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mmu_circGpam_1124
Basic information of circular RNA
PanCircBase ID:
mmu_circGpam_1124
mm39_Chr. Position ID:
chr19|55068815|55079681|-
Gene name:
Gpam
Transcript:
ENSMUST00000236859.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
13,12,11,10,9,8,7,6,5
Exon/intron offsets:
0,1008,1218,2817,3314,7001,7727,8414,10752
Genomic length:
10866
Exon/intron sizes in nt:
11,68,61,14,21,31,00,10,00,00,00,000
Flanking exon/introns:
chr19:55067718-55068815|chr19:55079681-55082350
Splice length:
1124
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCACAGAGGATGGCTGGCGAGACGGCTGTCTTACATCCTTTTTGTTCAAGAGCGAGACGTCCATAAGGGCATGTTTGCCACCAGTGTTACTGAGAATGTACTGAGCAGCAGCAGAGTCCAAGAGGCAATTGCTGAAGTGGCTGCGGAGTTGAACCCAGATGGATCTGCCCAGCAGCAGTCCAAAGCCATCCAGAAGGTGAAAAGGAAAGCCAGGAAGATCCTCCAGGAGATGGTCGCCACCGTCTCCCCAGGGATGATCAGGCTGACTGGCTGGGTGTTACTAAAGCTCTTCAACAGCTTCTTCTGGAACATTCAGATTCACAAGGGTCAACTCGAGATGGTCAAGGCTGCAACTGAGACGAACCTGCCGCTCTTGTTTCTGCCGGTGCACAGATCCCACATTGACTACCTGTTGCTCACCTTCATCCTCTTTTGCCACAACATCAAGGCGCCGTACATCGCCTCGGGCAATAATCTCAACATCCCCGTCTTCAGTACCTTGATTCACAAGCTTGGGGGCTTTTTCATAAGACGGAGGCTCGATGAAACCCCAGATGGACGCAAAGACATTCTGTACAGAGCGTTGCTCCATGGGCATGTAGTTGAACTCCTCCGACAGCAGCAGTTCCTGGAGATCTTCCTGGAAGGCACCCGCTCCCGCAGTGGCAAGACCTCCTGTGCCCGGGCAGGGCTCCTCTCAGTGGTAGTGGATACTCTGTCGTCCAACACCATCCCCGACATCCTCGTCATACCCGTGGGCATCTCGTATGATCGCATAATCGAAGGTCACTACAATGGCGAACAGTTGGGAAAGCCCAAGAAGAACGAGAGCCTCTGGAGTGTGGCGAGAGGCGTTATCAGAATGCTGCGGAAAAACTACGGCTACGTCCGAGTGGATTTTGCACAGCCATTTTCCTTGAAGGAATATTTAGAAGGCCAGAGTCAGAAACCTGTATCTGCCCCCCTTTCTCTGGAGCAAGCACTGTTACCAGCGATCCTTCCTTCAAGACCGAATGATGTTGCTGATGAACATCAAGACCTATCCAGTAACGAGTCCAGAAACCCAGCAGACGAAGCCTTCCGACGAAGGCTGATTGCAAACCTGGCTGAGCACATTCTCTTCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACGAGTCCAGAAACCCAGC
60.25
CCCTTATGGACGTCTCGCTC
59.97
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGAAACCCAGCAGACGAA
60.25
AACACTGGTGGCAAACATGC
59.9
157
PCR template sequence:
GATGAACATCAAGACCTATCCAGTAACGAGTCCAGAAACCCAGCAGACGAAGCCTTCCGACGAAGGCTGATTGCAAACCTGGCTGAGCACATTCTCTTCAGCACAGAGGATGGCTGGCGAGACGGCTGTCTTACATCCTTTTTGTTCAAGAGCGAGACGTCCATAAGGGCATGTTTGCCACCAGTGTTACTGAGAATGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-103-3p(1), mmu-miR-135a-5p(1), mmu-miR-19b-3p(1), mmu-miR-19a-3p(1), mmu-miR-196a-5p(1), mmu-miR-30d-5p(1), mmu-miR-127-3p(1), mmu-miR-431-5p(1), mmu-miR-194-5p(1), mmu-miR-362-5p(1), mmu-miR-107-3p(1), mmu-miR-129-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CACATTCTCTTCAGCACAGAGGATGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGPAM_1124_ORF_1
1.1004
0.309188322
0.99829307
1158
ORF sequence:
ATGTTTGCCACCAGTGTTACTGAGAATGTACTGAGCAGCAGCAGAGTCCAAGAGGCAATTGCTGAAGTGGCTGCGGAGTTGAACCCAGATGGATCTGCCCAGCAGCAGTCCAAAGCCATCCAGAAGGTGAAAAGGAAAGCCAGGAAGATCCTCCAGGAGATGGTCGCCACCGTCTCCCCAGGGATGATCAGGCTGACTGGCTGGGTGTTACTAAAGCTCTTCAACAGCTTCTTCTGGAACATTCAGATTCACAAGGGTCAACTCGAGATGGTCAAGGCTGCAACTGAGACGAACCTGCCGCTCTTGTTTCTGCCGGTGCACAGATCCCACATTGACTACCTGTTGCTCACCTTCATCCTCTTTTGCCACAACATCAAGGCGCCGTACATCGCCTCGGGCAATAATCTCAACATCCCCGTCTTCAGTACCTTGATTCACAAGCTTGGGGGCTTTTTCATAAGACGGAGGCTCGATGAAACCCCAGATGGACGCAAAGACATTCTGTACAGAGCGTTGCTCCATGGGCATGTAGTTGAACTCCTCCGACAGCAGCAGTTCCTGGAGATCTTCCTGGAAGGCACCCGCTCCCGCAGTGGCAAGACCTCCTGTGCCCGGGCAGGGCTCCTCTCAGTGGTAGTGGATACTCTGTCGTCCAACACCATCCCCGACATCCTCGTCATACCCGTGGGCATCTCGTATGATCGCATAATCGAAGGTCACTACAATGGCGAACAGTTGGGAAAGCCCAAGAAGAACGAGAGCCTCTGGAGTGTGGCGAGAGGCGTTATCAGAATGCTGCGGAAAAACTACGGCTACGTCCGAGTGGATTTTGCACAGCCATTTTCCTTGAAGGAATATTTAGAAGGCCAGAGTCAGAAACCTGTATCTGCCCCCCTTTCTCTGGAGCAAGCACTGTTACCAGCGATCCTTCCTTCAAGACCGAATGATGTTGCTGATGAACATCAAGACCTATCCAGTAACGAGTCCAGAAACCCAGCAGACGAAGCCTTCCGACGAAGGCTGATTGCAAACCTGGCTGAGCACATTCTCTTCAGCACAGAGGATGGCTGGCGAGACGGCTGTCTTACATCCTTTTTGTTCAAGAGCGAGACGTCCATAAGGGCATGTTTGCCACCAGTGTTACTGAGAATGTACTGA
Peptide sequence:
MFATSVTENVLSSSRVQEAIAEVAAELNPDGSAQQQSKAIQKVKRKARKILQEMVATVSPGMIRLTGWVLLKLFNSFFWNIQIHKGQLEMVKAATETNLPLLFLPVHRSHIDYLLLTFILFCHNIKAPYIASGNNLNIPVFSTLIHKLGGFFIRRRLDETPDGRKDILYRALLHGHVVELLRQQQFLEIFLEGTRSRSGKTSCARAGLLSVVVDTLSSNTIPDILVIPVGISYDRIIEGHYNGEQLGKPKKNESLWSVARGVIRMLRKNYGYVRVDFAQPFSLKEYLEGQSQKPVSAPLSLEQALLPAILPSRPNDVADEHQDLSSNESRNPADEAFRRRLIANLAEHILFSTEDGWRDGCLTSFLFKSETSIRACLPPVLLRMY
IRESfinder result
IRESfinder score
0.48790949
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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