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mmu_circSetx_1711
Basic information of circular RNA
PanCircBase ID:
mmu_circSetx_1711
mm39_Chr. Position ID:
chr2|29043949|29063733|+
Gene name:
Setx
Transcript:
ENSMUST00000061578.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
12,13,14,15,16,17,18,19,20,21,22,23
Exon/intron offsets:
0,3050,4160,4903,7534,7812,9040,10464,12330,17225,18378,19619
Genomic length:
19784
Exon/intron sizes in nt:
1,59,23,31,68,15,71,02,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr2:29040119-29043949|chr2:29063733-29066888
Splice length:
1711
Other database IDs:
circAtlas: mmu-Setx_0034
Human Ortholog IDs:
Mature spliced Sequence:
TTTACTTGAACGAATCTGAACTTGCTAAACAGCTTCACCCAAAGGAAAATGATCTGGTGTTTCTGGCTCCTGAGAAGAGTTATATGGACAGGCATGGCATGCAAGATTGCAGTCACTATTACTGTGGCTATGTTCATAAGTTTCGTCGCACTTCAGTTATGCGCAGTGGGAAAGCTGAGTGTTCATTATGCATACAGACACAAGATACCTTGCCAGCCAGTGTAAAAAATCTTACAAGATGCATTGTGATCAGTTCTCTGGTAACTACACAGAGGAAATTGAAAGCCATGTCTCTGTTGAGTAGTCGGAACCAGTTGGCCAGAGCTGTTCTAAATCCAAACCCCATGGACTTCTGTACCAAAGATCTACTAACTACAACTTCTGAAAGAATTGTTGCCTACTTAAAAGACTTTAATGAAGACCAAAAGAAAGCCATAGAAACTGCATATGCCATGGTGAAACACTCACCATCCGTTGCCAAAATCTGTCTGATTCATGGACCACCTGGAACAGGAAAATCCAAAACTATTGTTGGTCTCTTGTACCGCTTACTGACAGAGAACCAGAGGAAGGGCCATTCAGATGAAAATTTCAATGCCAAAATCAAACAAAATCGAGTCCTCGTGTGTGCACCTTCCAATGCGGCGGTTGATGAACTTATGAAAAAAATTATCCTCGAATTTAAAGAAAAATGTAAAGACAAGAAGAATCCTTTGGGAAACTGTGGAGATATAAATTTAGTACGACTAGGTCCAGAAAAGTCTATTAATACAGAGGTCTTAAAATTCAGTTTGGACAGCCAAGTCAACCATAGAATGAAAAAAGACTTGCCTTCTCATATTCAAGAAATGCTTAGAAGAAAAGAAATTCTAGATGCTCAACTTGATGAGCTTTCTCGTCAGCGAGCTCTGTGCCGAGGTGGGCGGGAGATGCAGAGGCAAGAATTAGATGAACACATTGCCATAGTCTCAAAAGAAAGGCAAGAACTTGCTTCGAAAATTAAAGAGGTTCAGGGACGCCCACAGAGAGCACAGAATACCATCATCTTGGAGTCCCATGTCATCTGCTGCACATTGAGCACTAGTGGTGGTTTATTGCTTGAGTCTGCTTTTCGAGGGCAAGGGGGTGTCCCCTTCAGTTGTGTCATCGTAGATGAGGCTGGGCAGTCTTGTGAAGTTGAGACACTTTCTCCACTCATCCACCGCTGCAATAAACTTATCCTAGTAGGAGACCCCAAACAGCTCCCTCCCACAGTCATCTCTATGAAAGCACAGGAGTATGGCTATGACCAGTCGATGATGGCCCGATTCTGCAAGCTGCTGGAAGAGAATGTGGAGCAGAACATGATTGGCAGGCTGCCGGTGTTACAGCTTACCATTCAGTACAGGATGCATCCAGACATATGTCTTTTCCCTTCTAATTACGTTTATAACAAAAACCTGAAGACAAATAGATTGACTGAATCCATTCGATGTTCATCAGAGTGGCCATTTCAGCCCTACCTCGTGTTTGATGTTGGAGATGGTTCAGAACGACGGGATAATGACTCATATATAAATGTTCAAGAAATAAAGTTGGTGATGGAAATAATTAAACTTATTAAAGAGAAAAGAAAAGATATTTCCTTCCGAAATATTGGCATAATAACCCATTACAAGGCTCAGAAGACGATGATCCAGAAGGATTTGGAGAAAGAATTTGATAAGAAAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCCATTACAAGGCTCAGAAGA
59.09
TCTCAGGAGCCAGAAACACC
59.31
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACCCATTACAAGGCTCAGAAGA
59.67
CTCAGGAGCCAGAAACACCA
59.6
140
PCR template sequence:
GAAAAGATATTTCCTTCCGAAATATTGGCATAATAACCCATTACAAGGCTCAGAAGACGATGATCCAGAAGGATTTGGAGAAAGAATTTGATAAGAAAGGTTTACTTGAACGAATCTGAACTTGCTAAACAGCTTCACCCAAAGGAAAATGATCTGGTGTTTCTGGCTCCTGAGAAGAGTTATATGGACAGGCATGGCAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
30
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(2), mmu-miR-335-3p(2), mmu-miR-9-5p(1), mmu-let-7a-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-let-7c-5p(1), mmu-miR-146a-5p(1), mmu-miR-18a-5p(1), mmu-miR-328-3p(1), mmu-let-7d-5p(1), mmu-miR-431-5p(1), mmu-miR-125a-5p(1), mmu-miR-182-5p(1), mmu-miR-382-5p(1), mmu-miR-511-3p(1), mmu-miR-34b-5p(1), mmu-miR-705(1), mmu-miR-1198-5p(1), mmu-miR-5101(1), mmu-miR-669d-5p(1), mmu-miR-452-3p(1), mmu-miR-3470b(1), mmu-miR-670-5p(1), mmu-miR-1904(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTGATAAGAAAGGTTTACTTGAACGA
siRNA sets
CAAGTAAACCTTTCTTATC, AAGTAAACCTTTCTTATCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSETX_1711_ORF_1
0.7763
0.100326758
0.999778758
1647
ORF sequence:
ATGGACAGGCATGGCATGCAAGATTGCAGTCACTATTACTGTGGCTATGTTCATAAGTTTCGTCGCACTTCAGTTATGCGCAGTGGGAAAGCTGAGTGTTCATTATGCATACAGACACAAGATACCTTGCCAGCCAGTGTAAAAAATCTTACAAGATGCATTGTGATCAGTTCTCTGGTAACTACACAGAGGAAATTGAAAGCCATGTCTCTGTTGAGTAGTCGGAACCAGTTGGCCAGAGCTGTTCTAAATCCAAACCCCATGGACTTCTGTACCAAAGATCTACTAACTACAACTTCTGAAAGAATTGTTGCCTACTTAAAAGACTTTAATGAAGACCAAAAGAAAGCCATAGAAACTGCATATGCCATGGTGAAACACTCACCATCCGTTGCCAAAATCTGTCTGATTCATGGACCACCTGGAACAGGAAAATCCAAAACTATTGTTGGTCTCTTGTACCGCTTACTGACAGAGAACCAGAGGAAGGGCCATTCAGATGAAAATTTCAATGCCAAAATCAAACAAAATCGAGTCCTCGTGTGTGCACCTTCCAATGCGGCGGTTGATGAACTTATGAAAAAAATTATCCTCGAATTTAAAGAAAAATGTAAAGACAAGAAGAATCCTTTGGGAAACTGTGGAGATATAAATTTAGTACGACTAGGTCCAGAAAAGTCTATTAATACAGAGGTCTTAAAATTCAGTTTGGACAGCCAAGTCAACCATAGAATGAAAAAAGACTTGCCTTCTCATATTCAAGAAATGCTTAGAAGAAAAGAAATTCTAGATGCTCAACTTGATGAGCTTTCTCGTCAGCGAGCTCTGTGCCGAGGTGGGCGGGAGATGCAGAGGCAAGAATTAGATGAACACATTGCCATAGTCTCAAAAGAAAGGCAAGAACTTGCTTCGAAAATTAAAGAGGTTCAGGGACGCCCACAGAGAGCACAGAATACCATCATCTTGGAGTCCCATGTCATCTGCTGCACATTGAGCACTAGTGGTGGTTTATTGCTTGAGTCTGCTTTTCGAGGGCAAGGGGGTGTCCCCTTCAGTTGTGTCATCGTAGATGAGGCTGGGCAGTCTTGTGAAGTTGAGACACTTTCTCCACTCATCCACCGCTGCAATAAACTTATCCTAGTAGGAGACCCCAAACAGCTCCCTCCCACAGTCATCTCTATGAAAGCACAGGAGTATGGCTATGACCAGTCGATGATGGCCCGATTCTGCAAGCTGCTGGAAGAGAATGTGGAGCAGAACATGATTGGCAGGCTGCCGGTGTTACAGCTTACCATTCAGTACAGGATGCATCCAGACATATGTCTTTTCCCTTCTAATTACGTTTATAACAAAAACCTGAAGACAAATAGATTGACTGAATCCATTCGATGTTCATCAGAGTGGCCATTTCAGCCCTACCTCGTGTTTGATGTTGGAGATGGTTCAGAACGACGGGATAATGACTCATATATAAATGTTCAAGAAATAAAGTTGGTGATGGAAATAATTAAACTTATTAAAGAGAAAAGAAAAGATATTTCCTTCCGAAATATTGGCATAATAACCCATTACAAGGCTCAGAAGACGATGATCCAGAAGGATTTGGAGAAAGAATTTGATAAGAAAGGTTTACTTGAACGAATCTGA
Peptide sequence:
MDRHGMQDCSHYYCGYVHKFRRTSVMRSGKAECSLCIQTQDTLPASVKNLTRCIVISSLVTTQRKLKAMSLLSSRNQLARAVLNPNPMDFCTKDLLTTTSERIVAYLKDFNEDQKKAIETAYAMVKHSPSVAKICLIHGPPGTGKSKTIVGLLYRLLTENQRKGHSDENFNAKIKQNRVLVCAPSNAAVDELMKKIILEFKEKCKDKKNPLGNCGDINLVRLGPEKSINTEVLKFSLDSQVNHRMKKDLPSHIQEMLRRKEILDAQLDELSRQRALCRGGREMQRQELDEHIAIVSKERQELASKIKEVQGRPQRAQNTIILESHVICCTLSTSGGLLLESAFRGQGGVPFSCVIVDEAGQSCEVETLSPLIHRCNKLILVGDPKQLPPTVISMKAQEYGYDQSMMARFCKLLEENVEQNMIGRLPVLQLTIQYRMHPDICLFPSNYVYNKNLKTNRLTESIRCSSEWPFQPYLVFDVGDGSERRDNDSYINVQEIKLVMEIIKLIKEKRKDISFRNIGIITHYKAQKTMIQKDLEKEFDKKGLLERI
IRESfinder result
IRESfinder score
0.584005585
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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