GgaINT0114642 @ galGal4
Intron Retention
Gene
ENSGALG00000027764 | CDX2
Description
caudal type homeobox 2 [Source:HGNC Symbol;Acc:HGNC:1806]
Coordinates
chr1:175317351-175317864:+
Coord C1 exon
chr1:175317351-175317564
Coord A exon
chr1:175317565-175317795
Coord C2 exon
chr1:175317796-175317864
Length
231 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTGT
5' ss Score
6.84
3' ss Seq
CACTCTCCCACTCCCGGCAGGTG
3' ss Score
11.25
Exon sequences
Seq C1 exon
GCCCCGTCTCGCTCGCCCCACTCGGCCCTTTCTCTTTTGCTTTCCCAACGCGGCTTTGTCCTCCGCAGTCAAAACCAGGACGAAGGACAAATACCGCGTGGTGTACACGGACCACCAGCGGTTGGAGCTGGAGAAGGAGTTCCACTACAGCCGCTATATCACCATCCGGAGGAAAGCTGAGCTGGCCTCCAGCCTGGGGCTGTCGGAGAGGCAG
Seq A exon
GTCTGTGGTACGGTGCGGGCTGCGCGGGGCTGGGATGCGCGGATCGAGTTGCGCGGGTCCGGTTGCGCAGGTTGGGATACGACGGACGGAAATACGCGGGACGGAGATGCGCGGATCGGGTTGCGCGGGTCGGGCTGCGTGGATTACGATGCGCGGATCGGCTTGCGCGCCCGCCGCTGAGCCCCGTGCTTTGAAACTGACTGCGCTTTTTCACTCTCCCACTCCCGGCAG
Seq C2 exon
GTGAAAATCTGGTTCCAGAACCGTCGGGCGAAGGAGAGGAAGATCAACAAGAAGAAGCTGCAGCAGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000027764:ENSGALT00000043833:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.139 A=NA C2=0.609
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PD(3.6=6.9),PF0004624=Homeobox=PU(73.7=58.3)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=56.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTCGCTCGCCCCACTC
R:
CCTGCTGCAGCTTCTTCTTGT
Band lengths:
276-507
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]