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mmu_circPcm1_3667
Basic information of circular RNA
PanCircBase ID:
mmu_circPcm1_3667
mm39_Chr. Position ID:
chr8|41728031|41775088|+
Gene name:
Pcm1
Transcript:
ENSMUST00000045218.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
21
Exon/intron indexes:
10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30
Exon/intron offsets:
0,658,931,4756,5027,7585,8561,10970,12687,13014,13636,15726,18463,28992,34525,35014,37163,38307,38850,40925,46859
Genomic length:
47057
Exon/intron sizes in nt:
17,41,55,22,71,43,13,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr8:41727335-41728031|chr8:41775088-41777991
Splice length:
3667
Other database IDs:
CIRCpedia: MMU_CIRCpedia_19598, circAtlas: mmu-Pcm1_0041
Human Ortholog IDs:
Mature spliced Sequence:
GAAGTTAAATGAAGTTCAAAAGAGATTGAATGAACTGAGAGAATTAGTTCATTATTATGAACAAACATCAGATATGATGACAGATGCTGTAAATGAAAATACAAAAGATGAAGAAACTGAAGAGTCAGAATATGATTCTGAACATGAAAATTCTGAACCTGTTACTAACATTAGAAATCCACAGGTAGCTTCTACCTGGAATGAAGTGAATACTAACAGTAATACACAGTGTGGTTCTAACAATAGAGATGGGAGACCAGTTAATTCTAACTGTGAAATTAATAACAGATCTGCTGCCAACATCAGAGCTCTAAACATGCCTCCATTAGACTGTCGATACAATAGAGAAGGAGAGCAGAGGTTGCATGTAGCACATGGAGAAGATGAGGAAGAAGAAGTAGAAGAGGAAGGAGTCAGTGGGGCTTCATTATCTAGTCGTAGGAGCAGTCTGGTCGATGAAGCACCAGAAGATGAAGAATTTGAACAGAAGATTAGTAGACTCATGGCTGCAAAAGAGAAACTTAAACAGCTCCAAGATCTTGTTGCTATGGTGCAGGATGATGATGCAACTCAAGTGGTTGTCCCTGCTGCATCAAATTTGGATGATTTCTATGCAGCAGAAGAAGATATCAAACAAAATTCCAATAATGCAAGAGAAAATTCTAATAAAATAGATACTGGAGTAAATGAAAAAACAAGAGAGAAATTTTATGAGGCTAAACTACAGCAGCAACAGAGAGAGCTTAAACAATTGCAGGAGGAAAGAAAGAAATTGATTGAAATTCAAGAGAAAATTCAAGCAGTGCAAAAGGCATGCCCTGACCTTCAGCTCTCAGCCACTAGTATAAGTAGTGGTCCCACAAAAAAATATCTACCAGCTATTACTTCAACTCCAACTGTTAATGAAAATGACAGCAGTACAAGCAAGTGTGTTATTGATCCTGAAGATTCTTCAGTGGTGGATAATGAGTTGTGGTCAGACATGAGAAGACATGAAATGTTAAGGGAAGAGCTACGGCAGAGAAGGAAGCAACTTGAAGCTCTAATGGCTGAACACCAGAGGAGGCAAGGTCTAGCTGAGACCTCATCTCCAGTGGCTATATCATTGAGAAGTGATGGATCTGAGAACCTGTGCACTCCTCAGCAAAGTAGAACAGAAAAAACAATGGCAACTTGGGGAGGTTCTACTCAGTGTGCATTAGATGAAGAAGGAGATGAGGATGGCTATCTTTCAGAAGGAATTGTTCGCACAGATGAAGAAGAGGAGGAGGAGCAGGATGCCAGTTCCAATGATAACTTCCCTATATACCCTCCTAGCATGAATCAAAATTCTTACAATGTAAAGGAAACCAAAACCAGGTGGAAGAGCAATCGCCCTGTTTCAGCAGATGGAAATTACCGTCCTTTAGCCAAGACAAGGCAGCAGAATATCAGCATGCAACGACAAGAAAACCTTCGATGGGTGTCAGAGCTCTCTTACATAGAAGAGAAGGAGCAGTGGCAAGAACAGATTAATCAGCTAAAGAAACAACTCGATTTCAGTGTCAATATTTGTCAGACTCTGATGCAAGACCAACAGACTTTATCTTGTTTGCTGCAGACTCTTCTAACAGGTCCGTACAGTGTTCTGCCTAGTAATGTGGCGTCCCCTCAAGTGCACCTTATCATGCATCAGCTGAACCAATGCTACACACAGCTAACATGGCAGCAGAACAATGTCCAGAGGTTAAAACAAATGCTAACTGAACTTATGCGCCAACAAAATCAGCACCCAGAAAAGCCTAGAAGCAAAGAAAGAGGCAGTAGTGCGTCACACCCTTCTTCTCCCAATTTATTTTGCCCTTTCAGCTTTCCAACACAGCCTGTAAATCTGTTTAACCTGCCTGGATTTACTAACTTTCCATCATTTGCACCAGGAATGAATTTCAGCCCTTTATTTCCTTCTAATTTTGGAGATTTTTCTCAGAATGTTTCTACACCTACTGAACAGCAGCAGCCATTAGCTCAAAATCCTTCAGGGAAAACAGAGTATATGGCTTTTCCAAAACCCTTTGAAAGCAGTTCTTCTCTTGGAGCAGAAAAGCAAAGGAATCAGAAACAGCCCGAAGAGGAAGCTGAAAACACTAAGACACCATGGTTATATGATCAAGAAGGTGGAGTAGAAAAACCATTTTTCAAGACTGGATTTACAGAGTCTGTAGAGAAAGCTACAAATAGTAACCGCAAAAATCAACCAGATACAAGCAGGAGAAGACGTCAGTTTGATGAAGAATCCTTGGAAAGCTTTAGCAGTATGCCTGATCCTATAGACCCAACAACAGTAACTAAAACATTTAAAACAAGAAAAGCATCTGCCCAGGCCAGCCTGGCCTCTAAGGACAAAACTCCCAAATCAAAGAGTAAGAAGAGGAATTCTACTCAGCTGAAAAGTAGAGTTAAAAATATTGGGTATGAAAGTGCCAGTGTGTCTAGCACATGTGAACCTTGCAAAAATAGGAACAGACATTCAGCCCAGACTGAAGAGCCTGTTCAAGCAAAATTATTCAGCAGAAAGAATCATGAACAGCTGGAAAAAATAATAAAATATAGTAGGTCTGCAGAAATATCTTCAGAGACTGGAAGTGATTTTTCCATGTTTGAAGCTTTACGGGATACTATTTATTCCGAAGTGGCTACATTAATTTCTCAAAATGAGTCTCGTCCACATTTTCTTATTGAACTTTTCCATGAGCTGCAGCTACTTAATACAGACTACTTGAGACAGAGAGCTTTATATGCATTGCAGGATATCGTATCCAGACACATTTCTGAAAGTGATGAAAGAGAAGGAGAAAATGTAAAGCCTGTGAACTCTGGCACTTGGGTAGCATCCAATTCAGAGCTTACTCCGAGTGAGAGCCTTGTTACTACTGACGATGAAACATTTGAGAAGAACTTTGAAAGAGAAACACATAAAGTAAGTGAACAGAATGATGCTGACAACGTGAGTGTCATGTCCGTATCCTCCAACTTTGAGCCATTTGCAACAGACGACTTAGGTAACACTGTGATTCACTTGGATCAAGCATTAGCCAGAATGAGAGAGTATGAGCGCATGAAGACCGAGACAGAAAGTCACTCAAATATGAGATGCACTTGCAGGGTTATTGAGGATGAAGATGGTGCTGCCGCCGCTGCCACAGTCAGTAATTCAGAAGAAACTCCCATTATTGAGAATCACAATTCACCACAACCTATAAGTGATGTTTCTGCCGTCCCCTGTCCTAGAATTGATACTCAGCAACTGGACCGCCAAATTAAAGCAATTATGAAAGAAGTCATTCCTTTTTTGAAGGAGCACATGGATGAAGTGTGTTCGTCTCAGCTTCTCACTTCAGTAAGACGTATGGTCTTGACCCTTACCCAGCAGAATGATGAGAGCAAAGAGTTTGTGAAGTTCTTTCATAAACAACTAGGAAGTATATTGCAGGATTCACTAGCAAAATTTGCAGGCAGAAAGCTGAAAGACTGTGGAGAAGATCTTCTTGTGGAGATCTCTGAAGTGTTGTTTAATGAATTGGCTTTCTTTAAGCTCATGCAAGACTTGGATAATAATAGCATAGCTGTTAAACAGAGGTGCAAGAGGAAAATTGAAGCAGCTGGAGTGAGGCAGTCTTATGCAAAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAAGAGGAAAATTGAAGCAGC
59.01
ACAGCATCTGTCATCATATCTGA
57.2
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGTGCAAGAGGAAAATTGAAGC
59.99
ACAGCATCTGTCATCATATCTGA
57.2
144
PCR template sequence:
TAAGCTCATGCAAGACTTGGATAATAATAGCATAGCTGTTAAACAGAGGTGCAAGAGGAAAATTGAAGCAGCTGGAGTGAGGCAGTCTTATGCAAAAGAGGAAGTTAAATGAAGTTCAAAAGAGATTGAATGAACTGAGAGAATTAGTTCATTATTATGAACAAACATCAGATATGATGACAGATGCTGTAAATGAAAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
34
Interacting miRNAs (#binding sites)
mmu-miR-335-3p(5), mmu-miR-5101(3), mmu-miR-1904(3), mmu-miR-129-5p(2), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-181a-5p(1), mmu-miR-19b-3p(1), mmu-miR-26a-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-146a-5p(1), mmu-miR-19a-3p(1), mmu-miR-18a-5p(1), mmu-miR-222-3p(1), mmu-miR-214-3p(1), mmu-miR-128-3p(1), mmu-miR-149-5p(1), mmu-miR-431-5p(1), mmu-miR-153-3p(1), mmu-miR-494-3p(1), mmu-miR-541-5p(1), mmu-miR-340-5p(1), mmu-miR-384-3p(1), mmu-miR-344d-3p(1), mmu-miR-207(1), mmu-miR-539-5p(1), mmu-miR-3470b(1), mmu-miR-670-5p(1), mmu-miR-323-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTATGCAAAAGAGGAAGTTAAATGAA
siRNA sets
TAACTTCCTCTTTTGCATA,TTTAACTTCCTCTTTTGCA,TTAACTTCCTCTTTTGCAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPCM1_3667_ORF_1
1.0834
0.063088613
1
3678
ORF sequence:
ATGCAAAAGAGGAAGTTAAATGAAGTTCAAAAGAGATTGAATGAACTGAGAGAATTAGTTCATTATTATGAACAAACATCAGATATGATGACAGATGCTGTAAATGAAAATACAAAAGATGAAGAAACTGAAGAGTCAGAATATGATTCTGAACATGAAAATTCTGAACCTGTTACTAACATTAGAAATCCACAGGTAGCTTCTACCTGGAATGAAGTGAATACTAACAGTAATACACAGTGTGGTTCTAACAATAGAGATGGGAGACCAGTTAATTCTAACTGTGAAATTAATAACAGATCTGCTGCCAACATCAGAGCTCTAAACATGCCTCCATTAGACTGTCGATACAATAGAGAAGGAGAGCAGAGGTTGCATGTAGCACATGGAGAAGATGAGGAAGAAGAAGTAGAAGAGGAAGGAGTCAGTGGGGCTTCATTATCTAGTCGTAGGAGCAGTCTGGTCGATGAAGCACCAGAAGATGAAGAATTTGAACAGAAGATTAGTAGACTCATGGCTGCAAAAGAGAAACTTAAACAGCTCCAAGATCTTGTTGCTATGGTGCAGGATGATGATGCAACTCAAGTGGTTGTCCCTGCTGCATCAAATTTGGATGATTTCTATGCAGCAGAAGAAGATATCAAACAAAATTCCAATAATGCAAGAGAAAATTCTAATAAAATAGATACTGGAGTAAATGAAAAAACAAGAGAGAAATTTTATGAGGCTAAACTACAGCAGCAACAGAGAGAGCTTAAACAATTGCAGGAGGAAAGAAAGAAATTGATTGAAATTCAAGAGAAAATTCAAGCAGTGCAAAAGGCATGCCCTGACCTTCAGCTCTCAGCCACTAGTATAAGTAGTGGTCCCACAAAAAAATATCTACCAGCTATTACTTCAACTCCAACTGTTAATGAAAATGACAGCAGTACAAGCAAGTGTGTTATTGATCCTGAAGATTCTTCAGTGGTGGATAATGAGTTGTGGTCAGACATGAGAAGACATGAAATGTTAAGGGAAGAGCTACGGCAGAGAAGGAAGCAACTTGAAGCTCTAATGGCTGAACACCAGAGGAGGCAAGGTCTAGCTGAGACCTCATCTCCAGTGGCTATATCATTGAGAAGTGATGGATCTGAGAACCTGTGCACTCCTCAGCAAAGTAGAACAGAAAAAACAATGGCAACTTGGGGAGGTTCTACTCAGTGTGCATTAGATGAAGAAGGAGATGAGGATGGCTATCTTTCAGAAGGAATTGTTCGCACAGATGAAGAAGAGGAGGAGGAGCAGGATGCCAGTTCCAATGATAACTTCCCTATATACCCTCCTAGCATGAATCAAAATTCTTACAATGTAAAGGAAACCAAAACCAGGTGGAAGAGCAATCGCCCTGTTTCAGCAGATGGAAATTACCGTCCTTTAGCCAAGACAAGGCAGCAGAATATCAGCATGCAACGACAAGAAAACCTTCGATGGGTGTCAGAGCTCTCTTACATAGAAGAGAAGGAGCAGTGGCAAGAACAGATTAATCAGCTAAAGAAACAACTCGATTTCAGTGTCAATATTTGTCAGACTCTGATGCAAGACCAACAGACTTTATCTTGTTTGCTGCAGACTCTTCTAACAGGTCCGTACAGTGTTCTGCCTAGTAATGTGGCGTCCCCTCAAGTGCACCTTATCATGCATCAGCTGAACCAATGCTACACACAGCTAACATGGCAGCAGAACAATGTCCAGAGGTTAAAACAAATGCTAACTGAACTTATGCGCCAACAAAATCAGCACCCAGAAAAGCCTAGAAGCAAAGAAAGAGGCAGTAGTGCGTCACACCCTTCTTCTCCCAATTTATTTTGCCCTTTCAGCTTTCCAACACAGCCTGTAAATCTGTTTAACCTGCCTGGATTTACTAACTTTCCATCATTTGCACCAGGAATGAATTTCAGCCCTTTATTTCCTTCTAATTTTGGAGATTTTTCTCAGAATGTTTCTACACCTACTGAACAGCAGCAGCCATTAGCTCAAAATCCTTCAGGGAAAACAGAGTATATGGCTTTTCCAAAACCCTTTGAAAGCAGTTCTTCTCTTGGAGCAGAAAAGCAAAGGAATCAGAAACAGCCCGAAGAGGAAGCTGAAAACACTAAGACACCATGGTTATATGATCAAGAAGGTGGAGTAGAAAAACCATTTTTCAAGACTGGATTTACAGAGTCTGTAGAGAAAGCTACAAATAGTAACCGCAAAAATCAACCAGATACAAGCAGGAGAAGACGTCAGTTTGATGAAGAATCCTTGGAAAGCTTTAGCAGTATGCCTGATCCTATAGACCCAACAACAGTAACTAAAACATTTAAAACAAGAAAAGCATCTGCCCAGGCCAGCCTGGCCTCTAAGGACAAAACTCCCAAATCAAAGAGTAAGAAGAGGAATTCTACTCAGCTGAAAAGTAGAGTTAAAAATATTGGGTATGAAAGTGCCAGTGTGTCTAGCACATGTGAACCTTGCAAAAATAGGAACAGACATTCAGCCCAGACTGAAGAGCCTGTTCAAGCAAAATTATTCAGCAGAAAGAATCATGAACAGCTGGAAAAAATAATAAAATATAGTAGGTCTGCAGAAATATCTTCAGAGACTGGAAGTGATTTTTCCATGTTTGAAGCTTTACGGGATACTATTTATTCCGAAGTGGCTACATTAATTTCTCAAAATGAGTCTCGTCCACATTTTCTTATTGAACTTTTCCATGAGCTGCAGCTACTTAATACAGACTACTTGAGACAGAGAGCTTTATATGCATTGCAGGATATCGTATCCAGACACATTTCTGAAAGTGATGAAAGAGAAGGAGAAAATGTAAAGCCTGTGAACTCTGGCACTTGGGTAGCATCCAATTCAGAGCTTACTCCGAGTGAGAGCCTTGTTACTACTGACGATGAAACATTTGAGAAGAACTTTGAAAGAGAAACACATAAAGTAAGTGAACAGAATGATGCTGACAACGTGAGTGTCATGTCCGTATCCTCCAACTTTGAGCCATTTGCAACAGACGACTTAGGTAACACTGTGATTCACTTGGATCAAGCATTAGCCAGAATGAGAGAGTATGAGCGCATGAAGACCGAGACAGAAAGTCACTCAAATATGAGATGCACTTGCAGGGTTATTGAGGATGAAGATGGTGCTGCCGCCGCTGCCACAGTCAGTAATTCAGAAGAAACTCCCATTATTGAGAATCACAATTCACCACAACCTATAAGTGATGTTTCTGCCGTCCCCTGTCCTAGAATTGATACTCAGCAACTGGACCGCCAAATTAAAGCAATTATGAAAGAAGTCATTCCTTTTTTGAAGGAGCACATGGATGAAGTGTGTTCGTCTCAGCTTCTCACTTCAGTAAGACGTATGGTCTTGACCCTTACCCAGCAGAATGATGAGAGCAAAGAGTTTGTGAAGTTCTTTCATAAACAACTAGGAAGTATATTGCAGGATTCACTAGCAAAATTTGCAGGCAGAAAGCTGAAAGACTGTGGAGAAGATCTTCTTGTGGAGATCTCTGAAGTGTTGTTTAATGAATTGGCTTTCTTTAAGCTCATGCAAGACTTGGATAATAATAGCATAGCTGTTAAACAGAGGTGCAAGAGGAAAATTGAAGCAGCTGGAGTGAGGCAGTCTTATGCAAAAGAG
Peptide sequence:
MQKRKLNEVQKRLNELRELVHYYEQTSDMMTDAVNENTKDEETEESEYDSEHENSEPVTNIRNPQVASTWNEVNTNSNTQCGSNNRDGRPVNSNCEINNRSAANIRALNMPPLDCRYNREGEQRLHVAHGEDEEEEVEEEGVSGASLSSRRSSLVDEAPEDEEFEQKISRLMAAKEKLKQLQDLVAMVQDDDATQVVVPAASNLDDFYAAEEDIKQNSNNARENSNKIDTGVNEKTREKFYEAKLQQQQRELKQLQEERKKLIEIQEKIQAVQKACPDLQLSATSISSGPTKKYLPAITSTPTVNENDSSTSKCVIDPEDSSVVDNELWSDMRRHEMLREELRQRRKQLEALMAEHQRRQGLAETSSPVAISLRSDGSENLCTPQQSRTEKTMATWGGSTQCALDEEGDEDGYLSEGIVRTDEEEEEEQDASSNDNFPIYPPSMNQNSYNVKETKTRWKSNRPVSADGNYRPLAKTRQQNISMQRQENLRWVSELSYIEEKEQWQEQINQLKKQLDFSVNICQTLMQDQQTLSCLLQTLLTGPYSVLPSNVASPQVHLIMHQLNQCYTQLTWQQNNVQRLKQMLTELMRQQNQHPEKPRSKERGSSASHPSSPNLFCPFSFPTQPVNLFNLPGFTNFPSFAPGMNFSPLFPSNFGDFSQNVSTPTEQQQPLAQNPSGKTEYMAFPKPFESSSSLGAEKQRNQKQPEEEAENTKTPWLYDQEGGVEKPFFKTGFTESVEKATNSNRKNQPDTSRRRRQFDEESLESFSSMPDPIDPTTVTKTFKTRKASAQASLASKDKTPKSKSKKRNSTQLKSRVKNIGYESASVSSTCEPCKNRNRHSAQTEEPVQAKLFSRKNHEQLEKIIKYSRSAEISSETGSDFSMFEALRDTIYSEVATLISQNESRPHFLIELFHELQLLNTDYLRQRALYALQDIVSRHISESDEREGENVKPVNSGTWVASNSELTPSESLVTTDDETFEKNFERETHKVSEQNDADNVSVMSVSSNFEPFATDDLGNTVIHLDQALARMREYERMKTETESHSNMRCTCRVIEDEDGAAAAATVSNSEETPIIENHNSPQPISDVSAVPCPRIDTQQLDRQIKAIMKEVIPFLKEHMDEVCSSQLLTSVRRMVLTLTQQNDESKEFVKFFHKQLGSILQDSLAKFAGRKLKDCGEDLLVEISEVLFNELAFFKLMQDLDNNSIAVKQRCKRKIEAAGVRQSYAKE
IRESfinder result
IRESfinder score
0.637957388
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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