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mmu_circAlg9_1307

Basic information of circular RNA
PanCircBase ID:

mmu_circAlg9_1307

mm39_Chr. Position ID:

chr9|50694557|50734015|+

Gene name:

Alg9

Transcript:

ENSMUST00000034561.11

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

11

Exon/intron indexes:

4,5,6,7,8,9,10,11,12,13,14

Exon/intron offsets:

0,4895,6239,8805,9044,16861,18680,22044,22964,25419,39327

Genomic length:

39458

Exon/intron sizes in nt:

71,89,136,88,106,123,155,130,148,130,131

Flanking exon/introns:

chr9:50690404-50694557|chr9:50734015-50754033

Splice length:

1307

Other database IDs:

circBase: mmu_circ_0015654, CIRCpedia: MMU_CIRCpedia_21940, circAtlas: mmu-Alg9_0007

CIRCpedia: HSA_CIRCpedia_75235

Human Ortholog IDs:
Mature spliced Sequence:

ATTCTTGTATTCTACTTTTTGAGATGTCTCCTGGCTTTTGTGAGCTGTGTTTGTGAACTTTACTTTTATAAGGCTGTGTGCAAGAAGTTTGGGCTGCATGTGAGTCGAATGATGCTGGCCTTCCTGGTGCTCAGCACGGGCATGTTCTGCTCATCATCTGCATTCCTCCCCAGCAGCTTCTGCATGTACACCACGCTGATCGCCATGACGGGATGGTATATGGACAAGACACCCATTGCTGTGCTGGGAGTAGCAGCTGGTGCCATCTTAGGGTGGCCGTTTAGTGCAGCTCTTGGTTTACCCATCGCCTTCGACTTGCTGGCCAGGAAGCACAGGTGGAAGAGTTTTCTCCTCTGGTCCCTGGTGGCCCTGGCTCTCTTCTTGGTGCCCGTGGTGGTCATTGACAGCTACTATTACGGGAAGTTGGTGGTTGCCCCTCTCAACATTGTTTTGTATAACGTCTTTACGTCTCATGGACCTGATCTTTATGGTACAGAACCATGGTATTTCTATTTAATCAATGGATTTCTGAACTTCAATGTTGCCTTTGCTTTGGCTCTTCTGGTTTTGCCACTGACTTTCCTTATGGAGTACCTGCTGCAGAGGTTCCATGTTCAGAATTTAGGACACCCGTATTGGCTGACCTTGGCGCCAATGTATATTTGGTTTATAATTTTCTTCATCCAGCCTCATAAAGAAGAGCGCTTTCTCTTCCCAGTCTATCCGCTCATATGCCTCTGTGGTGCTGTTGCTCTTTCTGCACTTCAGAAATGCTACCACTTTGTGTTTCAACGATACCGCCTGGAGCATTACACGGTGACGTCCAACTGGCTGGCGCTGGGCACAGTTTTCCTGTTTGGGCTCTTGTCGTTCTCCCGCTCTGTGGCTCTGTTCAGAGGATACCACGGGCCCCTTGATTTATATCCAGAATTTTACAGAATTGCCACAGACCCAACCATCCACACTGTCCCAGAAGGCAGGCCCGTGAACGTCTGTGTGGGAAAAGAGTGGTATCGATTTCCCAGTAGCTTCCTTCTGCCTGACAATTGGCAGCTTCAGTTCATTCCATCAGAGTTCAGAGGTCAGCTACCAAAGCCTTTCGCAGAGGGACCACTGGCCACCAGGACTGTTCCCACTCACATGAACGACCAGAACCGAGAGGAGCCTTCCAGATACATTGACATCAGCAAATGCCATTACTTAGTGGATTTGGATACCATGAGAGAAACACCTCGGGAGCCAAACTACTCATCCCACAGAGAAGAGTGGGTCAGCCTGGCTCACAGACCATTCCTGGATGCGTCTAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AGAGAAGAGTGGGTCAGCCT

59.88

ATGCAGCCCAAACTTCTTGC

59.68

149

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CCTCGGGAGCCAAACTACTC

59.82

ATGCAGCCCAAACTTCTTGC

59.68

176

PCR template sequence:

ATTTGGATACCATGAGAGAAACACCTCGGGAGCCAAACTACTCATCCCACAGAGAAGAGTGGGTCAGCCTGGCTCACAGACCATTCCTGGATGCGTCTAGATTCTTGTATTCTACTTTTTGAGATGTCTCCTGGCTTTTGTGAGCTGTGTTTGTGAACTTTACTTTTATAAGGCTGTGTGCAAGAAGTTTGGGCTGCATG

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

10

Interacting miRNAs (#binding sites)

mmu-miR-335-5p(1), mmu-miR-132-3p(1), mmu-miR-138-5p(1), mmu-miR-185-5p(1), mmu-miR-22-3p(1), mmu-miR-370-3p(1), mmu-miR-183-5p(1), mmu-miR-188-3p(1), mmu-miR-350-3p(1), mmu-miR-338-3p(1)

siRNAs for circular RNA silencing
Junction sequence

TGGATGCGTCTAGATTCTTGTATTCT

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCALG9_1307_ORF_1

0.8588

0.143121611

0.996628939

1221

ORF sequence:

ATGATGCTGGCCTTCCTGGTGCTCAGCACGGGCATGTTCTGCTCATCATCTGCATTCCTCCCCAGCAGCTTCTGCATGTACACCACGCTGATCGCCATGACGGGATGGTATATGGACAAGACACCCATTGCTGTGCTGGGAGTAGCAGCTGGTGCCATCTTAGGGTGGCCGTTTAGTGCAGCTCTTGGTTTACCCATCGCCTTCGACTTGCTGGCCAGGAAGCACAGGTGGAAGAGTTTTCTCCTCTGGTCCCTGGTGGCCCTGGCTCTCTTCTTGGTGCCCGTGGTGGTCATTGACAGCTACTATTACGGGAAGTTGGTGGTTGCCCCTCTCAACATTGTTTTGTATAACGTCTTTACGTCTCATGGACCTGATCTTTATGGTACAGAACCATGGTATTTCTATTTAATCAATGGATTTCTGAACTTCAATGTTGCCTTTGCTTTGGCTCTTCTGGTTTTGCCACTGACTTTCCTTATGGAGTACCTGCTGCAGAGGTTCCATGTTCAGAATTTAGGACACCCGTATTGGCTGACCTTGGCGCCAATGTATATTTGGTTTATAATTTTCTTCATCCAGCCTCATAAAGAAGAGCGCTTTCTCTTCCCAGTCTATCCGCTCATATGCCTCTGTGGTGCTGTTGCTCTTTCTGCACTTCAGAAATGCTACCACTTTGTGTTTCAACGATACCGCCTGGAGCATTACACGGTGACGTCCAACTGGCTGGCGCTGGGCACAGTTTTCCTGTTTGGGCTCTTGTCGTTCTCCCGCTCTGTGGCTCTGTTCAGAGGATACCACGGGCCCCTTGATTTATATCCAGAATTTTACAGAATTGCCACAGACCCAACCATCCACACTGTCCCAGAAGGCAGGCCCGTGAACGTCTGTGTGGGAAAAGAGTGGTATCGATTTCCCAGTAGCTTCCTTCTGCCTGACAATTGGCAGCTTCAGTTCATTCCATCAGAGTTCAGAGGTCAGCTACCAAAGCCTTTCGCAGAGGGACCACTGGCCACCAGGACTGTTCCCACTCACATGAACGACCAGAACCGAGAGGAGCCTTCCAGATACATTGACATCAGCAAATGCCATTACTTAGTGGATTTGGATACCATGAGAGAAACACCTCGGGAGCCAAACTACTCATCCCACAGAGAAGAGTGGGTCAGCCTGGCTCACAGACCATTCCTGGATGCGTCTAGATTCTTGTATTCTACTTTTTGA

Peptide sequence:

MMLAFLVLSTGMFCSSSAFLPSSFCMYTTLIAMTGWYMDKTPIAVLGVAAGAILGWPFSAALGLPIAFDLLARKHRWKSFLLWSLVALALFLVPVVVIDSYYYGKLVVAPLNIVLYNVFTSHGPDLYGTEPWYFYLINGFLNFNVAFALALLVLPLTFLMEYLLQRFHVQNLGHPYWLTLAPMYIWFIIFFIQPHKEERFLFPVYPLICLCGAVALSALQKCYHFVFQRYRLEHYTVTSNWLALGTVFLFGLLSFSRSVALFRGYHGPLDLYPEFYRIATDPTIHTVPEGRPVNVCVGKEWYRFPSSFLLPDNWQLQFIPSEFRGQLPKPFAEGPLATRTVPTHMNDQNREEPSRYIDISKCHYLVDLDTMRETPREPNYSSHREEWVSLAHRPFLDASRFLYSTF

IRESfinder result

IRESfinder score

0.740212241

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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