RnoINT0107831 @ rn6
Intron Retention
Gene
ENSRNOG00000000440 | Pbx2
Description
PBX homeobox 2 [Source:RGD Symbol;Acc:1303084]
Coordinates
chr20:4357733-4358956:+
Coord C1 exon
chr20:4357733-4358109
Coord A exon
chr20:4358110-4358882
Coord C2 exon
chr20:4358883-4358956
Length
773 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
CTTTTCTCTCCTCCCTTAAGGAA
3' ss Score
10.48
Exon sequences
Seq C1 exon
CTTCAGTGCCGGGGTGAACCCCCGAAGGGAGCCGGGAGGCGGGTTGCCGGGCGGGGTTGGGGCGGAGGGAGCAGCGGCCCCAGCGAGTTTGGGGGGGAAGTCACCCGGCGGGGGGAGGGGCGAGCAGGGAGGGGGCCTCAGGGCCCCCCCCCAGCTATGGACGAGCGGCTGCTGGGGCCGCCCCCTCCGGGCGGGGGCCGTGGGGGTCTGGGGCTGGTAGGTGGGGAGCCCGGGGGCCCTGGCGAGCCTCCCGGTGGCGGAGACCCCGGTGGGGGGAGTGGGGGGGTCCCGGGAGGCCGAGGGAAGCAAGACATCGGGGACATTCTGCAACAGATAATGACCATCACCGACCAGAGCCTGGACGAGGCCCAGGCCAA
Seq A exon
GTGAGTGCCCCCACCCCGGGACCCCGCTCACAGCTCTGAGTCCTCTGCCAGCCCCCCTCCCCCCAGGGCCCTCTCTGGATCTTGCAACTCTTTTCTTTCCTTAGTTCTAGTGTTCTCTCAAAGCTTGCTTTGCTCCTAGGCCCTAAAACCTCCACAGAGGGAACCCCAGGTGGTCTCACTCCCTCCTAACCTTTTGCTGACCCCTACAGTCTACACCGGCCCATCTCCTGGCTCCCAGACTTAGAAACTGTTCTCAGCCAAAGCTGTCCTCCCTAACTATCCGGCTAGCCCACCGCCTTCTCCACGTACGGATCCAGGATCTCCACACATTCCCTTCCGCTGAGGTCGGGGCCTCCAAGAGTCCTGCCTTTCCCTTGCTCAGCCCACACACCATACTGAACTCCCGGGCAGCCGGGCACCCCCTTCCCGGCCCCCTACCGCCTCACACTGACAGGCTCTGCTTCCCCTTCTCCGAAACCTACCTAGTCACCTTTATTTCTTCAGTCAGCTCTAGATCCTTTCTCCATCTTTTTGCTTGAACCATCCTTCTTAGCCTCAGCCCGCCCATAGTGACTTTAGCCCCATTGCCTGCACCTTCTGTTTCCCGTGGCCCAGCAGCTTCCAGACACCATGGCAGCCGATCTCAAGAACTTATCTCTCCGACTCCACACTACCCCATTCCCACTTACCCGCCTCACAGATTGTGTCCCCACCTTGCTCCCTGGCGCCCCTCTCCTGCCTGCCGCCTGAACTCTTTTCTCTCCTCCCTTAAG
Seq C2 exon
GAAACACGCCCTAAACTGTCACCGAATGAAGCCTGCCCTGTTTAGTGTCCTGTGTGAAATCAAGGAGAAAACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000440:ENSRNOT00000000509:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.231
Domain overlap (PFAM):
C1:
PF037928=PBC=PU(14.1=37.8)
A:
NA
C2:
PF037928=PBC=FE(12.6=100)
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:
TCAGTGCCGGGGTGAACC
R:
GGTGACAGTTTAGGGCGTGTT
Band lengths:
398-1171
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]