top of page
mmu_circVps13a_1666
Basic information of circular RNA
PanCircBase ID:
mmu_circVps13a_1666
mm39_Chr. Position ID:
chr19|16672822|16697831|-
Gene name:
Vps13a
Transcript:
ENSMUST00000068156.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
34,33,32,31,30,29,28,27,26,25,24,23
Exon/intron offsets:
0,3349,5662,8045,8229,9073,10416,11868,14812,15328,19590,24870
Genomic length:
25009
Exon/intron sizes in nt:
14,83,05,16,81,04,11,70,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr19:16669261-16672822|chr19:16697831-16699758
Splice length:
1666
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATTCAAGATTTCTGGAAAGTTACCTCTTGTTTCATTACGAATTTCGGATAAAAAACTGCAAGGCATTATGGAGTTGTTGGGAAGCATTCCAAAGCCTGAACCTGTAACTGATGTATCTGCCCCTGCCAGATCATTCCAGATTCAAGCATCTGCTTTGCCAGTATCACACATTTCTCAGAAGTTAATCCCTTTATTGGAACAGCCTGTTACTGAAGATGACTCAGAGGAAGAATTTTTTGATGCACCATGTAGTCCCTTGGAGGAGTGTCCTCAAGTGTCATGTAGAGATAAATGTACTCGACAGAAAAAATTACAAAAGAAAGATTGTGTGATGAATCTTATTCAACTTAGGATGAGATTTGAAGTAGCAGAGGTGTCCATTCAGTTTTATCACCTGGTGGGAGACTGTGAACTACCTGTGCTGGAAATGGGTGCTTTAGGATTGGGAACAGAAGCTGAGTTTAGAACATTTGACTTGAAAGGAAGTGCCTTTTTGAAAGAATTATGGCTAAAATGTCCAGAATATTTAGATGAAAACAAGAAACCAGTTTATTTGATCACGACCCTGGATAACACAATGGAAGATTTATTAACATTGGAATTCATGAAGGTTGAAAAAAATGCACCAAATTTGAATAGTACCTATAACAATGTTTTACAACTTATTAAGGTGAATTTTTCCTCTTTGGATATTCATTTACACACTGAAGCACTTCTGAATACAATGAATTATCTTAATAATATTCTTCCGGAATTAAGGGAAAAATCTGCCTCGGTGTCTGCTGCAGAGCCGGAAGACAAAGGGGACATCATTAAAAAACTTGCTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAAGGGCTTGATTCTGAGATGATTATGAAACCTCTAGTCACTGAAATAAATGCAAAGCTAAGGAATATAATTGTGTTAGATTCTGATAAAATGGCTATCTACAAAAAGGCTCTTTATATCACTGGAAAAGAAGTTTTCAGCTTCAAAATGATTTCTTACATGGATGCAACTGCTGGCTATGCATACACAGATATGAGTGTGGTTGACATTCGGGTTCATTTAACTGTTGGTTGCATTGAAGTAGTGTTCATCACAAAATTCCTGTATTCTATATTGGCATTTATAGATAATTTTCAAGCAGTTAAAGATGCCTTGGCTGAAGCAACTGTTCAAGCAGCAGAGATGGCTGCTGATGGTGTAAAGGAACTGGCTCGAAAGAGCTCTAGGTTTGCATTGGATGTTAACATCAAGGCTCCAGTTGTGCTCATTCCACAGTCTCCAGTGTCTCAGAACGTTTTTGTTGCTGATTTTGGATTAATTACAATGAAAAATATATTTGTTACTGTAACAGAGACCCAGAGTAATATCCCACCTGTAATTGATTTGATAACAATAAAGTTGAGTAAAATGAGACTATACAGGTCTCAGTTTAGGAATGATACATACCAGGAAGTGCTGGACCTGCTACTACCTTTGAACTTGGAAGTGATTGTCGAACGGAACTTATCCTGGGAATGGTACAAGGAAGTCCCTTGTTTTAATATAAAAGCTCAGCTAAAGCCCATGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAAGTGATTGTCGAACGGA
59.66
GGAATGCTTCCCAACAACTCC
59.45
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGAACGGAACTTATCCTGGGA
59.52
GGAATGCTTCCCAACAACTCC
59.45
166
PCR template sequence:
ACCTTTGAACTTGGAAGTGATTGTCGAACGGAACTTATCCTGGGAATGGTACAAGGAAGTCCCTTGTTTTAATATAAAAGCTCAGCTAAAGCCCATGGAGATTCAAGATTTCTGGAAAGTTACCTCTTGTTTCATTACGAATTTCGGATAAAAAACTGCAAGGCATTATGGAGTTGTTGGGAAGCATTCCAAAGCCTGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-196a-5p(2), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-326-3p(1), mmu-miR-214-3p(1), mmu-miR-153-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-541-5p(1), mmu-miR-425-5p(1), mmu-miR-802-5p(1), mmu-miR-466a-5p(1), mmu-miR-466p-5p(1), mmu-miR-539-5p(1), mmu-miR-335-3p(1), mmu-miR-532-5p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAGCCCATGGAGATTCAAGATTTCT
siRNA sets
AATCTTGAATCTCCATGGG, ATCTTGAATCTCCATGGGC, TCTTGAATCTCCATGGGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS13A_1666_ORF_1
0.8982
-0.009911725
0.999729718
1650
ORF sequence:
ATGGAGTTGTTGGGAAGCATTCCAAAGCCTGAACCTGTAACTGATGTATCTGCCCCTGCCAGATCATTCCAGATTCAAGCATCTGCTTTGCCAGTATCACACATTTCTCAGAAGTTAATCCCTTTATTGGAACAGCCTGTTACTGAAGATGACTCAGAGGAAGAATTTTTTGATGCACCATGTAGTCCCTTGGAGGAGTGTCCTCAAGTGTCATGTAGAGATAAATGTACTCGACAGAAAAAATTACAAAAGAAAGATTGTGTGATGAATCTTATTCAACTTAGGATGAGATTTGAAGTAGCAGAGGTGTCCATTCAGTTTTATCACCTGGTGGGAGACTGTGAACTACCTGTGCTGGAAATGGGTGCTTTAGGATTGGGAACAGAAGCTGAGTTTAGAACATTTGACTTGAAAGGAAGTGCCTTTTTGAAAGAATTATGGCTAAAATGTCCAGAATATTTAGATGAAAACAAGAAACCAGTTTATTTGATCACGACCCTGGATAACACAATGGAAGATTTATTAACATTGGAATTCATGAAGGTTGAAAAAAATGCACCAAATTTGAATAGTACCTATAACAATGTTTTACAACTTATTAAGGTGAATTTTTCCTCTTTGGATATTCATTTACACACTGAAGCACTTCTGAATACAATGAATTATCTTAATAATATTCTTCCGGAATTAAGGGAAAAATCTGCCTCGGTGTCTGCTGCAGAGCCGGAAGACAAAGGGGACATCATTAAAAAACTTGCTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAAGGGCTTGATTCTGAGATGATTATGAAACCTCTAGTCACTGAAATAAATGCAAAGCTAAGGAATATAATTGTGTTAGATTCTGATAAAATGGCTATCTACAAAAAGGCTCTTTATATCACTGGAAAAGAAGTTTTCAGCTTCAAAATGATTTCTTACATGGATGCAACTGCTGGCTATGCATACACAGATATGAGTGTGGTTGACATTCGGGTTCATTTAACTGTTGGTTGCATTGAAGTAGTGTTCATCACAAAATTCCTGTATTCTATATTGGCATTTATAGATAATTTTCAAGCAGTTAAAGATGCCTTGGCTGAAGCAACTGTTCAAGCAGCAGAGATGGCTGCTGATGGTGTAAAGGAACTGGCTCGAAAGAGCTCTAGGTTTGCATTGGATGTTAACATCAAGGCTCCAGTTGTGCTCATTCCACAGTCTCCAGTGTCTCAGAACGTTTTTGTTGCTGATTTTGGATTAATTACAATGAAAAATATATTTGTTACTGTAACAGAGACCCAGAGTAATATCCCACCTGTAATTGATTTGATAACAATAAAGTTGAGTAAAATGAGACTATACAGGTCTCAGTTTAGGAATGATACATACCAGGAAGTGCTGGACCTGCTACTACCTTTGAACTTGGAAGTGATTGTCGAACGGAACTTATCCTGGGAATGGTACAAGGAAGTCCCTTGTTTTAATATAAAAGCTCAGCTAAAGCCCATGGAGATTCAAGATTTCTGGAAAGTTACCTCTTGTTTCATTACGAATTTCGGATAA
Peptide sequence:
MELLGSIPKPEPVTDVSAPARSFQIQASALPVSHISQKLIPLLEQPVTEDDSEEEFFDAPCSPLEECPQVSCRDKCTRQKKLQKKDCVMNLIQLRMRFEVAEVSIQFYHLVGDCELPVLEMGALGLGTEAEFRTFDLKGSAFLKELWLKCPEYLDENKKPVYLITTLDNTMEDLLTLEFMKVEKNAPNLNSTYNNVLQLIKVNFSSLDIHLHTEALLNTMNYLNNILPELREKSASVSAAEPEDKGDIIKKLALKLPTNEDIITLQLLAELSCLQIFIQDQKQNISEIKIEGLDSEMIMKPLVTEINAKLRNIIVLDSDKMAIYKKALYITGKEVFSFKMISYMDATAGYAYTDMSVVDIRVHLTVGCIEVVFITKFLYSILAFIDNFQAVKDALAEATVQAAEMAADGVKELARKSSRFALDVNIKAPVVLIPQSPVSQNVFVADFGLITMKNIFVTVTETQSNIPPVIDLITIKLSKMRLYRSQFRNDTYQEVLDLLLPLNLEVIVERNLSWEWYKEVPCFNIKAQLKPMEIQDFWKVTSCFITNFG
IRESfinder result
IRESfinder score
0.782571151
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page