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mmu_circCsde1_1249

Basic information of circular RNA
PanCircBase ID:

mmu_circCsde1_1249

mm39_Chr. Position ID:

chr3|102952074|102962828|+

Gene name:

Csde1

Transcript:

ENSMUST00000198174.2

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

9

Exon/intron indexes:

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

Exon/intron offsets:

0,2026,2255,4862,5539,6281,8053,9896,10590

Genomic length:

10754

Exon/intron sizes in nt:

8,31,41,16,51,08,17,61,00,00,00,00,000

Flanking exon/introns:

chr3:102951247-102952074|chr3:102962828-102963660

Splice length:

1249

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

ACCGACGTGACAAATTGGAACGAGCAACCAACATAGAGGTTCTATCAAATACATTTCAGTTCACTAATGAAGCCAGAGAGATGGGTGTGATTGCTGCCATGAGAGATGGTTTTGGTTTCATCAAGTGTGTGGATCGTGATGCTCGTATGTTCTTCCACTTCAGTGAGATTCTAGATGGGAACCAGCTCCACATTGCAGATGAAGTAGAGTTTACTGTGGTTCCTGATATGCTCTCTGCCCAAAGAAATCATGCTATTAGGATTAAAAAACTTCCCAAGGGCACGGTTTCATTCCATTCCCATTCAGATCATCGTTTTCTGGGCACCGTAGAAAAAGAAGCCACTTTTTCCAATCCTAAAACTACAAGCCCAAATAAAGGCAAAGACAAGGAGGCAGAAGATGGCATTATAGCTTATGACGACTGTGGGGTGAAACTGACGATTGCTTTTCAAGCCAAGGATGTGGAAGGATCTACTTCTCCTCAAATAGGAGATAAGGTTGAATTTAGTATTAGTGACAAACAGAGGCCTGGACAGCAGATTGCAACTTGCGTGAGACTTTTAGGTCGTAATTCTAACTCCAAACGTCTCTTGGGTTATGTGGCAACTCTGAAAGATAATTTTGGATTTATAGAAACAGCTAATCATGATAAGGAAATATTTTTCCACTATAGTGAGTTCTCTGGTGATGTTGATAGCCTGGAACTGGGAGACATGGTTGAATACAGCTTGTCCAAAGGCAAAGGCAATAAAGTCAGTGCTGAGAAAGTAAACAAAGCCCACTCAGTGAATGGCATTACTGAGGAAGCTAATCCCACCATCTACTCTGGTAAAGTCATTCGCCCTCTGAGAGGTGTTGATCCAACACAGATTGAGTACCAAGGAATGATTGAGATTGTGGAGGAGGGGGATATGAAAGGTGAAGTGTATCCTTTTGGCATAGTTGGGATGGCCAACAAAGGGGATTGCCTACAGAAAGGGGAGAGTGTCAAGTTCCAGTTGTGTGTACTTGGCCAAAATGCACAAACTATGGCCTACAACATCACACCCCTTCGTAGGGCTACTGTGGAGTGTGTGAAAGATCAGTTTGGCTTTATTAACTATGAAGTAGGAGATAGCAAGAAGCTCTTTTTCCATGTGAAAGAAGTTCAGGATGGCGTTGAGCTACAGGCAGGAGATGAGGTGGAATTCTCAGTGATCCTTAATCAGCGCACTGGGAAGTGCAGTGCCTGTAATGTCTGGCGAGTCTG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CCTTAATCAGCGCACTGGGA

60.11

TCACACCCATCTCTCTGGCT

60.25

141

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TCCTTAATCAGCGCACTGGG

60.11

TCACACCCATCTCTCTGGCT

60.25

142

PCR template sequence:

AGGATGGCGTTGAGCTACAGGCAGGAGATGAGGTGGAATTCTCAGTGATCCTTAATCAGCGCACTGGGAAGTGCAGTGCCTGTAATGTCTGGCGAGTCTGACCGACGTGACAAATTGGAACGAGCAACCAACATAGAGGTTCTATCAAATACATTTCAGTTCACTAATGAAGCCAGAGAGATGGGTGTGATTGCTGCCAT

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

9

Interacting miRNAs (#binding sites)

mmu-miR-135a-5p(1), mmu-miR-216a-5p(1), mmu-miR-203-3p(1), mmu-miR-433-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-382-3p(1), mmu-miR-96-5p(1), mmu-miR-3087-3p(1), mmu-miR-697(1)

siRNAs for circular RNA silencing
Junction sequence

TCTGGCGAGTCTGACCGACGTGACAA

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCCSDE1_1249_ORF_1

1.0835

0.18936009

0.998644022

1263

ORF sequence:

ATGTCTGGCGAGTCTGACCGACGTGACAAATTGGAACGAGCAACCAACATAGAGGTTCTATCAAATACATTTCAGTTCACTAATGAAGCCAGAGAGATGGGTGTGATTGCTGCCATGAGAGATGGTTTTGGTTTCATCAAGTGTGTGGATCGTGATGCTCGTATGTTCTTCCACTTCAGTGAGATTCTAGATGGGAACCAGCTCCACATTGCAGATGAAGTAGAGTTTACTGTGGTTCCTGATATGCTCTCTGCCCAAAGAAATCATGCTATTAGGATTAAAAAACTTCCCAAGGGCACGGTTTCATTCCATTCCCATTCAGATCATCGTTTTCTGGGCACCGTAGAAAAAGAAGCCACTTTTTCCAATCCTAAAACTACAAGCCCAAATAAAGGCAAAGACAAGGAGGCAGAAGATGGCATTATAGCTTATGACGACTGTGGGGTGAAACTGACGATTGCTTTTCAAGCCAAGGATGTGGAAGGATCTACTTCTCCTCAAATAGGAGATAAGGTTGAATTTAGTATTAGTGACAAACAGAGGCCTGGACAGCAGATTGCAACTTGCGTGAGACTTTTAGGTCGTAATTCTAACTCCAAACGTCTCTTGGGTTATGTGGCAACTCTGAAAGATAATTTTGGATTTATAGAAACAGCTAATCATGATAAGGAAATATTTTTCCACTATAGTGAGTTCTCTGGTGATGTTGATAGCCTGGAACTGGGAGACATGGTTGAATACAGCTTGTCCAAAGGCAAAGGCAATAAAGTCAGTGCTGAGAAAGTAAACAAAGCCCACTCAGTGAATGGCATTACTGAGGAAGCTAATCCCACCATCTACTCTGGTAAAGTCATTCGCCCTCTGAGAGGTGTTGATCCAACACAGATTGAGTACCAAGGAATGATTGAGATTGTGGAGGAGGGGGATATGAAAGGTGAAGTGTATCCTTTTGGCATAGTTGGGATGGCCAACAAAGGGGATTGCCTACAGAAAGGGGAGAGTGTCAAGTTCCAGTTGTGTGTACTTGGCCAAAATGCACAAACTATGGCCTACAACATCACACCCCTTCGTAGGGCTACTGTGGAGTGTGTGAAAGATCAGTTTGGCTTTATTAACTATGAAGTAGGAGATAGCAAGAAGCTCTTTTTCCATGTGAAAGAAGTTCAGGATGGCGTTGAGCTACAGGCAGGAGATGAGGTGGAATTCTCAGTGATCCTTAATCAGCGCACTGGGAAGTGCAGTGCCTGTAATGTCTGGCGAGTC

Peptide sequence:

MSGESDRRDKLERATNIEVLSNTFQFTNEAREMGVIAAMRDGFGFIKCVDRDARMFFHFSEILDGNQLHIADEVEFTVVPDMLSAQRNHAIRIKKLPKGTVSFHSHSDHRFLGTVEKEATFSNPKTTSPNKGKDKEAEDGIIAYDDCGVKLTIAFQAKDVEGSTSPQIGDKVEFSISDKQRPGQQIATCVRLLGRNSNSKRLLGYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGNKVSAEKVNKAHSVNGITEEANPTIYSGKVIRPLRGVDPTQIEYQGMIEIVEEGDMKGEVYPFGIVGMANKGDCLQKGESVKFQLCVLGQNAQTMAYNITPLRRATVECVKDQFGFINYEVGDSKKLFFHVKEVQDGVELQAGDEVEFSVILNQRTGKCSACNVWRV

IRESfinder result

IRESfinder score

0.57288132

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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