top of page
mmu_circAlcam_1382
Basic information of circular RNA
PanCircBase ID:
mmu_circAlcam_1382
mm39_Chr. Position ID:
chr16|52073487|52117347|-
Gene name:
Alcam
Transcript:
ENSMUST00000023312.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
15,14,13,12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,15257,15665,17522,20785,21022,23663,35793,37752,41899,42538,43795
Genomic length:
43860
Exon/intron sizes in nt:
112,118,39,133,134,136,113,133,128,183,88,65
Flanking exon/introns:
chr16:52072009-52073487|chr16:52117347-52125921
Splice length:
1382
Other database IDs:
circAtlas: mmu-Alcam_0013
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_370310
Human Ortholog IDs:
Mature spliced Sequence:
AGCAACCATCTAAACCTGAAATTGTAAACAAAGCACCCTTTCTTGAAACAGATCAGCTGAAAAAGTTAGGTGACTGCATTTCAAGAGACAGTTACCCAGATGGCAACATCACATGGTACAGGAATGGCAAAGTGCTGCAACCTGTGGAAGGAGAGGTGGCCATACTTTTTAAAAAGGAAATTGATCCAGGAACTCAGTTGTATACCGTGACTTCCTCCTTGGAGTACAAGACAACCAGATCTGACATACAAATGCCATTCACCTGTTCTGTGACATATTATGGACCCTCCGGCCAGAAAACAATTTATTCCGAACAAGAAATCTTTGATATTTACTATCCTACAGAGCAGGTGACAATACAAGTGCTGCCACCAAAAAATGCCATCAAAGAAGGGGACAACATCACCCTTCAGTGTTTGGGGAATGGCAACCCACCTCCTGAGGAGTTCATGTTTTACTTACCAGGACAGCCTGAAGGCATAAGAAGCTCAAACACTTACACACTGACAGATGTGAGACGCAATGCCACAGGGGACTACAAATGCTCACTCATTGACAAAAGGAACATGGCGGCTTCAACGACCATCACAGTTCACTACTTGGATTTATCCTTAAACCCAAGTGGGGAGGTGACCAAGCAGATTGGCGATACCCTGCCTGTGTCATGCACAATATCTGCAAGTAGGAACGCGACTGTGGTGTGGATGAAGGATAACATCCGGCTCCGGTCCAGCCCTTCCTTTTCCAGTCTTCATTATCAGGATGCTGGGAACTATGTCTGTGAAACTGCTCTTCAGGAGGTTGAGGGACTGAAGAAAAGGGAGTCGCTGACCCTCATTGTAGAAGGGAAACCTCAAATCAAAATGACTAAGAAAACTGACCCCAGTGGACTGTCTAAAACTATAATCTGCCACGTGGAAGGGTTTCCAAAGCCAGCTATACATTGGACCATTACCGGCAGTGGGAGCGTCATAAACCAAACAGAGGAGTCTCCTTATATTAATGGCAGGTATTATAGTAAAATTATCATTTCCCCTGAGGAGAATGTAACATTAACTTGCACAGCAGAAAACCAACTGGAGAGAACAGTAAACTCCCTGAATGTCTCTGCGATAAGTATTCCAGAGCACGATGAGGCAGACGATATAAGTGATGAAAACAGAGAAAAGGTGAATGACCAGGCAAAACTGATTGTGGGAATTGTCGTTGGTCTCCTCCTCGCTGCCCTCGTTGCTGGTGTCGTCTACTGGCTGTACATGAAGAAGTCCAAAACTGCATCAAAACATGTAAACAAGGACCTTGGTAATATGGAGGAAAATAAAAAGCTGGAAGAAAACAATCACAAAACAGAAGCCTAAGAGAGGAGCGGATTGGATAGCCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGACCTTGGTAATATGGAGGA
57.7
TGTCTCTTGAAATGCAGTCACC
58.86
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAAGGACCTTGGTAATATGGAGG
59.83
TCTGTTTCAAGAAAGGGTGCT
57.7
144
PCR template sequence:
ACATGTAAACAAGGACCTTGGTAATATGGAGGAAAATAAAAAGCTGGAAGAAAACAATCACAAAACAGAAGCCTAAGAGAGGAGCGGATTGGATAGCCTGAGCAACCATCTAAACCTGAAATTGTAAACAAAGCACCCTTTCTTGAAACAGATCAGCTGAAAAAGTTAGGTGACTGCATTTCAAGAGACAGTTACCCAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-200c-3p(1), mmu-miR-205-5p(1), mmu-miR-211-5p(1), mmu-miR-483-5p(1), mmu-miR-5101(1), mmu-miR-369-3p(1), mmu-miR-335-3p(1), mmu-miR-188-3p(1), mmu-miR-574-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTGGATAGCCTGAGCAACCATCTAA
siRNA sets
TTAGATGGTTGCTCAGGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.497061698
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page