCCAGCAGTTTCTCTGAAGGAAACATCTGGGAAGTGTCCCGATGACCACGCAGTGCGGAATGAGGCTTATCACAGGAAGATCATCTCTTGGTTTGGAGATTCCCCCGTGGCCGTCTTTGGCTTACATCGTCTGATAGAGTTTGGGAAGAAGTCTGGGAAAAAAGCTGGCGATTGGTATGGACCAGCGGTGGTTGCTCACATTTTAAGAAAAGCAGTTGAAGAAGCAAGGCATCCGGATTTGCAAGGGCTAACTATTTATGTTGCCCAGGACTGTACAGTTTACAATTCTGACGTGATTGATAAGCAGACTGACTCCGTGACAGCTGGAGATGCACGTGACAAGGCTGTCATTATTTTAGTTCCTGTTAGACTCGGTGGAGAAAGGACCAATACCGACTATCTGGAGTTTGTGAAGGGTGTTTTAAGCCTTGAATACTGTGTAGGTATCATTGGCGGCAAACCTAAACAGTCATATTACTTTGCTGGATTTCAAGATGACAGTTTGATTTACATGGATCCTCATTACTGCCAGTCTTTTGTAGATGTCAGCATAAAGGATTTCCCTCTCGAGACATTCCACTGTCCATCTCCTAAAAAGATGTCATTTCGAAAAATGGATCCTAGTTGTACGATAGGATTTTACTGTCGAAATGTCCAGGACTTTGAACGAGCGTCTGAAGAAATCACTAAGATGAAAGCAAGATGTTGCCTGCAAGATCAGGATGTGCCATTGAAGATCATGTAA
Peptide sequence:
MLPARSGCAIEDHVIAGNVEEFRKDFISRIWLTYREEFPQIEASALTTDCGWGCTLRTGQMLLAQGLILHFLGRAWTWPDALHIENADSDSWTSNTVKKFTASFEASLSGDRELRTPAVSLKETSGKCPDDHAVRNEAYHRKIISWFGDSPVAVFGLHRLIEFGKKSGKKAGDWYGPAVVAHILRKAVEEARHPDLQGLTIYVAQDCTVYNSDVIDKQTDSVTAGDARDKAVIILVPVRLGGERTNTDYLEFVKGVLSLEYCVGIIGGKPKQSYYFAGFQDDSLIYMDPHYCQSFVDVSIKDFPLETFHCPSPKKMSFRKMDPSCTIGFYCRNVQDFERASEEITKMKARCCLQDQDVPLKIM
IRESfinder result
IRESfinder score
0.55570332
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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