GgaALTD0006647-2/3 @ galGal4
Alternative 5'ss
Gene
ENSGALG00000027764 | CDX2
Description
caudal type homeobox 2 [Source:HGNC Symbol;Acc:HGNC:1806]
Coordinates
chr1:175317351-175317864:+
Coord C1 exon
chr1:175317351-175317560
Coord A exon
chr1:175317561-175317564
Coord C2 exon
chr1:175317796-175317864
Length
4 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
GCCCCGTCTCGCTCGCCCCACTCGGCCCTTTCTCTTTTGCTTTCCCAACGCGGCTTTGTCCTCCGCAGTCAAAACCAGGACGAAGGACAAATACCGCGTGGTGTACACGGACCACCAGCGGTTGGAGCTGGAGAAGGAGTTCCACTACAGCCGCTATATCACCATCCGGAGGAAAGCTGAGCTGGCCTCCAGCCTGGGGCTGTCGGAGAG
Seq A exon
GCAG
Seq C2 exon
GTGAAAATCTGGTTCCAGAACCGTCGGGCGAAGGAGAGGAAGATCAACAAGAAGAAGCTGCAGCAGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000027764-6-6,7-6,8-6-2/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
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 Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCGCTATATCACCATCCGGA
R:
TGATCTTCCTCTCCTTCGCCC
Band lengths:
107-111
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]