top of page
mmu_circRaph1_780
Basic information of circular RNA
PanCircBase ID:
mmu_circRaph1_780
mm39_Chr. Position ID:
chr1|60535383|60542754|-
Gene name:
Raph1
Transcript:
ENSMUST00000140485.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
11,10,9,8,7,6,5
Exon/intron offsets:
0,2199,3255,4330,5531,6600,7293
Genomic length:
7371
Exon/intron sizes in nt:
99,111,144,66,122,160,78
Flanking exon/introns:
chr1:60534694-60535383|chr1:60542754-60564750
Splice length:
780
Other database IDs:
circAtlas: mmu-Raph1_0018
circAtlas: hsa-RAPH1_0023
Human Ortholog IDs:
Mature spliced Sequence:
GAAGAACAGGCAGCAAAACTGAAAGCTGAGAAGATCCGAGTTGCTCTGGAGAAAATTAAAGAGGCTCAAGTGAAAAAGCTGGTAATCAGGGTCCACATGTCTGATGACAGTTCTAAGACAATGATGGTGGATGAGAGACAGACAGTGAGACAAGTGCTGGATAACCTGATGGACAAATCTCACTGTGGCTACAGTTTAGACTGGTCGCTGGTGGAAACCATTTCCGAGTTACAAATGGAAAGAATCTTTGAAGACCATGAAAACTTGGTTGAAAATCTTCTTAATTGGACAAGAGACAGCCAAAATAAGCTTATATTTATGGAGCGTATAGAAAAATATGCACTTTTTAAAAACCCCCAGAATTATCTTCTAGGGAAAAAGGAAACAGCTGAAATGGCAGACAGAAACAAAGAAGTGCTGTTAGAGGAATGTTTTTGTGGAAGTTCTGTAACTGTCCCAGAAATTGAAGGAGTCCTTTGGTTAAAAGATGATGGCAAGAAGTCCTGGAAAAAGCGTTATTTTCTCTTGCGAGCATCTGGTATCTACTATGTCCCCAAAGGAAAAGCAAAGGTATCTCGGGATCTAGTGTGCTTTCTCCAGCTGGATCATGTAAATGTATACTATGGACAGGACTATCGGAACAAATACAAAGCACCCACAGACTGCTGCCTGGCATTAAAGCACCCACAGATCCAGAAGAAGTCTCAGTATATCAAGTACCTTTGCTGTGATGATGCAAGGACCCTGCATCAGTGGGTCAATGGAATCCGCATTGCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GATGATGCAAGGACCCTGCA
60.39
TGTGGACCCTGATTACCAGC
59.38
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGATGATGCAAGGACCCTGC
60.39
TGTGGACCCTGATTACCAGC
59.38
149
PCR template sequence:
GCACCCACAGATCCAGAAGAAGTCTCAGTATATCAAGTACCTTTGCTGTGATGATGCAAGGACCCTGCATCAGTGGGTCAATGGAATCCGCATTGCCAAGGAAGAACAGGCAGCAAAACTGAAAGCTGAGAAGATCCGAGTTGCTCTGGAGAAAATTAAAGAGGCTCAAGTGAAAAAGCTGGTAATCAGGGTCCACATGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-20a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-128-3p(1), mmu-miR-182-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCGCATTGCCAAGGAAGAACAGGCAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAPH1_780_ORF_1
0.9793
0.162427506
0.999578123
1464
ORF sequence:
ATGTCTGATGACAGTTCTAAGACAATGATGGTGGATGAGAGACAGACAGTGAGACAAGTGCTGGATAACCTGATGGACAAATCTCACTGTGGCTACAGTTTAGACTGGTCGCTGGTGGAAACCATTTCCGAGTTACAAATGGAAAGAATCTTTGAAGACCATGAAAACTTGGTTGAAAATCTTCTTAATTGGACAAGAGACAGCCAAAATAAGCTTATATTTATGGAGCGTATAGAAAAATATGCACTTTTTAAAAACCCCCAGAATTATCTTCTAGGGAAAAAGGAAACAGCTGAAATGGCAGACAGAAACAAAGAAGTGCTGTTAGAGGAATGTTTTTGTGGAAGTTCTGTAACTGTCCCAGAAATTGAAGGAGTCCTTTGGTTAAAAGATGATGGCAAGAAGTCCTGGAAAAAGCGTTATTTTCTCTTGCGAGCATCTGGTATCTACTATGTCCCCAAAGGAAAAGCAAAGGTATCTCGGGATCTAGTGTGCTTTCTCCAGCTGGATCATGTAAATGTATACTATGGACAGGACTATCGGAACAAATACAAAGCACCCACAGACTGCTGCCTGGCATTAAAGCACCCACAGATCCAGAAGAAGTCTCAGTATATCAAGTACCTTTGCTGTGATGATGCAAGGACCCTGCATCAGTGGGTCAATGGAATCCGCATTGCCAAGGAAGAACAGGCAGCAAAACTGAAAGCTGAGAAGATCCGAGTTGCTCTGGAGAAAATTAAAGAGGCTCAAGTGAAAAAGCTGGTAATCAGGGTCCACATGTCTGATGACAGTTCTAAGACAATGATGGTGGATGAGAGACAGACAGTGAGACAAGTGCTGGATAACCTGATGGACAAATCTCACTGTGGCTACAGTTTAGACTGGTCGCTGGTGGAAACCATTTCCGAGTTACAAATGGAAAGAATCTTTGAAGACCATGAAAACTTGGTTGAAAATCTTCTTAATTGGACAAGAGACAGCCAAAATAAGCTTATATTTATGGAGCGTATAGAAAAATATGCACTTTTTAAAAACCCCCAGAATTATCTTCTAGGGAAAAAGGAAACAGCTGAAATGGCAGACAGAAACAAAGAAGTGCTGTTAGAGGAATGTTTTTGTGGAAGTTCTGTAACTGTCCCAGAAATTGAAGGAGTCCTTTGGTTAAAAGATGATGGCAAGAAGTCCTGGAAAAAGCGTTATTTTCTCTTGCGAGCATCTGGTATCTACTATGTCCCCAAAGGAAAAGCAAAGGTATCTCGGGATCTAGTGTGCTTTCTCCAGCTGGATCATGTAAATGTATACTATGGACAGGACTATCGGAACAAATACAAAGCACCCACAGACTGCTGCCTGGCATTAAAGCACCCACAGATCCAGAAGAAGTCTCAGTATATCAAGTACCTTTGCTGTGATGATGCAAGGACCCTGCATCAGTGGGTCAATGGAATCCGCATTGCCAAG
Peptide sequence:
MSDDSSKTMMVDERQTVRQVLDNLMDKSHCGYSLDWSLVETISELQMERIFEDHENLVENLLNWTRDSQNKLIFMERIEKYALFKNPQNYLLGKKETAEMADRNKEVLLEECFCGSSVTVPEIEGVLWLKDDGKKSWKKRYFLLRASGIYYVPKGKAKVSRDLVCFLQLDHVNVYYGQDYRNKYKAPTDCCLALKHPQIQKKSQYIKYLCCDDARTLHQWVNGIRIAKEEQAAKLKAEKIRVALEKIKEAQVKKLVIRVHMSDDSSKTMMVDERQTVRQVLDNLMDKSHCGYSLDWSLVETISELQMERIFEDHENLVENLLNWTRDSQNKLIFMERIEKYALFKNPQNYLLGKKETAEMADRNKEVLLEECFCGSSVTVPEIEGVLWLKDDGKKSWKKRYFLLRASGIYYVPKGKAKVSRDLVCFLQLDHVNVYYGQDYRNKYKAPTDCCLALKHPQIQKKSQYIKYLCCDDARTLHQWVNGIRIAK
IRESfinder result
IRESfinder score
0.52225367
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page