GgaINT1020812 @ galGal4
Intron Retention
Gene
ENSGALG00000013419 | PBX4
Description
pre-B-cell leukemia homeobox 4 [Source:HGNC Symbol;Acc:HGNC:13403]
Coordinates
JH376279.1:108841-109641:+
Coord C1 exon
JH376279.1:108841-109082
Coord A exon
JH376279.1:109083-109450
Coord C2 exon
JH376279.1:109451-109641
Length
368 bp
Sequences
Splice sites
5' ss Seq
CAGGTGATC
5' ss Score
4.28
3' ss Seq
ACAAATATCTCCACTTTCAGGCC
3' ss Score
8.18
Exon sequences
Seq C1 exon
TGTTAAGTATTCGTGGTATTCAGGAAGAAGACCCCCCCGATGCCCAACTAATGAGGCTAGATAACATGTTGCTGGCGGAGGGCGTCTCCGGCCCCGAGAAAAGAGGAAGAGGAGCACCGATGGCTGTAGCAGCAACACCAGGTGGCTGTCCAAATGACAATAGCATTGAGCACTCTGACTACAGGGCCAAGCTGTCACAGATCCGACAGATATACCACTCTGAGCTAGAGAAATATGAACAG
Seq A exon
GTGATCTTTCTGCATGGAAGAGTTTTTATCATCTCAATTGAAAATAACCCTTTTTTTTTCTTTCCCCTTCGGTGTTGGTTTTAAGGAGGTATAATGAGTGCAGCTCAACGCGAGGTTATCACGTTTATGTGAGAGCTTATCTCAGTGTCGCAGGGATGAGATGAAATAGAGGGACTGGACATCGAGCTAAAGATTAATTAATGCCTCGTTTATCTTTGTTACAGTATTTTTAAGAGTAAATACGAATAAAGCCGAAACGTGAAAAGCCCTCTGCTGTTTTTTTTTGGGGGGGGGATATGTGTTCTTGTTGGGGGGGGTTAATTTGGGGCTGTTTTGTCGTTTCTCGATACAAATATCTCCACTTTCAG
Seq C2 exon
GCCTGCAGCGAGTTCACCACCCACGTCATGAACCTGCTCAGGGAACAGAGCCGGACGAGGCCCATTTCTCCCAAAGAAATCGAGCGGATGGTGAACATCATCCACGGCAAATTCAGCACCATTCAGATGCAGCTGAAGCAGAGCACGTGCGAGGCGGTGATGATCCTCCGCTCACGCTTCCTCGATGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013419:ENSGALT00000021886:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.679 A=NA C2=0.219
Domain overlap (PFAM):
C1:
PF037928=PBC=FE(41.0=100),PF070286=DUF1319=PU(43.0=49.4),PF040917=Sec15=PU(43.1=34.6)
A:
NA
C2:
PF037928=PBC=PD(31.3=95.3),PF070286=DUF1319=PD(54.8=79.7),PF040917=Sec15=PD(53.8=54.7),PF0004624=Homeobox=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCGATGCCCAACTAATGAGG
R:
TCAGCTGCATCTGAATGGTGC
Band lengths:
343-711
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]