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mmu_circVps16_2218
Basic information of circular RNA
PanCircBase ID:
mmu_circVps16_2218
mm39_Chr. Position ID:
chr2|130279541|130284603|+
Gene name:
Vps16
Transcript:
ENSMUST00000028900.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
21
Exon/intron indexes:
2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
Exon/intron offsets:
0,293,475,685,947,1161,1424,1814,1998,2219,2609,2830,3085,3278,3543,3773,3986,4172,4551,4713,4965
Genomic length:
5062
Exon/intron sizes in nt:
89,98,129,145,116,123,56,90,95,77,132,128,36,109,135,109,98,108,78,170,97
Flanking exon/introns:
chr2:130266367-130279541|chr2:130284603-130285215
Splice length:
2218
Other database IDs:
circAtlas: mmu-Vps16_0005
Human Ortholog IDs:
Mature spliced Sequence:
GAAGTATGAGCTGTACAGCATGGACTGGGACCTGAAGGAGGAGCTCAAGGATTGCCTGGTGGCTGCTGCACCCTATGGGGGTCCCATTGCTCTACTGAGGAACTGTTGGAGAAAAGAGAAAGCTGCCAGCGTGCGGCCAGTACTGGAGATCTACTCTGCATCTGGCTTACCACTGGCTAGCCTGCTGTGGAAGAGTGGGCCTGTGGTGGCCCTCGGCTGGTCAGCTGAGGAGGAGCTGCTCTGTGTGCAAGAAGATGGTGCAGTGCTAGTTTATGGCCTTCATGGAGACTTCCGGAGGCACTTCAGCATGGGCAATGAAGTGCTTCAGAACCGTGTCCTGGATGCCCGGATTTTTCACACTGAGTTTGGTTCAGGGGTGGCCATCCTTACAGGAGCCTATCGCTTTACTCTGAGTGCCAATGTGGGTGACCTCAAACTCCGTCGGATGCCAGAGGTGCCAGGTCTGCAAAGTGCACCCTCATGTTGGACCACACTGTGCCACGACCGAGTACCACACATTCTTCTGGCTGTAGGACCCGATCTTTACCTTCTGGATCATGCTACCTGCTCTGCAGTGACACCTGCTGGCTTAGCCCCAGGAGTGAGCAGCTTCCTACAGATGGCTGTATCCTTCACGTATCGTTACCTGGCACTCTTCACAGACACAGGCTACATCTGGATGGGGACAGCATCACTCAAGGAGAAGCTGTGTGAGTTCAACTGCAACATCCGGGCTCCCCCGAAGCAGATGGTCTGGTGTAGCCGTCCTCGGAGCAAGGAAAGGGCTGTTGTTGTGGCCTGGGAGAGGCGGCTGATGGTGGTGGGCAATGCGCCTGAAAGCATCCAGTTTGTGCTCGATGAGGACTCCTACTTAGTGCCTGAGCTTGATGGGGTCCGCATCTTCTCCCGAAGCACCCATGAGTTCCTGCATGAAGTCCCAGTGGCCAGTGAAGAGATCTTCAAAATTGCCTCAATGGCCCCTGGAGCACTGCTGTTAGAGGCCCAGAAGGAATATGAGAAAGAGAGCCAGAAAGCAGATGAGTACCTGCGGGAGATCCAGGAACTGGGCCAGCTGATCCAGGCTGTGCAGCAGTGCATTGAGGCTGCAGGACATGAGCACCAGCCAGACATGCAAAAGAGTCTGCTCAGGGCGGCTTCATTTGGAAAGTGTTTCCTTGACAGATTTCCACCTGACAGCTTCGTGCACATGTGTCAGGACCTTCGAGTGCTCAATGCTATTAGAGACTACCACATTGGGATCCCTCTCACCTACACCCAATACAAGCAGCTCACCATCCAGGTGCTGCTAGACAGGCTTGTGTTGCGGAGGCTTTATCCCCTGGCTATCCAGATATGCGAGTACCTGCGCCTTCCTGAAGTCCAGGGTGTCAGCAGGATCCTAGCCCACTGGGCCTGCTACAAGGTGCAGCAGAAAGATGTCTCAGATGAAGATGTAGCACGGGCTATTAATCAGAAGCTGGGTGACACGCCTGGTGTTTCATACTCTGACATTGCTGCGAGGGCCTATGGCTGTGGCCGCACTGAACTGGCCATTAAGCTGCTGGAGTATGAGCCACGCTCAGGGGAGCAGGTACCTCTTCTCCTAAAGATGAAGAGGAGCAAACTGGCACTGAGCAAGGCTATTGAGAGTGGAGACACTGACCTGGTGTTTACAGTGTTGCTGCACCTAAAGAATGAACTCAACCGAGGAGACTTTTTCATGACTCTCCGGAACCAACCCATGGCCCTGAGTTTGTATCGACAGTTCTGTAAGCATCAGGAGCTAGACACTCTGAAGGACCTTTACAATCAGGACGACAATCACCAGGAGTTGGGCAGCTTCCACATCAGAGCCAGCTATGCCGCTGAAGAGCGTATTGAAGGGCGAGTGGCAGCTCTGCAGACGGCAGCTGATGCCTTCTACAAAGCCAAGAATGAATTTGCAGCCAAGGCCACAGAGGATCAAATGAGGCTCCTGCGGATACAGCGACGCCTAGAGGATGAGCTAGGGGGCAGGTTCCTAGACCTATCTCTACACGACACTGTCACCACTCTTATCCTTGGAGGCCACAACAAGCGGGCAGAGCAGCTGGCACGTGACTTTCGCATCCCTGATAAGAGACTATGGTGGTTAAAGCTGGCTGCCCTGGCAGATTTGGAAGATTGGGAGGAGCTGGAGAAGTTTTCCAAAAGCAAGAAATCACCGATTGGTTACCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGAGGAGCTGGAGAAGTT
60.18
CAGTAGAGCAATGGGACCCC
59.82
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGGAGGAGCTGGAGAAGT
60.18
CAGTAGAGCAATGGGACCCC
59.82
152
PCR template sequence:
GAGACTATGGTGGTTAAAGCTGGCTGCCCTGGCAGATTTGGAAGATTGGGAGGAGCTGGAGAAGTTTTCCAAAAGCAAGAAATCACCGATTGGTTACCTGGAAGTATGAGCTGTACAGCATGGACTGGGACCTGAAGGAGGAGCTCAAGGATTGCCTGGTGGCTGCTGCACCCTATGGGGGTCCCATTGCTCTACTGAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
20
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(2), mmu-miR-214-3p(2), mmu-miR-22-3p(2), mmu-miR-15a-5p(1), mmu-miR-221-3p(1), mmu-miR-15b-5p(1), mmu-miR-222-3p(1), mmu-miR-149-5p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-676-3p(1), mmu-miR-541-5p(1), mmu-miR-342-3p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-207(1), mmu-miR-673-5p(1), mmu-miR-3087-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GATTGGTTACCTGGAAGTATGAGCTG
siRNA sets
TCATACTTCCAGGTAACCA, CTCATACTTCCAGGTAACC, ATACTTCCAGGTAACCAAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS16_2218_ORF_1
1.1534
0.366892418
0.999999341
2208
ORF sequence:
ATGGACTGGGACCTGAAGGAGGAGCTCAAGGATTGCCTGGTGGCTGCTGCACCCTATGGGGGTCCCATTGCTCTACTGAGGAACTGTTGGAGAAAAGAGAAAGCTGCCAGCGTGCGGCCAGTACTGGAGATCTACTCTGCATCTGGCTTACCACTGGCTAGCCTGCTGTGGAAGAGTGGGCCTGTGGTGGCCCTCGGCTGGTCAGCTGAGGAGGAGCTGCTCTGTGTGCAAGAAGATGGTGCAGTGCTAGTTTATGGCCTTCATGGAGACTTCCGGAGGCACTTCAGCATGGGCAATGAAGTGCTTCAGAACCGTGTCCTGGATGCCCGGATTTTTCACACTGAGTTTGGTTCAGGGGTGGCCATCCTTACAGGAGCCTATCGCTTTACTCTGAGTGCCAATGTGGGTGACCTCAAACTCCGTCGGATGCCAGAGGTGCCAGGTCTGCAAAGTGCACCCTCATGTTGGACCACACTGTGCCACGACCGAGTACCACACATTCTTCTGGCTGTAGGACCCGATCTTTACCTTCTGGATCATGCTACCTGCTCTGCAGTGACACCTGCTGGCTTAGCCCCAGGAGTGAGCAGCTTCCTACAGATGGCTGTATCCTTCACGTATCGTTACCTGGCACTCTTCACAGACACAGGCTACATCTGGATGGGGACAGCATCACTCAAGGAGAAGCTGTGTGAGTTCAACTGCAACATCCGGGCTCCCCCGAAGCAGATGGTCTGGTGTAGCCGTCCTCGGAGCAAGGAAAGGGCTGTTGTTGTGGCCTGGGAGAGGCGGCTGATGGTGGTGGGCAATGCGCCTGAAAGCATCCAGTTTGTGCTCGATGAGGACTCCTACTTAGTGCCTGAGCTTGATGGGGTCCGCATCTTCTCCCGAAGCACCCATGAGTTCCTGCATGAAGTCCCAGTGGCCAGTGAAGAGATCTTCAAAATTGCCTCAATGGCCCCTGGAGCACTGCTGTTAGAGGCCCAGAAGGAATATGAGAAAGAGAGCCAGAAAGCAGATGAGTACCTGCGGGAGATCCAGGAACTGGGCCAGCTGATCCAGGCTGTGCAGCAGTGCATTGAGGCTGCAGGACATGAGCACCAGCCAGACATGCAAAAGAGTCTGCTCAGGGCGGCTTCATTTGGAAAGTGTTTCCTTGACAGATTTCCACCTGACAGCTTCGTGCACATGTGTCAGGACCTTCGAGTGCTCAATGCTATTAGAGACTACCACATTGGGATCCCTCTCACCTACACCCAATACAAGCAGCTCACCATCCAGGTGCTGCTAGACAGGCTTGTGTTGCGGAGGCTTTATCCCCTGGCTATCCAGATATGCGAGTACCTGCGCCTTCCTGAAGTCCAGGGTGTCAGCAGGATCCTAGCCCACTGGGCCTGCTACAAGGTGCAGCAGAAAGATGTCTCAGATGAAGATGTAGCACGGGCTATTAATCAGAAGCTGGGTGACACGCCTGGTGTTTCATACTCTGACATTGCTGCGAGGGCCTATGGCTGTGGCCGCACTGAACTGGCCATTAAGCTGCTGGAGTATGAGCCACGCTCAGGGGAGCAGGTACCTCTTCTCCTAAAGATGAAGAGGAGCAAACTGGCACTGAGCAAGGCTATTGAGAGTGGAGACACTGACCTGGTGTTTACAGTGTTGCTGCACCTAAAGAATGAACTCAACCGAGGAGACTTTTTCATGACTCTCCGGAACCAACCCATGGCCCTGAGTTTGTATCGACAGTTCTGTAAGCATCAGGAGCTAGACACTCTGAAGGACCTTTACAATCAGGACGACAATCACCAGGAGTTGGGCAGCTTCCACATCAGAGCCAGCTATGCCGCTGAAGAGCGTATTGAAGGGCGAGTGGCAGCTCTGCAGACGGCAGCTGATGCCTTCTACAAAGCCAAGAATGAATTTGCAGCCAAGGCCACAGAGGATCAAATGAGGCTCCTGCGGATACAGCGACGCCTAGAGGATGAGCTAGGGGGCAGGTTCCTAGACCTATCTCTACACGACACTGTCACCACTCTTATCCTTGGAGGCCACAACAAGCGGGCAGAGCAGCTGGCACGTGACTTTCGCATCCCTGATAAGAGACTATGGTGGTTAAAGCTGGCTGCCCTGGCAGATTTGGAAGATTGGGAGGAGCTGGAGAAGTTTTCCAAAAGCAAGAAATCACCGATTGGTTACCTGGAAGTATGA
Peptide sequence:
MDWDLKEELKDCLVAAAPYGGPIALLRNCWRKEKAASVRPVLEIYSASGLPLASLLWKSGPVVALGWSAEEELLCVQEDGAVLVYGLHGDFRRHFSMGNEVLQNRVLDARIFHTEFGSGVAILTGAYRFTLSANVGDLKLRRMPEVPGLQSAPSCWTTLCHDRVPHILLAVGPDLYLLDHATCSAVTPAGLAPGVSSFLQMAVSFTYRYLALFTDTGYIWMGTASLKEKLCEFNCNIRAPPKQMVWCSRPRSKERAVVVAWERRLMVVGNAPESIQFVLDEDSYLVPELDGVRIFSRSTHEFLHEVPVASEEIFKIASMAPGALLLEAQKEYEKESQKADEYLREIQELGQLIQAVQQCIEAAGHEHQPDMQKSLLRAASFGKCFLDRFPPDSFVHMCQDLRVLNAIRDYHIGIPLTYTQYKQLTIQVLLDRLVLRRLYPLAIQICEYLRLPEVQGVSRILAHWACYKVQQKDVSDEDVARAINQKLGDTPGVSYSDIAARAYGCGRTELAIKLLEYEPRSGEQVPLLLKMKRSKLALSKAIESGDTDLVFTVLLHLKNELNRGDFFMTLRNQPMALSLYRQFCKHQELDTLKDLYNQDDNHQELGSFHIRASYAAEERIEGRVAALQTAADAFYKAKNEFAAKATEDQMRLLRIQRRLEDELGGRFLDLSLHDTVTTLILGGHNKRAEQLARDFRIPDKRLWWLKLAALADLEDWEELEKFSKSKKSPIGYLEV
IRESfinder result
IRESfinder score
0.394086389
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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