top of page
mmu_circSenp1_1439
Basic information of circular RNA
PanCircBase ID:
mmu_circSenp1_1439
mm39_Chr. Position ID:
chr15|97954709|97985014|-
Gene name:
Senp1
Transcript:
ENSMUST00000044189.16
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
13,12,11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,1367,2075,3087,7990,9575,9929,18980,19721,25414,28141,30257
Genomic length:
30305
Exon/intron sizes in nt:
132,156,85,39,55,272,104,172,160,85,131,48
Flanking exon/introns:
chr15:97946270-97954709|chr15:97985014-97991163
Splice length:
1439
Other database IDs:
CIRCpedia: MMU_CIRCpedia_35722, circAtlas: mmu-Senp1_0011
circBase: hsa_circ_0026023, circAtlas: hsa-SENP1_0008, CIRCpedia: HSA_CIRCpedia_8528
Human Ortholog IDs:
Mature spliced Sequence:
GATTCTGTGTCTTTACTAAAGCCAGTGATGTGAAGAGACCTGAAATGGATGACACAGCTGATGGGGTGAAGATGGACGCTGGGGAGGTGACCTTAGTGAACCACGGCTCCACTTTCAGAACCCACCGCCCGCCACAGTCAGGCTTTCCAGAGGAGCAGCTTCTGCTTTCTGACCAGCAGAGCTTGCCTTTCAGGCAGGGTACTTTAGATGGATCTTTCACGTGTTCTACAAGAAGCCCAGCCTATCGTCCAGATTATCACTCAGATAACCCTTCCTCAGACAGTTTCCTTGGCTCAGGTGACGTAAGAACCTTTGGTCAAAGTGCAAATGGACAATGGAGAAATTCCACTCCAGCGTCAGGCTCAGCGCCACAAAAACCAAGAAATAGCCGAAGTCTTTGCCTCGAAACCCGGAAGACCTCAAGTGGATTATCAAACACCTTTGTGGGCAAGTCCAATCACCACTGCCACATGTCTGCGTATGAAAAGTCATTTCCCATTAAGCCTGCCCCAAGTCCATCCTGGAGTGGGTCATGTCGTCGGAGTCTTTTAAGCCCTAAGAAAACTCAGAGGCGACATTTCAGCACAGCAGAAGAGACAGTTCAAGAAGAAGAGAAGGAGATCTACAGACAGCTGCTGCAGATGGTCACAGGGAAGCAGTTCTGTGTAGCGAAACCCACCACACATTTTCCGTTACGCCTGTCTCGGTGTCTTAGTTCCAATAAGAACTCTTTGAAAGACTCGCTGTTGAGAAACGGAAACTCTTGTGCATCTCATGTCATTGGTTCTGATACGTCATCCTCTGGATCTGCCAGCATTTTAACTGCACAGGAGCAGTTGTCCCACAGTGCACATTCCCTGTCATCTGGTACCCCAGATGTTGCCTTTGGATCCAAAGACTCTGATCCTCACCATCACCTCGCTGCACCTCATCAGCCAAATAGCTTACCAGCATCAAATACACAGTCCGAAGGGTCAGACTCTGTGATTTTACTTAAAGTGAAAGAATCTCAGACTCCAGCTTCCAGCCCTACGTTCTTCCAGGCAGAGCTATGGATCAAAGAATTAACTAGCGTTTATGACTCTCGAGCTCGGGAAAGATTGCGCCGGATTGAAGAGCAGAAAGCATTGGCACTACAGCTTCAAAACCAGCGACTGCAGGAGCAGGAACATGCAGTACTTGACTCCGTAGAGCTTCACCTTCGTGTGCCTCTTGAAAAGGAGATTCCTGTCACAGCTGCCCAAGAAACCAGGAAAAAAAGCCACCAGCTGACTGACAGTGAAGACGAATTTCCTGAAATTACAGAGGAAATGGAAAAAGAAATAAAGAATGTATTTCGTAACGGTAACCAGGATGAAGTCCTCAGTGAGGCATTCCGCTTGACCATTACACGCAAAGACATTCAGACTCTAAACCATCTAAACTGGCTCAATGATGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCATTCCGCTTGACCATT
60.32
TTCACCCCATCAGCTGTGTC
59.96
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCATTCCGCTTGACCATT
60.32
CTTCACCCCATCAGCTGTGT
59.96
142
PCR template sequence:
TAACGGTAACCAGGATGAAGTCCTCAGTGAGGCATTCCGCTTGACCATTACACGCAAAGACATTCAGACTCTAAACCATCTAAACTGGCTCAATGATGAGGATTCTGTGTCTTTACTAAAGCCAGTGATGTGAAGAGACCTGAAATGGATGACACAGCTGATGGGGTGAAGATGGACGCTGGGGAGGTGACCTTAGTGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(2), mmu-miR-1904(2), mmu-miR-26a-5p(1), mmu-miR-106b-5p(1), mmu-miR-26b-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-34b-5p(1), mmu-miR-27a-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-1187(1)
siRNAs for circular RNA silencing
Junction sequence
GCTCAATGATGAGGATTCTGTGTCTT
siRNA sets
AAGACACAGAATCCTCATC, AGACACAGAATCCTCATCA, ACAGAATCCTCATCATTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSENP1_1439_ORF_1
0.7881
0.129545255
0.999079592
1428
ORF sequence:
ATGGATGACACAGCTGATGGGGTGAAGATGGACGCTGGGGAGGTGACCTTAGTGAACCACGGCTCCACTTTCAGAACCCACCGCCCGCCACAGTCAGGCTTTCCAGAGGAGCAGCTTCTGCTTTCTGACCAGCAGAGCTTGCCTTTCAGGCAGGGTACTTTAGATGGATCTTTCACGTGTTCTACAAGAAGCCCAGCCTATCGTCCAGATTATCACTCAGATAACCCTTCCTCAGACAGTTTCCTTGGCTCAGGTGACGTAAGAACCTTTGGTCAAAGTGCAAATGGACAATGGAGAAATTCCACTCCAGCGTCAGGCTCAGCGCCACAAAAACCAAGAAATAGCCGAAGTCTTTGCCTCGAAACCCGGAAGACCTCAAGTGGATTATCAAACACCTTTGTGGGCAAGTCCAATCACCACTGCCACATGTCTGCGTATGAAAAGTCATTTCCCATTAAGCCTGCCCCAAGTCCATCCTGGAGTGGGTCATGTCGTCGGAGTCTTTTAAGCCCTAAGAAAACTCAGAGGCGACATTTCAGCACAGCAGAAGAGACAGTTCAAGAAGAAGAGAAGGAGATCTACAGACAGCTGCTGCAGATGGTCACAGGGAAGCAGTTCTGTGTAGCGAAACCCACCACACATTTTCCGTTACGCCTGTCTCGGTGTCTTAGTTCCAATAAGAACTCTTTGAAAGACTCGCTGTTGAGAAACGGAAACTCTTGTGCATCTCATGTCATTGGTTCTGATACGTCATCCTCTGGATCTGCCAGCATTTTAACTGCACAGGAGCAGTTGTCCCACAGTGCACATTCCCTGTCATCTGGTACCCCAGATGTTGCCTTTGGATCCAAAGACTCTGATCCTCACCATCACCTCGCTGCACCTCATCAGCCAAATAGCTTACCAGCATCAAATACACAGTCCGAAGGGTCAGACTCTGTGATTTTACTTAAAGTGAAAGAATCTCAGACTCCAGCTTCCAGCCCTACGTTCTTCCAGGCAGAGCTATGGATCAAAGAATTAACTAGCGTTTATGACTCTCGAGCTCGGGAAAGATTGCGCCGGATTGAAGAGCAGAAAGCATTGGCACTACAGCTTCAAAACCAGCGACTGCAGGAGCAGGAACATGCAGTACTTGACTCCGTAGAGCTTCACCTTCGTGTGCCTCTTGAAAAGGAGATTCCTGTCACAGCTGCCCAAGAAACCAGGAAAAAAAGCCACCAGCTGACTGACAGTGAAGACGAATTTCCTGAAATTACAGAGGAAATGGAAAAAGAAATAAAGAATGTATTTCGTAACGGTAACCAGGATGAAGTCCTCAGTGAGGCATTCCGCTTGACCATTACACGCAAAGACATTCAGACTCTAAACCATCTAAACTGGCTCAATGATGAGGATTCTGTGTCTTTACTAAAGCCAGTGATGTGA
Peptide sequence:
MDDTADGVKMDAGEVTLVNHGSTFRTHRPPQSGFPEEQLLLSDQQSLPFRQGTLDGSFTCSTRSPAYRPDYHSDNPSSDSFLGSGDVRTFGQSANGQWRNSTPASGSAPQKPRNSRSLCLETRKTSSGLSNTFVGKSNHHCHMSAYEKSFPIKPAPSPSWSGSCRRSLLSPKKTQRRHFSTAEETVQEEEKEIYRQLLQMVTGKQFCVAKPTTHFPLRLSRCLSSNKNSLKDSLLRNGNSCASHVIGSDTSSSGSASILTAQEQLSHSAHSLSSGTPDVAFGSKDSDPHHHLAAPHQPNSLPASNTQSEGSDSVILLKVKESQTPASSPTFFQAELWIKELTSVYDSRARERLRRIEEQKALALQLQNQRLQEQEHAVLDSVELHLRVPLEKEIPVTAAQETRKKSHQLTDSEDEFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEDSVSLLKPVM
IRESfinder result
IRESfinder score
0.626234763
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page