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mmu_circLrrcc1_642

Basic information of circular RNA
PanCircBase ID:

mmu_circLrrcc1_642

mm39_Chr. Position ID:

chr3|14612306|14616587|+

Gene name:

Lrrcc1

Transcript:

ENSMUST00000108370.9

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

8,9,10,11

Exon/intron offsets:

0,861,3004,4141

Genomic length:

4281

Exon/intron sizes in nt:

1,48,14,92,05,140

Flanking exon/introns:

chr3:14610752-14612306|chr3:14616587-14619363

Splice length:

642

Other database IDs:

CIRCpedia: MMU_CIRCpedia_222700, circAtlas: mmu-Lrrcc1_0012

circAtlas: hsa-LRRCC1_0032, CIRCpedia: HSA_CIRCpedia_151388

Human Ortholog IDs:
Mature spliced Sequence:

TTGTAATCGTAAAATGAGACAGCCTTACCTTAGAGATTTATATGTAAGATCATCTTTAGTAAACTGTAATAACTTACGAGACTTAGATGAGCAGAAGACTGGCGTAATTAAAGTAGACAAGAACTTCTCGGACAACAGCACCTACCGGTCCCTCGTGGAACAGTTAGACCAAGAGAGAGAGATGCGGTGGAAAGCTGAGCAAACGGAAAAGAAACTTATGGATTATATCGATGAGCTACATAAGCAAGCAGATGAGAAAAAAGATGTTCACAGCCAGGCTCTCATTACCACAGATAGACTAAAGGATGCTATTTTTAAGGAGAGACATTGCAAGGCTCAACTTGAAATTATAGTTCACAGACTTCAAAATGAAGTTAAAAAACTAACTATTGAATTAATGAAAGCGCGAGATCAACAGGAAGATCACATCAGACACCTGAGAACCCTGGAAAGGGCATTGGAAAAAATGGAGAAGCAGAAAGCACAGCAGCAGGCGGCACAGATAAGACTGATCCAAGAGGTGGAGCTCAAAGCCTCAGCTGCTGATCGAGAAATAAACTTACTTCGAACTTCTCTTCACCAAGAAAAGCAGCAAGTGCAACAACTTCATGAACTTCTGGCGTTGAAAGAGCAGGAACACAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TCACCAAGAAAAGCAGCAAGTG

59.9

GTCTTCTGCTCATCTAAGTCTCGT

59.9

165

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TCACCAAGAAAAGCAGCAAGTG

59.9

TCTTCTGCTCATCTAAGTCTCGT

58.73

164

PCR template sequence:

CTGATCGAGAAATAAACTTACTTCGAACTTCTCTTCACCAAGAAAAGCAGCAAGTGCAACAACTTCATGAACTTCTGGCGTTGAAAGAGCAGGAACACAGTTGTAATCGTAAAATGAGACAGCCTTACCTTAGAGATTTATATGTAAGATCATCTTTAGTAAACTGTAATAACTTACGAGACTTAGATGAGCAGAAGACT

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

4

Interacting miRNAs (#binding sites)

mmu-miR-136-5p(1), mmu-miR-382-5p(1), mmu-miR-370-3p(1), mmu-miR-1904(1)

siRNAs for circular RNA silencing
Junction sequence

AGCAGGAACACAGTTGTAATCGTAAA

siRNA sets

TTTACGATTACAACTGTGT,TTACAACTGTGTTCCTGCT,TTACGATTACAACTGTGTT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCLRRCC1_642_ORF_1

1.1356

0.169877627

0.998759223

1269

ORF sequence:

ATGAGACAGCCTTACCTTAGAGATTTATATGTAAGATCATCTTTAGTAAACTGTAATAACTTACGAGACTTAGATGAGCAGAAGACTGGCGTAATTAAAGTAGACAAGAACTTCTCGGACAACAGCACCTACCGGTCCCTCGTGGAACAGTTAGACCAAGAGAGAGAGATGCGGTGGAAAGCTGAGCAAACGGAAAAGAAACTTATGGATTATATCGATGAGCTACATAAGCAAGCAGATGAGAAAAAAGATGTTCACAGCCAGGCTCTCATTACCACAGATAGACTAAAGGATGCTATTTTTAAGGAGAGACATTGCAAGGCTCAACTTGAAATTATAGTTCACAGACTTCAAAATGAAGTTAAAAAACTAACTATTGAATTAATGAAAGCGCGAGATCAACAGGAAGATCACATCAGACACCTGAGAACCCTGGAAAGGGCATTGGAAAAAATGGAGAAGCAGAAAGCACAGCAGCAGGCGGCACAGATAAGACTGATCCAAGAGGTGGAGCTCAAAGCCTCAGCTGCTGATCGAGAAATAAACTTACTTCGAACTTCTCTTCACCAAGAAAAGCAGCAAGTGCAACAACTTCATGAACTTCTGGCGTTGAAAGAGCAGGAACACAGTTGTAATCGTAAAATGAGACAGCCTTACCTTAGAGATTTATATGTAAGATCATCTTTAGTAAACTGTAATAACTTACGAGACTTAGATGAGCAGAAGACTGGCGTAATTAAAGTAGACAAGAACTTCTCGGACAACAGCACCTACCGGTCCCTCGTGGAACAGTTAGACCAAGAGAGAGAGATGCGGTGGAAAGCTGAGCAAACGGAAAAGAAACTTATGGATTATATCGATGAGCTACATAAGCAAGCAGATGAGAAAAAAGATGTTCACAGCCAGGCTCTCATTACCACAGATAGACTAAAGGATGCTATTTTTAAGGAGAGACATTGCAAGGCTCAACTTGAAATTATAGTTCACAGACTTCAAAATGAAGTTAAAAAACTAACTATTGAATTAATGAAAGCGCGAGATCAACAGGAAGATCACATCAGACACCTGAGAACCCTGGAAAGGGCATTGGAAAAAATGGAGAAGCAGAAAGCACAGCAGCAGGCGGCACAGATAAGACTGATCCAAGAGGTGGAGCTCAAAGCCTCAGCTGCTGATCGAGAAATAAACTTACTTCGAACTTCTCTTCACCAAGAAAAGCAGCAAGTGCAACAACTTCATGAACTTCTGGCGTTGAAAGAGCAGGAACAC

Peptide sequence:

MRQPYLRDLYVRSSLVNCNNLRDLDEQKTGVIKVDKNFSDNSTYRSLVEQLDQEREMRWKAEQTEKKLMDYIDELHKQADEKKDVHSQALITTDRLKDAIFKERHCKAQLEIIVHRLQNEVKKLTIELMKARDQQEDHIRHLRTLERALEKMEKQKAQQQAAQIRLIQEVELKASAADREINLLRTSLHQEKQQVQQLHELLALKEQEHSCNRKMRQPYLRDLYVRSSLVNCNNLRDLDEQKTGVIKVDKNFSDNSTYRSLVEQLDQEREMRWKAEQTEKKLMDYIDELHKQADEKKDVHSQALITTDRLKDAIFKERHCKAQLEIIVHRLQNEVKKLTIELMKARDQQEDHIRHLRTLERALEKMEKQKAQQQAAQIRLIQEVELKASAADREINLLRTSLHQEKQQVQQLHELLALKEQEH

IRESfinder result

IRESfinder score

0.544483666

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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