RnoINT0107852 @ rn6
Intron Retention
Gene
ENSRNOG00000010736 | Pbx4
Description
PBX homeobox 4 [Source:RGD Symbol;Acc:1305100]
Coordinates
chr16:21305485-21306169:-
Coord C1 exon
chr16:21306016-21306169
Coord A exon
chr16:21305592-21306015
Coord C2 exon
chr16:21305485-21305591
Length
424 bp
Sequences
Splice sites
5' ss Seq
CAGGTGATG
5' ss Score
5.99
3' ss Seq
ACTCTGCCCCTTTCTCACAGACT
3' ss Score
9.91
Exon sequences
Seq C1 exon
GTCTCTAACTGGTTCGGCAACAAAAGAATCCGGTACAAAAAGAATACGGGGAAATTTCAAGAAGAAGCCACCATGTACACGGGGAAAACATCCACAGTCACTAAGACCCGGGTCTCCGGGGGTCAGACCAGCTGCCAGTCCACACCCAGCCCAG
Seq A exon
GTGATGAAGCCATGCCTTCTTTACCTGTAAGCTTTCTGTGGGGATAGGTGTGAGTCAAGCTACCTGGCCCCTGTAGACAGCCGGTGCCAACAGGAGGACAGCAAGAGTGTCTTAATGTCAGAGGCCAGCATCCCCCACTCAAGGCCAGGGGAAGAGCAGTGCCTGGGTGCTTTGGGGGTGGGTGTCAAATCCAGAATCTGTCTGTCTGCCTCCCGTCTCTGCCAAGACAGGGTTTCTCTGTGTAGAGCCCACTCTGTAGACCAGGCTGCCTACTGAGTGCTGGTGATTAAAAGTGAGTGCCGTCCTGCTTGGCCCAGAGTCTCTCTTGATGAGGGACTGAGCAGATGCCACCCGGAAATCTCTGTGACTACTGACCCTGCTTCTGCTGTGACACCCCCAAACTGACTCTGCCCCTTTCTCACAG
Seq C2 exon
ACTCCTGTGGCCCCTTCCCACTGACCAGTGGAAGTGACATGGTTCTCACCCTGCGGACCCTGGCCTTCCTCCAGCCCCCACCCGGAGGAGTCTGCCTACAGCCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010736:ENSRNOT00000014265:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.606 A=NA C2=0.361
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(21.7=25.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTCTAACTGGTTCGGCAACA
R:
CTGTAGGCAGACTCCTCCGG
Band lengths:
255-679
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]