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mmu_circHlcs_1685
Basic information of circular RNA
PanCircBase ID:
mmu_circHlcs_1685
mm39_Chr. Position ID:
chr16|94031922|94088785|-
Gene name:
Hlcs
Transcript:
ENSMUST00000163193.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,31528,36312,37472,56728
Genomic length:
56863
Exon/intron sizes in nt:
27,21,83,93,21,63,135
Flanking exon/introns:
chr16:93942275-94031922|chr16:94088785-94114376
Splice length:
1685
Other database IDs:
circAtlas: mmu-Hlcs_0012
circBase: hsa_circ_0061653, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_35429
Human Ortholog IDs:
Mature spliced Sequence:
TCTGTTGATGACTTGAACAAATGGGCCCTGTTTCTCGTGTCTCCCTTCATACTTGAGGCAGAACATATAGCATTTGTGACAGAGAGCATTTGGATACAAGGTACCAGTTTACAAGAGCCATCATCTTCAGAAACCGTTGTAAAATGGTCTGACTGCTGTCTGCCGTTAGCCTGCCGACCCGGGGACCCCTACCAGTTAATTGCTAAGGCAAGCGTGGACAACTTCAGCAAGCTTGGGGTGGCCTTCATGGAGGACAGGCTCCAGATGGACAACGGCCTGATAGCCCAGAAGATCGTTTCAGTCCACTTAAAGGACCCTGCTCTGAAGGAACTCGGCAAAGCCTCCGACAAGCAAGTGCAGGGCCCGCCCCCGGGCCCAGAAGCTTCCCCCGAGGCCCAGCCTGCACAAGGTGTCATGGAGCATGCTGGCCAAGGTGATTGCAAGGCCGCCGGTGAAGGCCCTTCCCCACGGAGGAGGGGCTGTGCCCCTGAAAGTGAGCCTGCTGCAGATGGGGACCCAGGGCTGAGCTCCCCGGAGCTCTGTCAGCTCCACCTGTCCATCTGTCACGAGTGTCTGGAGCTCGAGAACAGTACCATTGACTCGGTGAGGTCTGCGTCTGCGGAGAACATTCCAGACCTTCCCTGTGATCACAGCGGCGTGGAGGGTGCTGCGGGCGAACTCTGCCCCGAACGGAAAGGGAAGAGAGTCAACATTTCGGGAAAGGCGCCCAATATCTTGCTGTATGTGGGCTCTGGTTCCGAGGAAGCCCTGGGCCGGCTCCAGCAGGTGCGATCTGTCCTGACTGACTGTGTGGACACGGACAGCTACACTCTCTACCACCTGCTGGAAGACAGCGCTCTGAGGGACCCGTGGTCTGACAACTGCCTCCTGCTAGTTATTGCCAGCAGGGACCCCATCCCCAAAGACATACAGCACAAGTTCATGGCCTATCTTTCTCAGGGAGGGAAGGTGCTGGGCCTGTCTTCCCCCTTCACGTTGGGTGGCTTTCGGGTGACCAGGAGAGATGTGCTACGGAACACAGTCCAGAACTTGGTTTTCTCTAAGGCTGATGGGACTGAGGTACGGCTCAGTGTCCTGAGCAGCGGCTACGTTTATGAAGAAGGCCCGAGCTTGGGCAGGCTCCAGGGCCACCTGGAGAATGAGGACAAGGATAAAATGATTGTGCACGTGCCTTTTGGAACCCTCGGAGGGGAAGCCGTTCTCTGCCAGGTGCACCTGGAGCTCCCGCCCGGCGCCTCCCTGGTGCAGACTGCAGACGACTTTAACGTGCTCAAATCCAGCAATGTGAGAAGACACGAGGTCCTTAAGGAGATCCTGACTGCCCTCGGTCTGAGCTGTGACGCACCACAGGTTCCTGCCTTAACGCCCCTGTACTTACTGCTGGCCGCTGAGGAAACCCAGGATCCGTTCATGCAGTGGCTCGGGAGGCACACAGATCCTGAAGGAATCATAAAATCCAGCAAGCTCTCCCTTCAGTTTGTTTCCTCCTACACATCTGAAGCGGAGATCACCCCGTCTTCCATGCCTGTGGTCACTGACCCAGAAGCCTTTTCATCAGAGCACTTCAGCCTAGAGACCTATCGACAGAATCTGCAGACCACGCGCCTTGGGAAAGTGATTCTGTTTGCAGAAGTGACCTCCACCACCATGAGTCTCCTGGATGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGCCTAGAGACCTATCGACA
59.56
GGGAGACACGAGAAACAGGG
60.04
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCGCCTTGGGAAAGTGATTC
59.83
TGCTCTCTGTCACAAATGCT
57.44
151
PCR template sequence:
TCAGCCTAGAGACCTATCGACAGAATCTGCAGACCACGCGCCTTGGGAAAGTGATTCTGTTTGCAGAAGTGACCTCCACCACCATGAGTCTCCTGGATGGTCTGTTGATGACTTGAACAAATGGGCCCTGTTTCTCGTGTCTCCCTTCATACTTGAGGCAGAACATATAGCATTTGTGACAGAGAGCATTTGGATACAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
20
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-23b-3p(1), mmu-miR-7b-5p(1), mmu-miR-18a-5p(1), mmu-miR-328-3p(1), mmu-miR-298-5p(1), mmu-miR-217-5p(1), mmu-miR-7a-5p(1), mmu-miR-23a-3p(1), mmu-miR-339-5p(1), mmu-miR-214-3p(1), mmu-miR-382-5p(1), mmu-miR-511-3p(1), mmu-miR-370-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-673-5p(1), mmu-miR-484(1), mmu-miR-452-3p(1), mmu-miR-350-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCTCCTGGATGGTCTGTTGATGACT
siRNA sets
ATCAACAGACCATCCAGGA, AACAGACCATCCAGGAGAC, AGTCATCAACAGACCATCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHLCS_1685_ORF_1
1.2722
0.337122042
0.999866609
1455
ORF sequence:
ATGGAGGACAGGCTCCAGATGGACAACGGCCTGATAGCCCAGAAGATCGTTTCAGTCCACTTAAAGGACCCTGCTCTGAAGGAACTCGGCAAAGCCTCCGACAAGCAAGTGCAGGGCCCGCCCCCGGGCCCAGAAGCTTCCCCCGAGGCCCAGCCTGCACAAGGTGTCATGGAGCATGCTGGCCAAGGTGATTGCAAGGCCGCCGGTGAAGGCCCTTCCCCACGGAGGAGGGGCTGTGCCCCTGAAAGTGAGCCTGCTGCAGATGGGGACCCAGGGCTGAGCTCCCCGGAGCTCTGTCAGCTCCACCTGTCCATCTGTCACGAGTGTCTGGAGCTCGAGAACAGTACCATTGACTCGGTGAGGTCTGCGTCTGCGGAGAACATTCCAGACCTTCCCTGTGATCACAGCGGCGTGGAGGGTGCTGCGGGCGAACTCTGCCCCGAACGGAAAGGGAAGAGAGTCAACATTTCGGGAAAGGCGCCCAATATCTTGCTGTATGTGGGCTCTGGTTCCGAGGAAGCCCTGGGCCGGCTCCAGCAGGTGCGATCTGTCCTGACTGACTGTGTGGACACGGACAGCTACACTCTCTACCACCTGCTGGAAGACAGCGCTCTGAGGGACCCGTGGTCTGACAACTGCCTCCTGCTAGTTATTGCCAGCAGGGACCCCATCCCCAAAGACATACAGCACAAGTTCATGGCCTATCTTTCTCAGGGAGGGAAGGTGCTGGGCCTGTCTTCCCCCTTCACGTTGGGTGGCTTTCGGGTGACCAGGAGAGATGTGCTACGGAACACAGTCCAGAACTTGGTTTTCTCTAAGGCTGATGGGACTGAGGTACGGCTCAGTGTCCTGAGCAGCGGCTACGTTTATGAAGAAGGCCCGAGCTTGGGCAGGCTCCAGGGCCACCTGGAGAATGAGGACAAGGATAAAATGATTGTGCACGTGCCTTTTGGAACCCTCGGAGGGGAAGCCGTTCTCTGCCAGGTGCACCTGGAGCTCCCGCCCGGCGCCTCCCTGGTGCAGACTGCAGACGACTTTAACGTGCTCAAATCCAGCAATGTGAGAAGACACGAGGTCCTTAAGGAGATCCTGACTGCCCTCGGTCTGAGCTGTGACGCACCACAGGTTCCTGCCTTAACGCCCCTGTACTTACTGCTGGCCGCTGAGGAAACCCAGGATCCGTTCATGCAGTGGCTCGGGAGGCACACAGATCCTGAAGGAATCATAAAATCCAGCAAGCTCTCCCTTCAGTTTGTTTCCTCCTACACATCTGAAGCGGAGATCACCCCGTCTTCCATGCCTGTGGTCACTGACCCAGAAGCCTTTTCATCAGAGCACTTCAGCCTAGAGACCTATCGACAGAATCTGCAGACCACGCGCCTTGGGAAAGTGATTCTGTTTGCAGAAGTGACCTCCACCACCATGAGTCTCCTGGATGGTCTGTTGATGACTTGA
Peptide sequence:
MEDRLQMDNGLIAQKIVSVHLKDPALKELGKASDKQVQGPPPGPEASPEAQPAQGVMEHAGQGDCKAAGEGPSPRRRGCAPESEPAADGDPGLSSPELCQLHLSICHECLELENSTIDSVRSASAENIPDLPCDHSGVEGAAGELCPERKGKRVNISGKAPNILLYVGSGSEEALGRLQQVRSVLTDCVDTDSYTLYHLLEDSALRDPWSDNCLLLVIASRDPIPKDIQHKFMAYLSQGGKVLGLSSPFTLGGFRVTRRDVLRNTVQNLVFSKADGTEVRLSVLSSGYVYEEGPSLGRLQGHLENEDKDKMIVHVPFGTLGGEAVLCQVHLELPPGASLVQTADDFNVLKSSNVRRHEVLKEILTALGLSCDAPQVPALTPLYLLLAAEETQDPFMQWLGRHTDPEGIIKSSKLSLQFVSSYTSEAEITPSSMPVVTDPEAFSSEHFSLETYRQNLQTTRLGKVILFAEVTSTTMSLLDGLLMT
IRESfinder result
IRESfinder score
0.506175469
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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