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mmu_circGarem1_1304
Basic information of circular RNA
PanCircBase ID:
mmu_circGarem1_1304
mm39_Chr. Position ID:
chr18|21280788|21301923|-
Gene name:
Garem1
Transcript:
ENSMUST00000049260.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
4,3
Exon/intron offsets:
0,21004
Genomic length:
21135
Exon/intron sizes in nt:
11,73,131
Flanking exon/introns:
chr18:21264556-21280788|chr18:21301923-21369057
Splice length:
1304
Other database IDs:
circBase: mmu_circ_0007162, CIRCpedia: MMU_CIRCpedia_13153, circAtlas: mmu-Garem_0001
circBase: hsa_circ_0047385, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_23685
Human Ortholog IDs:
Mature spliced Sequence:
GACAATTCAAGCTGCTGGAACAAGACCGGGATATAAAGGAGCCGGTGCAATATTTCAACAGCGTGGAGGAAGTGGCCAAAGCATTTCCTGAACGTGTGTACGTCATGGAGGAGATTACATTCAACGTGAAGGTGGCGTCGGGTGAATGCAATGAAGACACTGAAGTTTACAACATCACCCTGTGCACCGGGGATGAACTCACCCTAATGGGGCAGGCAGAAATCCTTTATGCAAAGACCTTCAAGGAGAAGTCACGTCTCAACACCATCTTCAAAAAGATTGGGAAGCTCAATTCCATCAGCAAGCTGGGGAAAGGCAAAATGCCCTGCCTCATTTGCATGAATCACCGGACCAATGAAAGCATCAGCCTTCCATTCCAGTGCAAGGGCAGATTTAGCACCCGAAGTCCCCTGGAACTTCAGATGCAGGAAGGGGAACACACCATCCGAAACATCGTGGAGAAGACTCGACTCCCCGTGAATGTGACAGTGCCCAGTCCCCCACCCAGAAATCCCTATGACCTCCACTTCATTAGAGAGGGGCACCGCTACAAGTTTGTGAACATCCAGACCAAGACAGTGGTGGTTTGTTGTGTGCTGCGCAACAACAAGATCCTCCCCATGCACTTCCCTTTGCACTTGACTGTCCCCAAGTTCAGCCTCCCGGAACACCAGGTGAAGGGAGACATGTGGCCAGAAACACTAGTCCATCACTGGCTTGGTATCTGCCAAGAGCAGTTTGACATCGATGAGTATTCACGGGCTGTGCGTGATGTGAAAACGGACTGGAATGAAGACTGCAAGAGCCCCAAAAAGGGCCGCTGCTCTGGCCACAACCATTTACCCAATTCCCTCAGCTATGCCCGCGATGAGCTCACCCAGTCCTTCCACCGACTCTCAGTCTGTGTGTATGGCAACAATCTCCATGGCAATAGTGAGGTGAATCTCCATGGCTGCAGGGACCTTGGGGGAGAGTGGGCCCCTTTTCCCCATGATATCCTTCCCTATCAAGACTCTGGTGACAGTGGGAGCGACTACCTTTTCCCGGAAGCTAATGAGGAGTCAGCGGGCATCCCGGGGAAAACAGAAGTTCCCTATGAAGAGCTGTGGCTGGAGGAAGGCAAGCCCAGCCGCCAGCCTCTCACTCGCTCACTCAGTGAGAAGAGCAGGTGCGACACCTTGAGAGGCTCCACGAGGTCCACGTGTGCACCCTCTTCTCCTCCCACCCCTGCGACCCTGGGAGCCACAATTAAGTCTTCAGAAATCGCCCTACCTCCACCTCCAGTGCCTCCCAAATCTGAAGCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACCCTGGGAGCCACAATTA
59.38
CACTTCCTCCACGCTGTTGA
60.25
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACCCTGGGAGCCACAATTA
59.38
ACTTCCTCCACGCTGTTGAA
59.53
146
PCR template sequence:
TGCACCCTCTTCTCCTCCCACCCCTGCGACCCTGGGAGCCACAATTAAGTCTTCAGAAATCGCCCTACCTCCACCTCCAGTGCCTCCCAAATCTGAAGCTGACAATTCAAGCTGCTGGAACAAGACCGGGATATAAAGGAGCCGGTGCAATATTTCAACAGCGTGGAGGAAGTGGCCAAAGCATTTCCTGAACGTGTGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-382-3p(2), mmu-miR-23b-3p(1), mmu-miR-7b-5p(1), mmu-let-7e-5p(1), mmu-miR-92a-3p(1), mmu-miR-196a-5p(1), mmu-miR-709(1), mmu-miR-203-3p(1), mmu-miR-23a-3p(1), mmu-miR-363-3p(1), mmu-miR-130b-3p(1), mmu-miR-541-5p(1), mmu-miR-666-5p(1), mmu-miR-705(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAAATCTGAAGCTGACAATTCAAGCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGAREM1_1304_ORF_1
0.9702
0.31135902
0.99876142
1236
ORF sequence:
ATGGAGGAGATTACATTCAACGTGAAGGTGGCGTCGGGTGAATGCAATGAAGACACTGAAGTTTACAACATCACCCTGTGCACCGGGGATGAACTCACCCTAATGGGGCAGGCAGAAATCCTTTATGCAAAGACCTTCAAGGAGAAGTCACGTCTCAACACCATCTTCAAAAAGATTGGGAAGCTCAATTCCATCAGCAAGCTGGGGAAAGGCAAAATGCCCTGCCTCATTTGCATGAATCACCGGACCAATGAAAGCATCAGCCTTCCATTCCAGTGCAAGGGCAGATTTAGCACCCGAAGTCCCCTGGAACTTCAGATGCAGGAAGGGGAACACACCATCCGAAACATCGTGGAGAAGACTCGACTCCCCGTGAATGTGACAGTGCCCAGTCCCCCACCCAGAAATCCCTATGACCTCCACTTCATTAGAGAGGGGCACCGCTACAAGTTTGTGAACATCCAGACCAAGACAGTGGTGGTTTGTTGTGTGCTGCGCAACAACAAGATCCTCCCCATGCACTTCCCTTTGCACTTGACTGTCCCCAAGTTCAGCCTCCCGGAACACCAGGTGAAGGGAGACATGTGGCCAGAAACACTAGTCCATCACTGGCTTGGTATCTGCCAAGAGCAGTTTGACATCGATGAGTATTCACGGGCTGTGCGTGATGTGAAAACGGACTGGAATGAAGACTGCAAGAGCCCCAAAAAGGGCCGCTGCTCTGGCCACAACCATTTACCCAATTCCCTCAGCTATGCCCGCGATGAGCTCACCCAGTCCTTCCACCGACTCTCAGTCTGTGTGTATGGCAACAATCTCCATGGCAATAGTGAGGTGAATCTCCATGGCTGCAGGGACCTTGGGGGAGAGTGGGCCCCTTTTCCCCATGATATCCTTCCCTATCAAGACTCTGGTGACAGTGGGAGCGACTACCTTTTCCCGGAAGCTAATGAGGAGTCAGCGGGCATCCCGGGGAAAACAGAAGTTCCCTATGAAGAGCTGTGGCTGGAGGAAGGCAAGCCCAGCCGCCAGCCTCTCACTCGCTCACTCAGTGAGAAGAGCAGGTGCGACACCTTGAGAGGCTCCACGAGGTCCACGTGTGCACCCTCTTCTCCTCCCACCCCTGCGACCCTGGGAGCCACAATTAAGTCTTCAGAAATCGCCCTACCTCCACCTCCAGTGCCTCCCAAATCTGAAGCTGACAATTCAAGCTGCTGGAACAAGACCGGGATATAA
Peptide sequence:
MEEITFNVKVASGECNEDTEVYNITLCTGDELTLMGQAEILYAKTFKEKSRLNTIFKKIGKLNSISKLGKGKMPCLICMNHRTNESISLPFQCKGRFSTRSPLELQMQEGEHTIRNIVEKTRLPVNVTVPSPPPRNPYDLHFIREGHRYKFVNIQTKTVVVCCVLRNNKILPMHFPLHLTVPKFSLPEHQVKGDMWPETLVHHWLGICQEQFDIDEYSRAVRDVKTDWNEDCKSPKKGRCSGHNHLPNSLSYARDELTQSFHRLSVCVYGNNLHGNSEVNLHGCRDLGGEWAPFPHDILPYQDSGDSGSDYLFPEANEESAGIPGKTEVPYEELWLEEGKPSRQPLTRSLSEKSRCDTLRGSTRSTCAPSSPPTPATLGATIKSSEIALPPPPVPPKSEADNSSCWNKTGI
IRESfinder result
IRESfinder score
0.496625574
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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