RnoINT0107849 @ rn6
Intron Retention
Gene
ENSRNOG00000010736 | Pbx4
Description
PBX homeobox 4 [Source:RGD Symbol;Acc:1305100]
Coordinates
chr16:21310460-21311162:-
Coord C1 exon
chr16:21310921-21311162
Coord A exon
chr16:21310651-21310920
Coord C2 exon
chr16:21310460-21310650
Length
270 bp
Sequences
Splice sites
5' ss Seq
CAGGTGATC
5' ss Score
4.28
3' ss Seq
CCCATCTTTTCCCACCCCAGGCC
3' ss Score
9.48
Exon sequences
Seq C1 exon
CTGTGAGCGTCCAGACGCAGGAAGAGGACCCTCCCGATGCCCAGCTGCTGAGGTTGGATAACATGCTGCTGGCTGAGGGTGTGTCCAGGCCAGAGAAGCGAGGACGAGGAGGAGCAGCGGCAGGCAGCACAGCAACACCAGGTGGCTGCCCAAATGACAATAGCATTGAACACTCAGACTACAGGGCCAAGCTGTCCCAGATCCGACAGATTTACCACTCAGAGCTAGAGAAGTATGAACAG
Seq A exon
GTGATCTTTCTGCACGCAAGAGTTTGTCATGTGAATGTGCACTGGCCACAGGCAGGTGTGGACACGAGCCCCTCCTCTGTGCAGAGCAGGGACAGCCCGCCGCAGTGAGTTGCTGCAGAGGCGGCTGGTGTCACTGAAAGCGCCTTTCCCTCCTCAGAGGTGACCTGAGTGTGAGCTGTGGGGGTGGCAGATGTGGTCAGCTGTGGAGCCTTACTGCCCTGCACCACCTGGCTGCTGAGTCACAGACTGGCCCATCTTTTCCCACCCCAG
Seq C2 exon
GCCTGTCGTGAGTTCACCACGCACGTCACCAACCTTCTCCGGGAACAGAGTAGGGTGAGGCCCGTGTCCTCCGGGGAGATCGAGCACATGGTGAGCACCATTCACAGCAAGTTCAGTGCCATCCAGAGGCAGCTGAAACAGAGCACCTGTGAGGCTGTGATGACCCTACGCTCACGGTTCCTGGATGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010736:ENSRNOT00000014265:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.716 A=NA C2=0.188
Domain overlap (PFAM):
C1:
PF037928=PBC=FE(40.8=100),PF070286=DUF1319=PU(32.9=34.6),PF083976=IMD=PU(20.3=30.9)
A:
NA
C2:
PF037928=PBC=PD(31.1=95.3),PF070286=DUF1319=PD(64.7=85.9),PF083976=IMD=FE(51.2=100),PF0004624=Homeobox=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGATAACATGCTGCTGGCTG
R:
ACTTGCTGTGAATGGTGCTCA
Band lengths:
300-570
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]