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mmu_circUbap2_767

Basic information of circular RNA
PanCircBase ID:

mmu_circUbap2_767

mm39_Chr. Position ID:

chr4|41216565|41235594|-

Gene name:

Ubap2

Transcript:

ENSMUST00000108068.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

9

Exon/intron indexes:

11,10,9,8,7,6,5,4,3

Exon/intron offsets:

0,1745,4990,6790,9714,10633,13129,17038,18951

Genomic length:

19029

Exon/intron sizes in nt:

68,53,66,104,55,78,154,111,78

Flanking exon/introns:

chr4:41211894-41216565|chr4:41235594-41251534

Splice length:

767

Other database IDs:

circBase: mmu_circ_0011600, CIRCpedia: MMU_CIRCpedia_37382, circAtlas: mmu-Ubap2_0022

circAtlas: hsa-UBAP2_0048

Human Ortholog IDs:
Mature spliced Sequence:

GCAACAGCTGAGCAGATGCGGCTTGCTCAAGTGATCTTTGATAAGAATGATTCAGATTTTGAAGCTAAAGTTAAGCAGCTTATGGAAGTGACGGGAAAAAATCAGGATGAATGCATCGTGGCCCTACATGACTGTAATGGTGATGTGAACAAAGCTATCAATATACTGTTGGAAGGGAATTCTGACACCACTTCATGGGAGACTGTAGGAGGGAAGAAGAAGAATTTTGGAAGAGAAAGTTCAGAAAACAAAGAAAACAGAGAGAAGAGGACGGAGAGAGAAGCGAGTCGTGGACGGGGAACCAACAACCGCAAGGGAAGAGGCGGCAACCGAGTCCGAGAGTTCAAAGGTGAAGAGAATGGGATTGACTGCAGCCAAGGAGACAAGCCTGCGGAGCGGGGCAAGCGGGCCCGAGGCAGAGGATTTGGACGTGGCAGGGGCAGAGGGACAGGAAGGTTCTCCGCTCAAAGCATGGGGACATTCAATCCTGCAGACTATTCAGAGTCCATGTCTACAGATGGCTGTGGGACAAAGTTGGCAGTTTGGGAAGCTGCTCAGAATGGTACAGATGAGGGACCGGAAGGGCTGGCCAAGTCTCACAGTATGTCTCAGGAACCGCCAAGTAAAAGTTCTTATGGACTTAAAGGTGCCTGGAAGAATTCTGTGGAAGAGTGGACAACAGAAGACTGGACTGAAGATCTCTCTGAAACAAAGGTATTCACTGCTTCATCTGCTCCAGCAGAGAACCATGTCACACCTGGGCACAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ACTGCTTCATCTGCTCCAGC

60.39

CCGTCACTTCCATAAGCTGC

58.99

141

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

ACTGCTTCATCTGCTCCAGC

60.39

TCCCGTCACTTCCATAAGCTG

59.79

143

PCR template sequence:

AAGAGTGGACAACAGAAGACTGGACTGAAGATCTCTCTGAAACAAAGGTATTCACTGCTTCATCTGCTCCAGCAGAGAACCATGTCACACCTGGGCACAGGCAACAGCTGAGCAGATGCGGCTTGCTCAAGTGATCTTTGATAAGAATGATTCAGATTTTGAAGCTAAAGTTAAGCAGCTTATGGAAGTGACGGGAAAAA

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

2

Interacting miRNAs (#binding sites)

mmu-miR-532-5p(1), mmu-miR-3105-3p(1)

siRNAs for circular RNA silencing
Junction sequence

CACCTGGGCACAGGCAACAGCTGAGC

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCUBAP2_767_ORF_1

0.8431

0.202916796

0.942163364

786

ORF sequence:

ATGCGGCTTGCTCAAGTGATCTTTGATAAGAATGATTCAGATTTTGAAGCTAAAGTTAAGCAGCTTATGGAAGTGACGGGAAAAAATCAGGATGAATGCATCGTGGCCCTACATGACTGTAATGGTGATGTGAACAAAGCTATCAATATACTGTTGGAAGGGAATTCTGACACCACTTCATGGGAGACTGTAGGAGGGAAGAAGAAGAATTTTGGAAGAGAAAGTTCAGAAAACAAAGAAAACAGAGAGAAGAGGACGGAGAGAGAAGCGAGTCGTGGACGGGGAACCAACAACCGCAAGGGAAGAGGCGGCAACCGAGTCCGAGAGTTCAAAGGTGAAGAGAATGGGATTGACTGCAGCCAAGGAGACAAGCCTGCGGAGCGGGGCAAGCGGGCCCGAGGCAGAGGATTTGGACGTGGCAGGGGCAGAGGGACAGGAAGGTTCTCCGCTCAAAGCATGGGGACATTCAATCCTGCAGACTATTCAGAGTCCATGTCTACAGATGGCTGTGGGACAAAGTTGGCAGTTTGGGAAGCTGCTCAGAATGGTACAGATGAGGGACCGGAAGGGCTGGCCAAGTCTCACAGTATGTCTCAGGAACCGCCAAGTAAAAGTTCTTATGGACTTAAAGGTGCCTGGAAGAATTCTGTGGAAGAGTGGACAACAGAAGACTGGACTGAAGATCTCTCTGAAACAAAGGTATTCACTGCTTCATCTGCTCCAGCAGAGAACCATGTCACACCTGGGCACAGGCAACAGCTGAGCAGATGCGGCTTGCTCAAGTGA

Peptide sequence:

MRLAQVIFDKNDSDFEAKVKQLMEVTGKNQDECIVALHDCNGDVNKAINILLEGNSDTTSWETVGGKKKNFGRESSENKENREKRTEREASRGRGTNNRKGRGGNRVREFKGEENGIDCSQGDKPAERGKRARGRGFGRGRGRGTGRFSAQSMGTFNPADYSESMSTDGCGTKLAVWEAAQNGTDEGPEGLAKSHSMSQEPPSKSSYGLKGAWKNSVEEWTTEDWTEDLSETKVFTASSAPAENHVTPGHRQQLSRCGLLK

IRESfinder result

IRESfinder score

0.334164484

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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Institute of Life sciences, Bhubaneswar, India

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