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mmu_circPgap1_463

Basic information of circular RNA
PanCircBase ID:

mmu_circPgap1_463

mm39_Chr. Position ID:

chr1|54551755|54567754|-

Gene name:

Pgap1

Transcript:

ENSMUST00000097739.5

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

7

Exon/intron indexes:

16,15,14,13,12,11,10

Exon/intron offsets:

0,175,2240,8695,11719,12771,15915

Genomic length:

15999

Exon/intron sizes in nt:

52,74,76,78,52,47,84

Flanking exon/introns:

chr1:54551126-54551755|chr1:54567754-54569275

Splice length:

463

Other database IDs:

CIRCpedia: MMU_CIRCpedia_22859, circAtlas: mmu-Pgap1_0008

circAtlas: hsa-SCAF8_0001

Human Ortholog IDs:
Mature spliced Sequence:

GAATCTGATAAGATTTACTTTGCATTTCCTCTTGCAAATCATAGAAAAATCTACACTCATGCCTATTGTCAGAGCACCATGCTGGATACAAATAGTTGGATTTTTGGCTGCATAAACAGCACTTCCATGTGCCGGCAAGGGGTTGATTTGTCATGGAAAGCTGAGCTGTTACCAACAATTAAGTCTCTGACGCTAAGACTTCAAGACTATCCATCCTTGTCGCATATTGTTGTCTATGTGCCATCTGTCCACGGAAGTAAGTTTGTTGTCGACTGTGAATTCTTTAAGAAAGAAGCGAGATCCATGCAGCTCCCTGTGACTCACCTTTTTTCCTTTGGACTGTCTTCCAGGAAGGTGACGTTAAATACAAACGGCCTATACTACAACATAGAGCTGCTGAACTTTGGACAGATATACCAAGCTTTTAAAGTCAACGTGGTCAGCAAGTGCACTGGAAGCAAAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AGCTGCTGAACTTTGGACAGA

59.86

TGGTGCTCTGACAATAGGCA

59.02

151

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

AGAGCTGCTGAACTTTGGACA

59.86

TGGTGCTCTGACAATAGGCA

59.02

153

PCR template sequence:

AATACAAACGGCCTATACTACAACATAGAGCTGCTGAACTTTGGACAGATATACCAAGCTTTTAAAGTCAACGTGGTCAGCAAGTGCACTGGAAGCAAAGGAATCTGATAAGATTTACTTTGCATTTCCTCTTGCAAATCATAGAAAAATCTACACTCATGCCTATTGTCAGAGCACCATGCTGGATACAAATAGTTGGA

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

7

Interacting miRNAs (#binding sites)

mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-93-5p(1), mmu-miR-148a-3p(1), mmu-miR-194-5p(1), mmu-miR-3065-5p(1), mmu-miR-338-3p(1)

siRNAs for circular RNA silencing
Junction sequence

ACTGGAAGCAAAGGAATCTGATAAGA

siRNA sets

TCTTATCAGATTCCTTTGC, TATCAGATTCCTTTGCTTC, TCAGATTCCTTTGCTTCCA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCPGAP1_463_ORF_1

0.5893

0.029942825

0.229619304

393

ORF sequence:

ATGCTGGATACAAATAGTTGGATTTTTGGCTGCATAAACAGCACTTCCATGTGCCGGCAAGGGGTTGATTTGTCATGGAAAGCTGAGCTGTTACCAACAATTAAGTCTCTGACGCTAAGACTTCAAGACTATCCATCCTTGTCGCATATTGTTGTCTATGTGCCATCTGTCCACGGAAGTAAGTTTGTTGTCGACTGTGAATTCTTTAAGAAAGAAGCGAGATCCATGCAGCTCCCTGTGACTCACCTTTTTTCCTTTGGACTGTCTTCCAGGAAGGTGACGTTAAATACAAACGGCCTATACTACAACATAGAGCTGCTGAACTTTGGACAGATATACCAAGCTTTTAAAGTCAACGTGGTCAGCAAGTGCACTGGAAGCAAAGGAATCTGA

Peptide sequence:

MLDTNSWIFGCINSTSMCRQGVDLSWKAELLPTIKSLTLRLQDYPSLSHIVVYVPSVHGSKFVVDCEFFKKEARSMQLPVTHLFSFGLSSRKVTLNTNGLYYNIELLNFGQIYQAFKVNVVSKCTGSKGI

IRESfinder result

IRESfinder score

0.707253348

IRES/non IRES

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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