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mmu_circSycp2_1056
Basic information of circular RNA
PanCircBase ID:
mmu_circSycp2_1056
mm39_Chr. Position ID:
chr2|178022646|178037716|-
Gene name:
Sycp2
Transcript:
ENSMUST00000081134.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
18,17,16,15,14,13,12,11,10,9,8,7
Exon/intron offsets:
0,985,1479,2612,8599,10837,11489,13122,13262,14095,14367,14984
Genomic length:
15070
Exon/intron sizes in nt:
100,126,75,149,61,96,46,53,143,35,86,86
Flanking exon/introns:
chr2:178021341-178022646|chr2:178037716-178043413
Splice length:
1056
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAAAACCAAGTATTGGAAAGTTTCATACCTCAAATCTGTGCCCTGGTTATTGATTCAAGAGTGAATTTTTGCATTCAGCAGGAGGCTTTAAAAAAAATGAATTTGATGCTTGACAGAATACCTCAAGATGCCAACAAAATACTTTCTAATCAAGAAATGTTAACTCTCATGAGTAATATGGGAGAAAGGATTTTAGATGTAGGAGATTATGAATTACAGGTAGGCATTGTGGAAGCTTTGTGTAGAATGACCACAGAAAAACGGAGACAAGAACTGGCATATGAATGGTTTTCAATGGACTTTATTGCTAATGCATTTAAGGAAATTAAAGACTGTGAATTTGAAACAGATTGCAGAATATTTCTCAACTTGGTAAATGGCATTCTTGGTGATAAAAGAAGGGTCTATACATTTCCTTGCTTGTCAGCATTTCTTGGTAAATATGAGCTGCAGATACCATCAGATGAAAAACTTGAGGAATTCTGGATCGATTTTAATCTTGGGAGCCACACTCTGTCATTCTACATTGCTGGAGATGAAGAAGATCACCAATGGGAAGCTGTCACTGTACCTGAAGAAAAAGTTCAGATGTACAACATTGAAGTGAGAGAATCAAAGAAGCTACTGACTCTAACTTTGAAAAATATAGTAAAAATTAGTAAAAAAGAAGGAAAAGAGTTACTTTTTTATTTTGATGAATCATTAGAAATCACCAACGTGACTAAAAAAGTTTTTGGTGGAAATAAGTATAAGGAATTTACCAGAAAACAAGGTATTTCAGTTGCCAAAACATCTATTCATGTACTTTTTGATGCAAGTGGATCACAGATTCTAGTACCAGAAAGTCAACCATCTCCAGTCAAAGAAAACCTCATTCATCTAAAAGAGAAATCCGACATCCAAAAGAAACTTGTAAACCCTCTAGAACTAGGCAATAGCAGCAGCCAGGATGAGATCACTACACCTAGCAGAAAGAAAATGTCTGAAGCATCAATGATTGTTCCTGATACAGACAGATACACTGTGCGAAGCCCAATACTTTTAATCAACACAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCACTACACCTAGCAGAAAGA
55.75
CCAGGGCACAGATTTGAGGT
59.96
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCACTACACCTAGCAGAAAGA
55.75
ACCAGGGCACAGATTTGAGG
59.96
148
PCR template sequence:
ATCACTACACCTAGCAGAAAGAAAATGTCTGAAGCATCAATGATTGTTCCTGATACAGACAGATACACTGTGCGAAGCCCAATACTTTTAATCAACACATGTAAAAACCAAGTATTGGAAAGTTTCATACCTCAAATCTGTGCCCTGGTTATTGATTCAAGAGTGAATTTTTGCATTCAGCAGGAGGCTTTAAAAAAAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-128-3p(1), mmu-miR-182-5p(1), mmu-miR-370-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTAATCAACACATGTAAAAACCAAGT
siRNA sets
TTGGTTTTTACATGTGTTG, TTTTACATGTGTTGATTAA, TTTTTACATGTGTTGATTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSYCP2_1056_ORF_1
0.8856
-0.015601842
0.999979947
2013
ORF sequence:
ATGAATTTGATGCTTGACAGAATACCTCAAGATGCCAACAAAATACTTTCTAATCAAGAAATGTTAACTCTCATGAGTAATATGGGAGAAAGGATTTTAGATGTAGGAGATTATGAATTACAGGTAGGCATTGTGGAAGCTTTGTGTAGAATGACCACAGAAAAACGGAGACAAGAACTGGCATATGAATGGTTTTCAATGGACTTTATTGCTAATGCATTTAAGGAAATTAAAGACTGTGAATTTGAAACAGATTGCAGAATATTTCTCAACTTGGTAAATGGCATTCTTGGTGATAAAAGAAGGGTCTATACATTTCCTTGCTTGTCAGCATTTCTTGGTAAATATGAGCTGCAGATACCATCAGATGAAAAACTTGAGGAATTCTGGATCGATTTTAATCTTGGGAGCCACACTCTGTCATTCTACATTGCTGGAGATGAAGAAGATCACCAATGGGAAGCTGTCACTGTACCTGAAGAAAAAGTTCAGATGTACAACATTGAAGTGAGAGAATCAAAGAAGCTACTGACTCTAACTTTGAAAAATATAGTAAAAATTAGTAAAAAAGAAGGAAAAGAGTTACTTTTTTATTTTGATGAATCATTAGAAATCACCAACGTGACTAAAAAAGTTTTTGGTGGAAATAAGTATAAGGAATTTACCAGAAAACAAGGTATTTCAGTTGCCAAAACATCTATTCATGTACTTTTTGATGCAAGTGGATCACAGATTCTAGTACCAGAAAGTCAACCATCTCCAGTCAAAGAAAACCTCATTCATCTAAAAGAGAAATCCGACATCCAAAAGAAACTTGTAAACCCTCTAGAACTAGGCAATAGCAGCAGCCAGGATGAGATCACTACACCTAGCAGAAAGAAAATGTCTGAAGCATCAATGATTGTTCCTGATACAGACAGATACACTGTGCGAAGCCCAATACTTTTAATCAACACATGTAAAAACCAAGTATTGGAAAGTTTCATACCTCAAATCTGTGCCCTGGTTATTGATTCAAGAGTGAATTTTTGCATTCAGCAGGAGGCTTTAAAAAAAATGAATTTGATGCTTGACAGAATACCTCAAGATGCCAACAAAATACTTTCTAATCAAGAAATGTTAACTCTCATGAGTAATATGGGAGAAAGGATTTTAGATGTAGGAGATTATGAATTACAGGTAGGCATTGTGGAAGCTTTGTGTAGAATGACCACAGAAAAACGGAGACAAGAACTGGCATATGAATGGTTTTCAATGGACTTTATTGCTAATGCATTTAAGGAAATTAAAGACTGTGAATTTGAAACAGATTGCAGAATATTTCTCAACTTGGTAAATGGCATTCTTGGTGATAAAAGAAGGGTCTATACATTTCCTTGCTTGTCAGCATTTCTTGGTAAATATGAGCTGCAGATACCATCAGATGAAAAACTTGAGGAATTCTGGATCGATTTTAATCTTGGGAGCCACACTCTGTCATTCTACATTGCTGGAGATGAAGAAGATCACCAATGGGAAGCTGTCACTGTACCTGAAGAAAAAGTTCAGATGTACAACATTGAAGTGAGAGAATCAAAGAAGCTACTGACTCTAACTTTGAAAAATATAGTAAAAATTAGTAAAAAAGAAGGAAAAGAGTTACTTTTTTATTTTGATGAATCATTAGAAATCACCAACGTGACTAAAAAAGTTTTTGGTGGAAATAAGTATAAGGAATTTACCAGAAAACAAGGTATTTCAGTTGCCAAAACATCTATTCATGTACTTTTTGATGCAAGTGGATCACAGATTCTAGTACCAGAAAGTCAACCATCTCCAGTCAAAGAAAACCTCATTCATCTAAAAGAGAAATCCGACATCCAAAAGAAACTTGTAAACCCTCTAGAACTAGGCAATAGCAGCAGCCAGGATGAGATCACTACACCTAGCAGAAAGAAAATGTCTGAAGCATCAATGATTGTTCCTGATACAGACAGATACACTGTGCGAAGCCCAATACTTTTAATCAACACA
Peptide sequence:
MNLMLDRIPQDANKILSNQEMLTLMSNMGERILDVGDYELQVGIVEALCRMTTEKRRQELAYEWFSMDFIANAFKEIKDCEFETDCRIFLNLVNGILGDKRRVYTFPCLSAFLGKYELQIPSDEKLEEFWIDFNLGSHTLSFYIAGDEEDHQWEAVTVPEEKVQMYNIEVRESKKLLTLTLKNIVKISKKEGKELLFYFDESLEITNVTKKVFGGNKYKEFTRKQGISVAKTSIHVLFDASGSQILVPESQPSPVKENLIHLKEKSDIQKKLVNPLELGNSSSQDEITTPSRKKMSEASMIVPDTDRYTVRSPILLINTCKNQVLESFIPQICALVIDSRVNFCIQQEALKKMNLMLDRIPQDANKILSNQEMLTLMSNMGERILDVGDYELQVGIVEALCRMTTEKRRQELAYEWFSMDFIANAFKEIKDCEFETDCRIFLNLVNGILGDKRRVYTFPCLSAFLGKYELQIPSDEKLEEFWIDFNLGSHTLSFYIAGDEEDHQWEAVTVPEEKVQMYNIEVRESKKLLTLTLKNIVKISKKEGKELLFYFDESLEITNVTKKVFGGNKYKEFTRKQGISVAKTSIHVLFDASGSQILVPESQPSPVKENLIHLKEKSDIQKKLVNPLELGNSSSQDEITTPSRKKMSEASMIVPDTDRYTVRSPILLINT
IRESfinder result
IRESfinder score
0.768047483
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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