top of page
mmu_circR3hdm1_1020
Basic information of circular RNA
PanCircBase ID:
mmu_circR3hdm1_1020
mm39_Chr. Position ID:
chr1|128079480|128106919|+
Gene name:
R3hdm1
Transcript:
ENSMUST00000191016.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
2,3,4,5,6,7,8,9
Exon/intron offsets:
0,1445,16149,17235,23205,23348,27139,27343
Genomic length:
27439
Exon/intron sizes in nt:
209,211,115,79,60,141,109,96
Flanking exon/introns:
chr1:128031220-128079480|chr1:128106919-128109453
Splice length:
1020
Other database IDs:
circAtlas: mmu-R3hdm1_0021
circBase: hsa_circ_0117368, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_146158
Human Ortholog IDs:
Mature spliced Sequence:
GCCACTGAAAGGTATGATATATTTGATCCAAGACAGTCCATTTCAGCCCAGGAATCTACAGTGGTGACAAGGACATGGGACTCCTCCCGCCAGATTACTGTTGGTTCAATACATTTGACATCCTGGCTGACAACTGTGAAGAGGAACCTTGGGTTATTTTATTTTATTTTTGTGGAACACCACAATCTCAGATCCATAGGACACATCAGGCTTCAAGTTCCCTGTAGAATTCTAAAATAACCTTTGCTAATGAGGATGTCTGATATTGTTATTATAAAAGATGAAACTGAAACAATGAAGGATTTGGAGGCAGAAATGAGAGATACAACCAGAGTTGAAAATCTTATCAAATCAGAAAACTATGGGAAGATTTCGGCAGAGAAGAATGAACATTGTATTGACAACAATATTGATTTGCAGGAGAAAATTCAGATACAGTTAACACAATCATTTGAAAAAGAGGAAAAGCCCTCAAAAGATGAAACAGATAAAGAAAAAGCCAGTGATAAGTTACCCAGAAAAATGTTATCAAGAGATTCCAGCCAAGAATACACTGATTCAACTGGCATAGATCTACATGAATTTTTAGTAAATACATTAAAAAACAATCCCAGGGACAGAATGATGCTGCTGAAATTGGAACAAGAAATTTTAGATTTCATTGGTAATAATGAGTCCCCACGTAAGAAGTTTCCCCCGATGACATCTTACCACAGGATGCTGTTACACAGAGTGGCTGCCTACTTTGGATTAGACCACAATGTTGATCAGAGTGGGAAGTCTGTCATAGTGAACAAAACTAGCAACACAAGAATACCTGATCAGAAATTTAATGAACATATAAAGGATGATAGAGGTGAAGACTTTCAGAAACGATACATCCTTAAGAGAGATAACTCTAGCTTTGACAAAGATGATAGCCAGATGAGAATACGTTTGAAAGATGACAGAAGAAGCAAATCTATAGAAGAAAGAGAAGAAGAATACCAGAGAGCTAGAGACCGAATATTTTCCCAAGAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAATACCAGAGAGCTAGAGACC
58.27
CAGTAATCTGGCGGGAGGAG
59.61
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAATACCAGAGAGCTAGAGACCG
60.75
CAGTAATCTGGCGGGAGGAG
59.61
140
PCR template sequence:
CCAGATGAGAATACGTTTGAAAGATGACAGAAGAAGCAAATCTATAGAAGAAAGAGAAGAAGAATACCAGAGAGCTAGAGACCGAATATTTTCCCAAGATGCCACTGAAAGGTATGATATATTTGATCCAAGACAGTCCATTTCAGCCCAGGAATCTACAGTGGTGACAAGGACATGGGACTCCTCCCGCCAGATTACTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-103-3p(1), mmu-miR-135a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-434-3p(1), mmu-miR-194-5p(1), mmu-miR-107-3p(1), mmu-miR-669d-5p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
ATTTTCCCAAGATGCCACTGAAAGGT
siRNA sets
TTTCAGTGGCATCTTGGGA, TTCAGTGGCATCTTGGGAA, CTTTCAGTGGCATCTTGGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCR3HDM1_1020_ORF_1
0.8072
0.023976565
0.973507525
1011
ORF sequence:
ATGAGGATGTCTGATATTGTTATTATAAAAGATGAAACTGAAACAATGAAGGATTTGGAGGCAGAAATGAGAGATACAACCAGAGTTGAAAATCTTATCAAATCAGAAAACTATGGGAAGATTTCGGCAGAGAAGAATGAACATTGTATTGACAACAATATTGATTTGCAGGAGAAAATTCAGATACAGTTAACACAATCATTTGAAAAAGAGGAAAAGCCCTCAAAAGATGAAACAGATAAAGAAAAAGCCAGTGATAAGTTACCCAGAAAAATGTTATCAAGAGATTCCAGCCAAGAATACACTGATTCAACTGGCATAGATCTACATGAATTTTTAGTAAATACATTAAAAAACAATCCCAGGGACAGAATGATGCTGCTGAAATTGGAACAAGAAATTTTAGATTTCATTGGTAATAATGAGTCCCCACGTAAGAAGTTTCCCCCGATGACATCTTACCACAGGATGCTGTTACACAGAGTGGCTGCCTACTTTGGATTAGACCACAATGTTGATCAGAGTGGGAAGTCTGTCATAGTGAACAAAACTAGCAACACAAGAATACCTGATCAGAAATTTAATGAACATATAAAGGATGATAGAGGTGAAGACTTTCAGAAACGATACATCCTTAAGAGAGATAACTCTAGCTTTGACAAAGATGATAGCCAGATGAGAATACGTTTGAAAGATGACAGAAGAAGCAAATCTATAGAAGAAAGAGAAGAAGAATACCAGAGAGCTAGAGACCGAATATTTTCCCAAGATGCCACTGAAAGGTATGATATATTTGATCCAAGACAGTCCATTTCAGCCCAGGAATCTACAGTGGTGACAAGGACATGGGACTCCTCCCGCCAGATTACTGTTGGTTCAATACATTTGACATCCTGGCTGACAACTGTGAAGAGGAACCTTGGGTTATTTTATTTTATTTTTGTGGAACACCACAATCTCAGATCCATAGGACACATCAGGCTTCAAGTTCCCTGTAGAATTCTAAAATAA
Peptide sequence:
MRMSDIVIIKDETETMKDLEAEMRDTTRVENLIKSENYGKISAEKNEHCIDNNIDLQEKIQIQLTQSFEKEEKPSKDETDKEKASDKLPRKMLSRDSSQEYTDSTGIDLHEFLVNTLKNNPRDRMMLLKLEQEILDFIGNNESPRKKFPPMTSYHRMLLHRVAAYFGLDHNVDQSGKSVIVNKTSNTRIPDQKFNEHIKDDRGEDFQKRYILKRDNSSFDKDDSQMRIRLKDDRRSKSIEEREEEYQRARDRIFSQDATERYDIFDPRQSISAQESTVVTRTWDSSRQITVGSIHLTSWLTTVKRNLGLFYFIFVEHHNLRSIGHIRLQVPCRILK
IRESfinder result
IRESfinder score
0.687942125
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page