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mmu_circNrf1_1513
Basic information of circular RNA
PanCircBase ID:
mmu_circNrf1_1513
mm39_Chr. Position ID:
chr6|30088831|30126358|+
Gene name:
Nrf1
Transcript:
ENSMUST00000115212.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
2,3,4,5,6,7,8,9,10,11
Exon/intron offsets:
0,1082,6507,9616,13336,26180,27263,28223,30116,37402
Genomic length:
37527
Exon/intron sizes in nt:
156,232,115,127,141,159,198,102,158,125
Flanking exon/introns:
chr6:30048112-30088831|chr6:30126358-30151512
Splice length:
1513
Other database IDs:
circBase: mmu_circ_0013269, CIRCpedia: MMU_CIRCpedia_15712, circAtlas: mmu-Nrf1_0011
Human Ortholog IDs:
Mature spliced Sequence:
GTCGAATGGTATGTGGTTCATGTAGACCACATTTTGTTTCCCTCTCACCCATTGATGGACACTTGGGTAGCTTCCATTTTTGGCTGTTGTGAATAATGCTGCTATGAACATGGGTGTGCACAGAGCTCTCTGAGACGCTGCTTTCAGTCCTTCTGGTAGATCTTCATGGAGGAGCACGGAGTGACCCAAACTGAACACATGGCTACCATAGAAGCCCATGCAGTGGCCCAGCAAGTCCAGCAGGTCCATGTAGCCACGTACACTGAGCACAGTATGCTAAGTGCTGATGAAGACTCCCCTTCCTCCCCCGAGGACACTTCTTATGATGACTCGGACATCCTCAACTCCACGGCAGCTGATGAGGTAACTGCCCATCTGGCTGCTGCAGGTCCTGTGGGAATGGCCGCTGCTGCTGCTGTGGCAACAGGGAAGAAACGGAAACGGCCTCATGTGTTTGAGTCTAATCCATCTATCCGAAAGAGACAGCAGACACGTTTGCTTCGGAAACTCAGAGCCACGTTGGATGAGTACACGACGCGAGTGGGACAGCAAGCGATTGTACTCTGCATCTCACCCTCCAAACCCAACCCTGTCTTCAAGGTGTTTGGCGCAGCACCTTTGGAGAATGTGGTGCGAAAGTACAAGAGCATGATCCTGGAAGACCTCGAGTCTGCTCTGGCAGAACACGCCCCTGCGCCACAGGAGGTTAATTCAGAGCTGCCGCCTCTCACCATCGATGGGATTCCAGTCTCTGTGGACAAAATGACCCAGGCTCAGCTTCGGGCATTTATCCCAGAGATGCTCAAGTATTCCACAGGTCGGGGGAAACCAGGCTGGGGGAAAGAAAGCTGCAAGCCTATCTGGTGGCCAGAAGATATCCCATGGGCCAATGTCCGCAGTGATGTCCGCACAGAAGAGCAAAAACAAAGGGTTTCATGGACCCAGGCATTACGGACCATAGTTAAAAATTGCTATAAGCAACATGGGCGGGAGGATCTTTTATATGCTTTTGAAGATCAGCAAACACAAACTCAGGCCACCACCACACACAGTATAGCTCATCTCGTACCATCACAGACCGTAGTACAGACCTTCAGCAACCCTGATGGCACCGTGTCGCTCATCCAGGTTGGTACAGGGGCAACAGTAGCCACATTGGCTGATGCTTCAGAACTGCCAACCACAGTCACTGTTGCCCAAGTGAATTACTCTGCTGTGGCTGATGGAGAGGTGGAACAAAACTGGGCCACGTTACAGGGCGGTGAAATGACCATCCAGACGACGCAAGCATCAGAGGCCACCCAGGCGGTAGCATCACTGGCAGAAGCCGCAGTGGCAGCTTCTCAGGAGATGCAGCAGGGAGCCACTGTCACCATGGCCCTCAACAGTGAAGCTGCCGCCCATGCTGTCGCCACTCTGGCGGAAGCCACCTTACAAGGTGGGGGACAGATAGTCCTGTCTGGGGAAACCGCAGCAGCCGTCGGAGCACTTACTGGAGTCCAAGATGCTAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTTACAAGGTGGGGGACAG
59.67
GGAAGCTACCCAAGTGTCCA
59.31
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTTACAAGGTGGGGGACAG
59.67
TGGAAGCTACCCAAGTGTCC
59.31
160
PCR template sequence:
ACTCTGGCGGAAGCCACCTTACAAGGTGGGGGACAGATAGTCCTGTCTGGGGAAACCGCAGCAGCCGTCGGAGCACTTACTGGAGTCCAAGATGCTAATGGTCGAATGGTATGTGGTTCATGTAGACCACATTTTGTTTCCCTCTCACCCATTGATGGACACTTGGGTAGCTTCCATTTTTGGCTGTTGTGAATAATGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-296-3p(2), mmu-miR-134-5p(1), mmu-miR-103-3p(1), mmu-miR-221-3p(1), mmu-miR-322-5p(1), mmu-miR-222-3p(1), mmu-miR-503-5p(1), mmu-miR-22-3p(1), mmu-miR-370-3p(1), mmu-miR-107-3p(1), mmu-miR-1198-5p(1), mmu-miR-129-5p(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAAGATGCTAATGGTCGAATGGTATG
siRNA sets
ATACCATTCGACCATTAGC, ATTCGACCATTAGCATCTT, TACCATTCGACCATTAGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNRF1_1513_ORF_1
1.0911
0.255340946
0.999711558
1440
ORF sequence:
ATGGAGGAGCACGGAGTGACCCAAACTGAACACATGGCTACCATAGAAGCCCATGCAGTGGCCCAGCAAGTCCAGCAGGTCCATGTAGCCACGTACACTGAGCACAGTATGCTAAGTGCTGATGAAGACTCCCCTTCCTCCCCCGAGGACACTTCTTATGATGACTCGGACATCCTCAACTCCACGGCAGCTGATGAGGTAACTGCCCATCTGGCTGCTGCAGGTCCTGTGGGAATGGCCGCTGCTGCTGCTGTGGCAACAGGGAAGAAACGGAAACGGCCTCATGTGTTTGAGTCTAATCCATCTATCCGAAAGAGACAGCAGACACGTTTGCTTCGGAAACTCAGAGCCACGTTGGATGAGTACACGACGCGAGTGGGACAGCAAGCGATTGTACTCTGCATCTCACCCTCCAAACCCAACCCTGTCTTCAAGGTGTTTGGCGCAGCACCTTTGGAGAATGTGGTGCGAAAGTACAAGAGCATGATCCTGGAAGACCTCGAGTCTGCTCTGGCAGAACACGCCCCTGCGCCACAGGAGGTTAATTCAGAGCTGCCGCCTCTCACCATCGATGGGATTCCAGTCTCTGTGGACAAAATGACCCAGGCTCAGCTTCGGGCATTTATCCCAGAGATGCTCAAGTATTCCACAGGTCGGGGGAAACCAGGCTGGGGGAAAGAAAGCTGCAAGCCTATCTGGTGGCCAGAAGATATCCCATGGGCCAATGTCCGCAGTGATGTCCGCACAGAAGAGCAAAAACAAAGGGTTTCATGGACCCAGGCATTACGGACCATAGTTAAAAATTGCTATAAGCAACATGGGCGGGAGGATCTTTTATATGCTTTTGAAGATCAGCAAACACAAACTCAGGCCACCACCACACACAGTATAGCTCATCTCGTACCATCACAGACCGTAGTACAGACCTTCAGCAACCCTGATGGCACCGTGTCGCTCATCCAGGTTGGTACAGGGGCAACAGTAGCCACATTGGCTGATGCTTCAGAACTGCCAACCACAGTCACTGTTGCCCAAGTGAATTACTCTGCTGTGGCTGATGGAGAGGTGGAACAAAACTGGGCCACGTTACAGGGCGGTGAAATGACCATCCAGACGACGCAAGCATCAGAGGCCACCCAGGCGGTAGCATCACTGGCAGAAGCCGCAGTGGCAGCTTCTCAGGAGATGCAGCAGGGAGCCACTGTCACCATGGCCCTCAACAGTGAAGCTGCCGCCCATGCTGTCGCCACTCTGGCGGAAGCCACCTTACAAGGTGGGGGACAGATAGTCCTGTCTGGGGAAACCGCAGCAGCCGTCGGAGCACTTACTGGAGTCCAAGATGCTAATGGTCGAATGGTATGTGGTTCATGTAGACCACATTTTGTTTCCCTCTCACCCATTGATGGACACTTGGGTAGCTTCCATTTTTGGCTGTTGTGA
Peptide sequence:
MEEHGVTQTEHMATIEAHAVAQQVQQVHVATYTEHSMLSADEDSPSSPEDTSYDDSDILNSTAADEVTAHLAAAGPVGMAAAAAVATGKKRKRPHVFESNPSIRKRQQTRLLRKLRATLDEYTTRVGQQAIVLCISPSKPNPVFKVFGAAPLENVVRKYKSMILEDLESALAEHAPAPQEVNSELPPLTIDGIPVSVDKMTQAQLRAFIPEMLKYSTGRGKPGWGKESCKPIWWPEDIPWANVRSDVRTEEQKQRVSWTQALRTIVKNCYKQHGREDLLYAFEDQQTQTQATTTHSIAHLVPSQTVVQTFSNPDGTVSLIQVGTGATVATLADASELPTTVTVAQVNYSAVADGEVEQNWATLQGGEMTIQTTQASEATQAVASLAEAAVAASQEMQQGATVTMALNSEAAAHAVATLAEATLQGGGQIVLSGETAAAVGALTGVQDANGRMVCGSCRPHFVSLSPIDGHLGSFHFWLL
IRESfinder result
IRESfinder score
0.356585241
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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