top of page
mmu_circGmps_1003
Basic information of circular RNA
PanCircBase ID:
mmu_circGmps_1003
mm39_Chr. Position ID:
chr3|63889831|63901394|+
Gene name:
Gmps
Transcript:
ENSMUST00000029405.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
3,4,5,6,7,8,9
Exon/intron offsets:
0,3189,5248,7744,8106,10780,11389
Genomic length:
11563
Exon/intron sizes in nt:
1,15,98,10,41,94,16,61,00,000
Flanking exon/introns:
chr3:63887738-63889831|chr3:63901394-63904227
Splice length:
1003
Other database IDs:
circBase: hsa_circ_0122492, circAtlas: hsa-GMPS_0044, CIRCpedia: HSA_CIRCpedia_44149
Human Ortholog IDs:
Mature spliced Sequence:
GGCTATTATCATATCTGGAGGACCTAATTCTGTGTATGCAGAGGATGCTCCCTGGTTTGATCCAGCAATATTTACCATTGGCAAGCCTATTCTAGGAATTTGCTATGGCATGCAGATGATGAATAAAGTCTTTGGAGGCACTGTGCATAAAAAAAGTGTTAGAGAGGATGGAGTTTTCAACATTAGTATGGATAATACGTGTTCATTATTCAGGGGCCTGCAGAAGGAAGAAATTGTTTTACTTACACATGGAGACAGTGTAGACAAAGTTGCTGATGGATTCAAGGTTGTAGCACGTTCTGGGAACATTGTGGCAGGTATAGCCAATGAATCTAAAAAGCTATACGGTGTACAGTTCCACCCTGAAGTTGGGCTTACAGAAAATGGGAAGGTAATACTGAAGAATTTCCTGTATGATATAGCTGGATGCAGTGGGAACTTTACTGTGCAGAACCGAGAACTTGAATGCATTCGAGAGATTAAAGAGAAAGTAGGAACATCAAAAGTGTTGGTTTTACTCAGTGGTGGTGTAGATTCAACTGTTTGTACAGCTTTGCTAAATCGTGCTTTGAACCAAGATCAAGTCATTGCTGTACACATTGATAATGGCTTTATGAGAAAACGAGAAAGCCAATCTGTTGAAGAGGCCCTCAAAAAGCTTGGAATTCAAGTCAAAGTGATAAATGCTGCTCATTCCTTCTACAATGGAACAACTACTCTACCAATCTCAGATGAAGACAGGACCCCACGGAAAAGAATTAGCAAAACATTAAATATGACAACAAGTCCTGAGGAGAAAAGAAAAATTATTGGTGATACTTTCGTTAAGATTGCCAATGAAGTAATTGGAGAAATGAGTCTGAAGCCCGAGGAGGTTTTTCTCGCCCAAGGCACTTTACGGCCTGATCTAATCGAAAGTGCGTCCCTTGTTGCCAGTGGTAAAGCCGAACTCATCAAAACCCACCACAACGACACAGAACTTATCAGGAAGTTAAGGGAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATCGAAAGTGCGTCCCTTGT
59.97
TGGATCAAACCAGGGAGCAT
59
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGAAAGTGCGTCCCTTGTTG
60.04
TGGATCAAACCAGGGAGCAT
59
155
PCR template sequence:
TGATCTAATCGAAAGTGCGTCCCTTGTTGCCAGTGGTAAAGCCGAACTCATCAAAACCCACCACAACGACACAGAACTTATCAGGAAGTTAAGGGAAGAGGGCTATTATCATATCTGGAGGACCTAATTCTGTGTATGCAGAGGATGCTCCCTGGTTTGATCCAGCAATATTTACCATTGGCAAGCCTATTCTAGGAATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-322-5p(1), mmu-miR-182-5p(1), mmu-miR-511-3p(1), mmu-miR-384-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTTAAGGGAAGAGGGCTATTATCATA
siRNA sets
ATGATAATAGCCCTCTTCC, TATGATAATAGCCCTCTTC, TGATAATAGCCCTCTTCCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGMPS_1003_ORF_1
0.9692
0.06791966
0.968820183
921
ORF sequence:
ATGCAGATGATGAATAAAGTCTTTGGAGGCACTGTGCATAAAAAAAGTGTTAGAGAGGATGGAGTTTTCAACATTAGTATGGATAATACGTGTTCATTATTCAGGGGCCTGCAGAAGGAAGAAATTGTTTTACTTACACATGGAGACAGTGTAGACAAAGTTGCTGATGGATTCAAGGTTGTAGCACGTTCTGGGAACATTGTGGCAGGTATAGCCAATGAATCTAAAAAGCTATACGGTGTACAGTTCCACCCTGAAGTTGGGCTTACAGAAAATGGGAAGGTAATACTGAAGAATTTCCTGTATGATATAGCTGGATGCAGTGGGAACTTTACTGTGCAGAACCGAGAACTTGAATGCATTCGAGAGATTAAAGAGAAAGTAGGAACATCAAAAGTGTTGGTTTTACTCAGTGGTGGTGTAGATTCAACTGTTTGTACAGCTTTGCTAAATCGTGCTTTGAACCAAGATCAAGTCATTGCTGTACACATTGATAATGGCTTTATGAGAAAACGAGAAAGCCAATCTGTTGAAGAGGCCCTCAAAAAGCTTGGAATTCAAGTCAAAGTGATAAATGCTGCTCATTCCTTCTACAATGGAACAACTACTCTACCAATCTCAGATGAAGACAGGACCCCACGGAAAAGAATTAGCAAAACATTAAATATGACAACAAGTCCTGAGGAGAAAAGAAAAATTATTGGTGATACTTTCGTTAAGATTGCCAATGAAGTAATTGGAGAAATGAGTCTGAAGCCCGAGGAGGTTTTTCTCGCCCAAGGCACTTTACGGCCTGATCTAATCGAAAGTGCGTCCCTTGTTGCCAGTGGTAAAGCCGAACTCATCAAAACCCACCACAACGACACAGAACTTATCAGGAAGTTAAGGGAAGAGGGCTATTATCATATCTGGAGGACCTAA
Peptide sequence:
MQMMNKVFGGTVHKKSVREDGVFNISMDNTCSLFRGLQKEEIVLLTHGDSVDKVADGFKVVARSGNIVAGIANESKKLYGVQFHPEVGLTENGKVILKNFLYDIAGCSGNFTVQNRELECIREIKEKVGTSKVLVLLSGGVDSTVCTALLNRALNQDQVIAVHIDNGFMRKRESQSVEEALKKLGIQVKVINAAHSFYNGTTTLPISDEDRTPRKRISKTLNMTTSPEEKRKIIGDTFVKIANEVIGEMSLKPEEVFLAQGTLRPDLIESASLVASGKAELIKTHHNDTELIRKLREEGYYHIWRT
IRESfinder result
IRESfinder score
0.608296693
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page