RnoINT0107838 @ rn6
Intron Retention
Gene
ENSRNOG00000000440 | Pbx2
Description
PBX homeobox 2 [Source:RGD Symbol;Acc:1303084]
Coordinates
chr20:4360950-4362682:+
Coord C1 exon
chr20:4360950-4361036
Coord A exon
chr20:4361037-4361156
Coord C2 exon
chr20:4361157-4362682
Length
120 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
GACTCTCATTCTCTTACCAGGCC
3' ss Score
9.58
Exon sequences
Seq C1 exon
GTGGAATCTCTCCGACACTCGATGGGGCCAGCGAGCTATGGGGATAACATCGGGGGAGGCCAGATATATAGTCCTCGAGAAATGCGG
Seq A exon
GTGAGTGAGTTGAAGGGCCTTAGTGCCTCCAGCTTTTGGCTCTACCAGGGCAGGAGTGTGCCCCCGCACCCCCCACCCCTACATTGGAGTTTCCCATTCTGACTCTCATTCTCTTACCAG
Seq C2 exon
GCCAATGGTGGCTGGCAGGAGGCTGTGACCCCGTCCTCGGTGACATCCCCGACAGAGGGACCAGGAAGTGTTCACTCTGACACCTCCAACTGACCTTGCCCCTCAAGGTCACAGGGTTGGGGGCTCCCACCAGGCAACTCTTGAGGAGGACTCTGGGCACCTAGAGGACTAACCCCACAGAAGCACAAAACAGGGCGATTGGGGTTGTGCCCTCCCCAACTAGACACTCGGTGCTGGGGTGCTGACTACATGGCAGGGAGAGTGGGGTGTCTCCGTTTCTTTTCTCCCCCTCCACGAAAAACAGATACTTATTTCTCAGATATCTCTCTTAAATCTACAACGTAATGCCAATTGTGTTTGGCTTGGGCTCCCCCTACTTCTATTCCCCACCCCACTTGTATACTCTGGAATCTGAAGACGTCAGCCCTGCCCGACCCAGAGATGCCAAAAATGGGGACTCTTGGACAGAGGCCCTGGGACGACACCCCCTCCCCCATGCATCCCCACCTTCTGCCCCTCCAGACGGCTTTATTACCTCATACGCAGCTCATCTTAAACCAATAGAATCGCTCGGTGGACAAGAGTGTCTGACTCAGATATCTACCTCGGAGGGACTTTCTGCTACTTTAGAGAATTGTTGACCAGGTTTTGAAGTTGGACTTTTTTTTTTTTTTAGAAAAGAAACCCTGAATCTGTATTTTTTTTTTTTGTTTGTTTTGTTTTTGTTTTTGTTGGTAGTGGTGATCATTAATTTTTTAATAGTTTGAAGAAGTAGGGTTTGGGGTGTGTATGTGGGTGTGTGTGTGTATGTTTTAAATAAACATGCTGATTTATTTTTGTTTACCCACTCGAGAAGTAAGCGCCAAAGGGGCCTAGTAAGAGAACAGACAGCGCTGGTGGTGGCTATTTGCTCCAGGCCTACCAGTGGGGAAGTGGATTTTGCGGGACACCGTGTCCTCAGCCTGGACACTTAGGTGTTTCTTAGCTTGTGCAGCCAAATCCCTGCTGTATCTGATGTGGATCACGATGCAGCTGTAGCCTCCTGTCTCCCCCCACACCTCCCCAGTAACCTTTGGGCAAGGCTGGACTGAACTCAGTGATTTTTGAAAAAGTCAAAAAGCTTTCGGTTTTGTTTTTTAAACTGTTTGCAGAATGGAGAAGATCGATCAGGAAGGGGAGTTCTTGCCAAATACGCTAAATACGGGCTGGGTGCTTCTCTACGTGTCTCCGCCAGTTTCCCAGAAATAAGTCTTTCTATTCAGTTCTTAATCTCATGCCAAAATCAAGGGGGTGGGGAGAGGAGGGAGGTCATGCAAAGCCAGGTATGAGGGAAGATTAAAAGTGTCTCATCTCAGCCCGGAACCCTTCTATCTGACCCTTCAGACATCCTCAGGATCTTCCAGACCTGTCACAGTGGGAACCCCTCCCATCAGTGGCCCAGGCGGGCCGGAGGGAGTGTGTGGAGAGGGCGGTGGGAGGGTGCCAGGGGCAGTTTCTCTCCTCACTTGTAAACTTGTAGATTCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000440:ENSRNOT00000000509:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.931 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCTCTCCGACACTCGATGGG
R:
CTCTAGGTGCCCAGAGTCCTC
Band lengths:
248-368
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]