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mmu_circAkap9_3671
Basic information of circular RNA
PanCircBase ID:
mmu_circAkap9_3671
mm39_Chr. Position ID:
chr5|4004791|4026326|+
Gene name:
Akap9
Transcript:
ENSMUST00000044492.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
4,5,6,7,8,9,10,11,12,13
Exon/intron offsets:
0,1365,2832,5320,13788,15872,17110,17964,20807,21336
Genomic length:
21535
Exon/intron sizes in nt:
17,11,56,17,72,34,62,10,00,00,00,00,00,000
Flanking exon/introns:
chr5:4001734-4004791|chr5:4026326-4031117
Splice length:
3671
Other database IDs:
circBase: mmu_circ_0012635, CIRCpedia: MMU_CIRCpedia_217050, circAtlas: mmu-Akap9_0012
circBase: hsa_circ_0135001, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_132765
Human Ortholog IDs:
Mature spliced Sequence:
GAAGAAGAATTTTCACTTGATGACTCCTCCTCTGAGCAAGGAGCTCAGTCCAGTCAGACCTGTCTTCAGATGGTAGAAAAGGAGTTGGCCGAGAAGCAGCATGATATTGAAGAGTTGACTCAGGAGTTGGAAGAGATGAGGGCCAGCTTTGGGACCGAAGGGCTGAAGCAGTTACAAGAATTTGAAGCCGCCATTAAACAGCGAGACGGCATCATAACTCAGCTCACAGCTAACTTGCAGCAAGCAAGGAGAGAGAAGGATGACACGATGGTAGAATTCTTAGAGCTGACAGAACAAAGTCAAAAACTGCAGATTCAGTTCCAGCACTTACAGGCTAATGAAACTTTGCAAAACAGCACTCTCAGCCGAACTGCGACAGATTTACTGCAGGCCAAACGACAGATCTTCACTCAACAGCAACAGCTGCAAGATTATCAGAAAAAGGAGGAGGACCTCCAAGCGCAGATTTCTTTTTTACAAGAGAAATTAAGAGCGTTTGAAATGGAAAAAGACAGAAAAATAGAAAACTTAAATGCAAAAGAAATACAGGAGAAGCAGGCACTCATTGATGAGTTGAATACAAGAGTAGTAGAAGAAGAGAAGAAAACTGTTGAGTTAAAGAATAAAGTAACAACTGCTGATGAGTTACTAGGAGGGTTACACGAACAGCTTACACAGAGGAATCAGGAGATCCAAAGCCTGAAACTAGAACTGGGCAACTCTCAGCAGAACGAGCGGAAGTGTTCAGAGGAAATCAAAGAGCTAATGAGGACAGTTGAAGAACTCCAGAAGAGAAACCTTAAAGATAGCTGGCTGGAAACTAGCGCCGTGCGAAGGGTGGAACAGGAAACCCAACGGAAATTAAGCCATCTCCAAGCAGAGCTGGATGAGATGTATGGGAAGCAAATAGTGCAAATGAAACAAGAGTTAATAAATCAGCACATGTCTCAGATAGAGGAGCTCAAATCCCAACATAAGAGAGAAATGGAGAACACCTTAAAGTCGGATACAAATGCTGCCATCAGTAAAGAACAAGTAAATTTAATGAATGCCGCCATAAATGAACTCAATGTAAGATTACAGGAGACTCATGCTCAAAAGGAGGAACTCAAGGGAGAGCTTGGCGTAGTTCTGGGAGAAAAGTCAGCTTTGCAAAGTCAGTCTAATGACCTCTTAGAAGAGGTAAGGTTTTTAAGAGAGCAAGTTCAGAAAGCTAGGCAGACAATCGCAGAGCAAGAGAACAGGCTGAGTGAGGCGCGCAAGTCCCTGAGCACAGTGGAAGACCTAAAAGCTGAGATCGTGGCTGCCTCCGAATCCAGAAAGGAACTCGAGCTCAAGCATGAAGCCGAGATTACAAATTATAAAATAAAACTTGAAATGCTAGAAAAAGAAAAAAATGCTGTGCTAGACAGAATGGCGGAATCCCAAGAAGCAGAGCTGGAGAGGCTGAGAACACAGCTCCTCTTTAGTCATGAGGAAGAATTGTCTAAACTAAAAGAAGATTTAGAAGTAGAACATCGAATAAATATTGAAAAACTTAAAGATAATTTAGGCATTCACTACAAGCAACAGATAGACGGCTTACAGAATGAAATGAATAGGAAGATGGAAAGTATGCAGTGTGAAACAGACAACCTGATAACCCAGCAGAATCAGTTAATTCTGGAAAATTCAAAGCTAAGAGATTTACAGGAATGCCTTGTTAACTCAAAATCAGAAGAAATGAATCTTCAAATCAATGAACTGCAAAAAGAGATTGAAATCCTCAAACAAGAAGAAAAGGAGAAAGGTACCCTTGAGCAGGAAGTCCAGGAGTTGCAACTTAAAACTGAACAATTGGAGAAACAGCTGAAGGAGAAGGAAGATGACCTTCAAGAAAAATGTGCACAGCTGGACGCAGAGAACAACATTCTCAAAGAGGAGAAGAGAGTCCTTGAAGACAAGTTGAAAATGTACAGTCCTTCGGAACAAGAGGAGAGATCCATTGCCGTAGATCCCAGCACAAGCAAGTCGGCAGACTCGAGGTGGCAAAAAGAAGTAGCGATGCTGAGGAAGGAGACCGAGGACCTTCAACAACAATGCCTTTATCTAAATGAAGAGATCGAGAAGCAAAGGAATACGTTTGCGTTTGCTGAAAAGAACTTTGAAGTTAACTATCAAGAGTTACAGAGGGAGTATACTTGTCTGCTCAAGATAAGAGATGATTTAGAGGCCACACAGACCAAGCAGGCATTGGAATATGAGAGCAAGCTGAGAGCGCTGGAGGAAGAGCTCCTTTCGAAAAGAGGAAATCCAGCCGCGCCAAAGGGGAAGAGTTCTGGAATTTTCCCATCTGAGACGCTGGAAATTGGGGAAGTTGTAGAAAAAGATACAACAGAGCTTATGGAGAAGCTAGAAGTAACCAAGCGAGAAAAGTTGGAGCTCTCAGAGAAAGTCTCTGGCCTTTCTGAACAACTAAAGCAGACCCATTGTACCATCAATTCTCTAAGTGCAGAGGTCAGAGCCTTAAAGCAAGAGAAGGAACAGCTTTTATTGAGATGTGGAGAACTTGAACTCCTCGCTAACCCTAGTGGAACAGAAAATGCAGCTGTCTGCCCTGTGCAGATGAGTTCTTACCAAGCTGGGCTTGTGATGGGCAAGGTCGGGGATTCTGGGGGATCTATTTCTAAAATTAGTAAAGATTTGGCTGAAGAATCAAAACCAATGATAGAAGATAAAATTCCCTTTAAAGAAAGTGGGAGAGAACAGTTGCTCTTGCCAACAAGAGCACAAAAACCGTCTCATGCGACAGTTGAACCATGTGAAAGTGAAAAACTCCAGCAAGAGCTTCATGCCCTCAAAGCCGAGCAGGATGATCTAAGGCTGCAGATGGAGGCCCAGCGCATATGCCTTTTTGTGGTTTACTCAACTCATGCGGATCAGGTTCGTGCACACATGGAAAAGGAGAGGGAGGAAGCTCTTTGCAGCCTTAAAGATGAGCTCATTTCCGCTCAACAGAAAAAGATCGACGAACTTCATAAAATGCACCAGTGCCAGCTCCAGAATTTTAAAATACAGGAGACAGGTGATGAGCCTTTACAGGTGCTCATTGAACGACTTCAACAGGCAGTGTCTGAGAAATGCTTTCACATTTCAAAGACCCTAAACAATGTTTTCGATGAATGCTATACTCCTTTAAAATGTGAAATGAATATAGAAGAGAAAGAGAATTCTGGTGTTTACACTTCTCAAAATCAAAGCCCAGAATTACAAGAGTATAGATACGAAGTTCAAGACTTTCAAGAGAGCATGCAAGTCCTTCTTGGTAAAGTGACGGAAGAATGCCGCAAACTCTCAGGACTGCAGACGCGCTTAGGCAAGATCCATGAACAACAGACAGATGGTGTGGCACTAGAGTTTGCTGAACAAAATGCGGCAGAAGAGGAAGCAGGTCTTCTGTCAGGTTGTTCTCAGAGTGCTTTACAGAGCACAGATGTCAGTCTTGAGAGCAAGGTGTCTTCTCTGCCTGCGAGTGAGAAAAGCAGAGAATGTGAGAGGCAAGTCCAAGAGTTACAGAGCCCTGTGGCTGCCGGACAGCTGCAGCTCACGGAAACCGAAGCAAACCACAGAGCAGAAACTGAGTCTTTGCAGCAGAGACTTGAGGCTGTCAGTGAGGCTCCGGTTCAGCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGAAGCAAACCACAGAGCAG
59.76
CAGGTCTGACTGGACTGAGC
59.75
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGAAGCAAACCACAGAGCAG
59.76
GCTTCTCGGCCAACTCCTTT
60.61
175
PCR template sequence:
GACAGCTGCAGCTCACGGAAACCGAAGCAAACCACAGAGCAGAAACTGAGTCTTTGCAGCAGAGACTTGAGGCTGTCAGTGAGGCTCCGGTTCAGCCAAGGAAGAAGAATTTTCACTTGATGACTCCTCCTCTGAGCAAGGAGCTCAGTCCAGTCAGACCTGTCTTCAGATGGTAGAAAAGGAGTTGGCCGAGAAGCAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
23
Interacting miRNAs (#binding sites)
mmu-miR-207(4), mmu-miR-129-5p(2), mmu-miR-9-5p(1), mmu-miR-23b-3p(1), mmu-miR-141-3p(1), mmu-miR-103-3p(1), mmu-miR-135a-5p(1), mmu-miR-335-5p(1), mmu-miR-30c-5p(1), mmu-miR-328-3p(1), mmu-miR-203-3p(1), mmu-miR-23a-3p(1), mmu-miR-149-5p(1), mmu-miR-136-5p(1), mmu-miR-96-5p(1), mmu-miR-182-5p(1), mmu-miR-107-3p(1), mmu-miR-1187(1), mmu-miR-5101(1), mmu-miR-452-3p(1), mmu-miR-3470b(1), mmu-miR-1904(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGGTTCAGCCAAGGAAGAAGAATTTT
siRNA sets
AAAATTCTTCTTCCTTGGC, TTCTTCCTTGGCTGAACCG, AATTCTTCTTCCTTGGCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAKAP9_3671_ORF_1
1.1709
0.197574651
1
3678
ORF sequence:
ATGGTAGAAAAGGAGTTGGCCGAGAAGCAGCATGATATTGAAGAGTTGACTCAGGAGTTGGAAGAGATGAGGGCCAGCTTTGGGACCGAAGGGCTGAAGCAGTTACAAGAATTTGAAGCCGCCATTAAACAGCGAGACGGCATCATAACTCAGCTCACAGCTAACTTGCAGCAAGCAAGGAGAGAGAAGGATGACACGATGGTAGAATTCTTAGAGCTGACAGAACAAAGTCAAAAACTGCAGATTCAGTTCCAGCACTTACAGGCTAATGAAACTTTGCAAAACAGCACTCTCAGCCGAACTGCGACAGATTTACTGCAGGCCAAACGACAGATCTTCACTCAACAGCAACAGCTGCAAGATTATCAGAAAAAGGAGGAGGACCTCCAAGCGCAGATTTCTTTTTTACAAGAGAAATTAAGAGCGTTTGAAATGGAAAAAGACAGAAAAATAGAAAACTTAAATGCAAAAGAAATACAGGAGAAGCAGGCACTCATTGATGAGTTGAATACAAGAGTAGTAGAAGAAGAGAAGAAAACTGTTGAGTTAAAGAATAAAGTAACAACTGCTGATGAGTTACTAGGAGGGTTACACGAACAGCTTACACAGAGGAATCAGGAGATCCAAAGCCTGAAACTAGAACTGGGCAACTCTCAGCAGAACGAGCGGAAGTGTTCAGAGGAAATCAAAGAGCTAATGAGGACAGTTGAAGAACTCCAGAAGAGAAACCTTAAAGATAGCTGGCTGGAAACTAGCGCCGTGCGAAGGGTGGAACAGGAAACCCAACGGAAATTAAGCCATCTCCAAGCAGAGCTGGATGAGATGTATGGGAAGCAAATAGTGCAAATGAAACAAGAGTTAATAAATCAGCACATGTCTCAGATAGAGGAGCTCAAATCCCAACATAAGAGAGAAATGGAGAACACCTTAAAGTCGGATACAAATGCTGCCATCAGTAAAGAACAAGTAAATTTAATGAATGCCGCCATAAATGAACTCAATGTAAGATTACAGGAGACTCATGCTCAAAAGGAGGAACTCAAGGGAGAGCTTGGCGTAGTTCTGGGAGAAAAGTCAGCTTTGCAAAGTCAGTCTAATGACCTCTTAGAAGAGGTAAGGTTTTTAAGAGAGCAAGTTCAGAAAGCTAGGCAGACAATCGCAGAGCAAGAGAACAGGCTGAGTGAGGCGCGCAAGTCCCTGAGCACAGTGGAAGACCTAAAAGCTGAGATCGTGGCTGCCTCCGAATCCAGAAAGGAACTCGAGCTCAAGCATGAAGCCGAGATTACAAATTATAAAATAAAACTTGAAATGCTAGAAAAAGAAAAAAATGCTGTGCTAGACAGAATGGCGGAATCCCAAGAAGCAGAGCTGGAGAGGCTGAGAACACAGCTCCTCTTTAGTCATGAGGAAGAATTGTCTAAACTAAAAGAAGATTTAGAAGTAGAACATCGAATAAATATTGAAAAACTTAAAGATAATTTAGGCATTCACTACAAGCAACAGATAGACGGCTTACAGAATGAAATGAATAGGAAGATGGAAAGTATGCAGTGTGAAACAGACAACCTGATAACCCAGCAGAATCAGTTAATTCTGGAAAATTCAAAGCTAAGAGATTTACAGGAATGCCTTGTTAACTCAAAATCAGAAGAAATGAATCTTCAAATCAATGAACTGCAAAAAGAGATTGAAATCCTCAAACAAGAAGAAAAGGAGAAAGGTACCCTTGAGCAGGAAGTCCAGGAGTTGCAACTTAAAACTGAACAATTGGAGAAACAGCTGAAGGAGAAGGAAGATGACCTTCAAGAAAAATGTGCACAGCTGGACGCAGAGAACAACATTCTCAAAGAGGAGAAGAGAGTCCTTGAAGACAAGTTGAAAATGTACAGTCCTTCGGAACAAGAGGAGAGATCCATTGCCGTAGATCCCAGCACAAGCAAGTCGGCAGACTCGAGGTGGCAAAAAGAAGTAGCGATGCTGAGGAAGGAGACCGAGGACCTTCAACAACAATGCCTTTATCTAAATGAAGAGATCGAGAAGCAAAGGAATACGTTTGCGTTTGCTGAAAAGAACTTTGAAGTTAACTATCAAGAGTTACAGAGGGAGTATACTTGTCTGCTCAAGATAAGAGATGATTTAGAGGCCACACAGACCAAGCAGGCATTGGAATATGAGAGCAAGCTGAGAGCGCTGGAGGAAGAGCTCCTTTCGAAAAGAGGAAATCCAGCCGCGCCAAAGGGGAAGAGTTCTGGAATTTTCCCATCTGAGACGCTGGAAATTGGGGAAGTTGTAGAAAAAGATACAACAGAGCTTATGGAGAAGCTAGAAGTAACCAAGCGAGAAAAGTTGGAGCTCTCAGAGAAAGTCTCTGGCCTTTCTGAACAACTAAAGCAGACCCATTGTACCATCAATTCTCTAAGTGCAGAGGTCAGAGCCTTAAAGCAAGAGAAGGAACAGCTTTTATTGAGATGTGGAGAACTTGAACTCCTCGCTAACCCTAGTGGAACAGAAAATGCAGCTGTCTGCCCTGTGCAGATGAGTTCTTACCAAGCTGGGCTTGTGATGGGCAAGGTCGGGGATTCTGGGGGATCTATTTCTAAAATTAGTAAAGATTTGGCTGAAGAATCAAAACCAATGATAGAAGATAAAATTCCCTTTAAAGAAAGTGGGAGAGAACAGTTGCTCTTGCCAACAAGAGCACAAAAACCGTCTCATGCGACAGTTGAACCATGTGAAAGTGAAAAACTCCAGCAAGAGCTTCATGCCCTCAAAGCCGAGCAGGATGATCTAAGGCTGCAGATGGAGGCCCAGCGCATATGCCTTTTTGTGGTTTACTCAACTCATGCGGATCAGGTTCGTGCACACATGGAAAAGGAGAGGGAGGAAGCTCTTTGCAGCCTTAAAGATGAGCTCATTTCCGCTCAACAGAAAAAGATCGACGAACTTCATAAAATGCACCAGTGCCAGCTCCAGAATTTTAAAATACAGGAGACAGGTGATGAGCCTTTACAGGTGCTCATTGAACGACTTCAACAGGCAGTGTCTGAGAAATGCTTTCACATTTCAAAGACCCTAAACAATGTTTTCGATGAATGCTATACTCCTTTAAAATGTGAAATGAATATAGAAGAGAAAGAGAATTCTGGTGTTTACACTTCTCAAAATCAAAGCCCAGAATTACAAGAGTATAGATACGAAGTTCAAGACTTTCAAGAGAGCATGCAAGTCCTTCTTGGTAAAGTGACGGAAGAATGCCGCAAACTCTCAGGACTGCAGACGCGCTTAGGCAAGATCCATGAACAACAGACAGATGGTGTGGCACTAGAGTTTGCTGAACAAAATGCGGCAGAAGAGGAAGCAGGTCTTCTGTCAGGTTGTTCTCAGAGTGCTTTACAGAGCACAGATGTCAGTCTTGAGAGCAAGGTGTCTTCTCTGCCTGCGAGTGAGAAAAGCAGAGAATGTGAGAGGCAAGTCCAAGAGTTACAGAGCCCTGTGGCTGCCGGACAGCTGCAGCTCACGGAAACCGAAGCAAACCACAGAGCAGAAACTGAGTCTTTGCAGCAGAGACTTGAGGCTGTCAGTGAGGCTCCGGTTCAGCCAAGGAAGAAGAATTTTCACTTGATGACTCCTCCTCTGAGCAAGGAGCTCAGTCCAGTCAGACCTGTCTTCAGATGGTAG
Peptide sequence:
MVEKELAEKQHDIEELTQELEEMRASFGTEGLKQLQEFEAAIKQRDGIITQLTANLQQARREKDDTMVEFLELTEQSQKLQIQFQHLQANETLQNSTLSRTATDLLQAKRQIFTQQQQLQDYQKKEEDLQAQISFLQEKLRAFEMEKDRKIENLNAKEIQEKQALIDELNTRVVEEEKKTVELKNKVTTADELLGGLHEQLTQRNQEIQSLKLELGNSQQNERKCSEEIKELMRTVEELQKRNLKDSWLETSAVRRVEQETQRKLSHLQAELDEMYGKQIVQMKQELINQHMSQIEELKSQHKREMENTLKSDTNAAISKEQVNLMNAAINELNVRLQETHAQKEELKGELGVVLGEKSALQSQSNDLLEEVRFLREQVQKARQTIAEQENRLSEARKSLSTVEDLKAEIVAASESRKELELKHEAEITNYKIKLEMLEKEKNAVLDRMAESQEAELERLRTQLLFSHEEELSKLKEDLEVEHRINIEKLKDNLGIHYKQQIDGLQNEMNRKMESMQCETDNLITQQNQLILENSKLRDLQECLVNSKSEEMNLQINELQKEIEILKQEEKEKGTLEQEVQELQLKTEQLEKQLKEKEDDLQEKCAQLDAENNILKEEKRVLEDKLKMYSPSEQEERSIAVDPSTSKSADSRWQKEVAMLRKETEDLQQQCLYLNEEIEKQRNTFAFAEKNFEVNYQELQREYTCLLKIRDDLEATQTKQALEYESKLRALEEELLSKRGNPAAPKGKSSGIFPSETLEIGEVVEKDTTELMEKLEVTKREKLELSEKVSGLSEQLKQTHCTINSLSAEVRALKQEKEQLLLRCGELELLANPSGTENAAVCPVQMSSYQAGLVMGKVGDSGGSISKISKDLAEESKPMIEDKIPFKESGREQLLLPTRAQKPSHATVEPCESEKLQQELHALKAEQDDLRLQMEAQRICLFVVYSTHADQVRAHMEKEREEALCSLKDELISAQQKKIDELHKMHQCQLQNFKIQETGDEPLQVLIERLQQAVSEKCFHISKTLNNVFDECYTPLKCEMNIEEKENSGVYTSQNQSPELQEYRYEVQDFQESMQVLLGKVTEECRKLSGLQTRLGKIHEQQTDGVALEFAEQNAAEEEAGLLSGCSQSALQSTDVSLESKVSSLPASEKSRECERQVQELQSPVAAGQLQLTETEANHRAETESLQQRLEAVSEAPVQPRKKNFHLMTPPLSKELSPVRPVFRW
IRESfinder result
IRESfinder score
0.471099699
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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