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mmu_circUbxn4_1197
Basic information of circular RNA
PanCircBase ID:
mmu_circUbxn4_1197
mm39_Chr. Position ID:
chr1|128183169|128202741|+
Gene name:
Ubxn4
Transcript:
ENSMUST00000027592.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
3,4,5,6,7,8,9,10,11,12
Exon/intron offsets:
0,686,3399,4011,5401,7360,10857,14436,17388,19369
Genomic length:
19572
Exon/intron sizes in nt:
29,11,91,72,94,55,16,50,00,00,00,00,000
Flanking exon/introns:
chr1:128180042-128183169|chr1:128202741-128204693
Splice length:
1197
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TGAAGCCTGTCTGCAGTTTTCACAAATTTATCCTGTAGTATGTGTTCCATCCAGTTTCTTTATAGGAGACAGTGGAATCCCTTTGGAAGTAATAGCGGGGAGTGTTTCTGCAGATGAGCTTGTTACAAGAATTCATAAAGTCCAACAGATGCACTCGTCAAAAGGTGAAGCATCAGTGACAAATGACAACCAGTCAGAAAGTTCAGTATCTACCCCATCTGCCTCATTTGAACCTGATGTATGTGAAAATCCCGAGTCCAAAAATACAGAGCTTTGTGAGACACCAGCTACCTCTGACACAAAGTCAGATACTGCAACAGGAGGAGAATGCACAGGTCATGACAGCCACTCTCAGGAGCCTCATGGATGTTCAAACCAGAGACCAGCCGAGGACCTCACCGTCAGAGTAGAAAGACTAACAAAAAAACTTGAAGAAAGGAGAGAAGAGAAGCGGAAGGAAGAAGCACAGAGAGAGATTAAGAAGGAAATTGAAAGGAGAAAAACTGGAAAGGAAATGTTGGATTATAAAAGAAAACAAGAAGAAGAATTAACAAAAAGAATGTTAGAAGAAAGAAGCAGAGAGAAGGCAGAAGATAGAGCGGCTCGAGAGCGCATCAAGCAGCAGATTGCCCTGGATCGTGCAGAAAGAGCTGCTCGTTTTGCAAAGACAAAGGAAGCAGAAGCTGCCAAAGCTGCTGCCTTGCTGACCAAACAGGCAGGAACGGAAGTCAAGAGAGAGTCTACAGCACGAGACAGAAGCACCATTGCAAGAATTCAGTTCCGGCTGCCTGATGGTTCTTCCTTTACAAACCAGTTTCCTTCTGATGCTCCTCTAGAAGAAGCGAGGCAGTTTGCTGCACAGACCGTGGGCAACACCTATGGCAATTTTTCATTAGCCACCATGTTTCCCAGAAGAGAGTTCACCAGAGAAGACTATAAGAGGAGGCTGCTGGATCTGGAGCTCGCCCCCAGCGCCTCTGTGGTGCTGCTGCCAGCAGGACGGCCAGCCACATCCATTGTCCACTCTTCTAGTGGAGACATTTGGACATTACTGGGGACGGTGCTTTATCCATTCCTGGCCATATGGAGATTAATTAGCAATTTTTTATTTAGCAATCCTCCTCCTGCACAGACTTCAGCAAGAGCCACATCCACAGAGCCTTCAAACTCTGCATCATCCAGCAAATCAGAGAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCCTGCACAGACTTCAGCA
59.97
CCCGCTATTACTTCCAAAGGGA
59.83
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGAGCCACATCCACAGAGC
60.04
CCCGCTATTACTTCCAAAGGGA
59.83
156
PCR template sequence:
GCAATTTTTTATTTAGCAATCCTCCTCCTGCACAGACTTCAGCAAGAGCCACATCCACAGAGCCTTCAAACTCTGCATCATCCAGCAAATCAGAGAAAAGTGAAGCCTGTCTGCAGTTTTCACAAATTTATCCTGTAGTATGTGTTCCATCCAGTTTCTTTATAGGAGACAGTGGAATCCCTTTGGAAGTAATAGCGGGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-miR-15a-5p(1), mmu-miR-103-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-15b-5p(1), mmu-miR-709(1), mmu-miR-138-5p(1), mmu-let-7d-5p(1), mmu-miR-370-3p(1), mmu-miR-541-5p(1), mmu-miR-340-5p(1), mmu-miR-107-3p(1), mmu-miR-383-5p(1), mmu-miR-98-5p(1), mmu-miR-539-5p(1), mmu-miR-350-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AATCAGAGAAAAGTGAAGCCTGTCTG
siRNA sets
CAGGCTTCACTTTTCTCTG, GACAGGCTTCACTTTTCTC, ACAGGCTTCACTTTTCTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUBXN4_1197_ORF_1
0.8845
0.133248103
0.999997922
2244
ORF sequence:
ATGCACTCGTCAAAAGGTGAAGCATCAGTGACAAATGACAACCAGTCAGAAAGTTCAGTATCTACCCCATCTGCCTCATTTGAACCTGATGTATGTGAAAATCCCGAGTCCAAAAATACAGAGCTTTGTGAGACACCAGCTACCTCTGACACAAAGTCAGATACTGCAACAGGAGGAGAATGCACAGGTCATGACAGCCACTCTCAGGAGCCTCATGGATGTTCAAACCAGAGACCAGCCGAGGACCTCACCGTCAGAGTAGAAAGACTAACAAAAAAACTTGAAGAAAGGAGAGAAGAGAAGCGGAAGGAAGAAGCACAGAGAGAGATTAAGAAGGAAATTGAAAGGAGAAAAACTGGAAAGGAAATGTTGGATTATAAAAGAAAACAAGAAGAAGAATTAACAAAAAGAATGTTAGAAGAAAGAAGCAGAGAGAAGGCAGAAGATAGAGCGGCTCGAGAGCGCATCAAGCAGCAGATTGCCCTGGATCGTGCAGAAAGAGCTGCTCGTTTTGCAAAGACAAAGGAAGCAGAAGCTGCCAAAGCTGCTGCCTTGCTGACCAAACAGGCAGGAACGGAAGTCAAGAGAGAGTCTACAGCACGAGACAGAAGCACCATTGCAAGAATTCAGTTCCGGCTGCCTGATGGTTCTTCCTTTACAAACCAGTTTCCTTCTGATGCTCCTCTAGAAGAAGCGAGGCAGTTTGCTGCACAGACCGTGGGCAACACCTATGGCAATTTTTCATTAGCCACCATGTTTCCCAGAAGAGAGTTCACCAGAGAAGACTATAAGAGGAGGCTGCTGGATCTGGAGCTCGCCCCCAGCGCCTCTGTGGTGCTGCTGCCAGCAGGACGGCCAGCCACATCCATTGTCCACTCTTCTAGTGGAGACATTTGGACATTACTGGGGACGGTGCTTTATCCATTCCTGGCCATATGGAGATTAATTAGCAATTTTTTATTTAGCAATCCTCCTCCTGCACAGACTTCAGCAAGAGCCACATCCACAGAGCCTTCAAACTCTGCATCATCCAGCAAATCAGAGAAAAGTGAAGCCTGTCTGCAGTTTTCACAAATTTATCCTGTAGTATGTGTTCCATCCAGTTTCTTTATAGGAGACAGTGGAATCCCTTTGGAAGTAATAGCGGGGAGTGTTTCTGCAGATGAGCTTGTTACAAGAATTCATAAAGTCCAACAGATGCACTCGTCAAAAGGTGAAGCATCAGTGACAAATGACAACCAGTCAGAAAGTTCAGTATCTACCCCATCTGCCTCATTTGAACCTGATGTATGTGAAAATCCCGAGTCCAAAAATACAGAGCTTTGTGAGACACCAGCTACCTCTGACACAAAGTCAGATACTGCAACAGGAGGAGAATGCACAGGTCATGACAGCCACTCTCAGGAGCCTCATGGATGTTCAAACCAGAGACCAGCCGAGGACCTCACCGTCAGAGTAGAAAGACTAACAAAAAAACTTGAAGAAAGGAGAGAAGAGAAGCGGAAGGAAGAAGCACAGAGAGAGATTAAGAAGGAAATTGAAAGGAGAAAAACTGGAAAGGAAATGTTGGATTATAAAAGAAAACAAGAAGAAGAATTAACAAAAAGAATGTTAGAAGAAAGAAGCAGAGAGAAGGCAGAAGATAGAGCGGCTCGAGAGCGCATCAAGCAGCAGATTGCCCTGGATCGTGCAGAAAGAGCTGCTCGTTTTGCAAAGACAAAGGAAGCAGAAGCTGCCAAAGCTGCTGCCTTGCTGACCAAACAGGCAGGAACGGAAGTCAAGAGAGAGTCTACAGCACGAGACAGAAGCACCATTGCAAGAATTCAGTTCCGGCTGCCTGATGGTTCTTCCTTTACAAACCAGTTTCCTTCTGATGCTCCTCTAGAAGAAGCGAGGCAGTTTGCTGCACAGACCGTGGGCAACACCTATGGCAATTTTTCATTAGCCACCATGTTTCCCAGAAGAGAGTTCACCAGAGAAGACTATAAGAGGAGGCTGCTGGATCTGGAGCTCGCCCCCAGCGCCTCTGTGGTGCTGCTGCCAGCAGGACGGCCAGCCACATCCATTGTCCACTCTTCTAGTGGAGACATTTGGACATTACTGGGGACGGTGCTTTATCCATTCCTGGCCATATGGAGATTAATTAGCAATTTTTTATTTAGCAATCCTCCTCCTGCACAGACTTCAGCAAGAGCCACATCCACAGAGCCTTCAAACTCTGCATCATCCAGCAAATCAGAGAAA
Peptide sequence:
MHSSKGEASVTNDNQSESSVSTPSASFEPDVCENPESKNTELCETPATSDTKSDTATGGECTGHDSHSQEPHGCSNQRPAEDLTVRVERLTKKLEERREEKRKEEAQREIKKEIERRKTGKEMLDYKRKQEEELTKRMLEERSREKAEDRAARERIKQQIALDRAERAARFAKTKEAEAAKAAALLTKQAGTEVKRESTARDRSTIARIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVGNTYGNFSLATMFPRREFTREDYKRRLLDLELAPSASVVLLPAGRPATSIVHSSSGDIWTLLGTVLYPFLAIWRLISNFLFSNPPPAQTSARATSTEPSNSASSSKSEKSEACLQFSQIYPVVCVPSSFFIGDSGIPLEVIAGSVSADELVTRIHKVQQMHSSKGEASVTNDNQSESSVSTPSASFEPDVCENPESKNTELCETPATSDTKSDTATGGECTGHDSHSQEPHGCSNQRPAEDLTVRVERLTKKLEERREEKRKEEAQREIKKEIERRKTGKEMLDYKRKQEEELTKRMLEERSREKAEDRAARERIKQQIALDRAERAARFAKTKEAEAAKAAALLTKQAGTEVKRESTARDRSTIARIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVGNTYGNFSLATMFPRREFTREDYKRRLLDLELAPSASVVLLPAGRPATSIVHSSSGDIWTLLGTVLYPFLAIWRLISNFLFSNPPPAQTSARATSTEPSNSASSSKSEK
IRESfinder result
IRESfinder score
0.5637832
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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