GgaALTA0009112-2/3 @ galGal4
Alternative 3'ss
Gene
ENSGALG00000023419 | HOXD4
Description
homeobox protein Hox-D4 [Source:RefSeq peptide;Acc:NP_001012293]
Coordinates
chr7:15778332-15779976:-
Coord C1 exon
chr7:15778828-15779976
Coord A exon
chr7:15778433-15778529
Coord C2 exon
chr7:15778332-15778432
Length
97 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
TCTCCGTGTTTCTTTCCCAGTGA
3' ss Score
10.25
Exon sequences
Seq C1 exon
TTTATTCAGTTGACAGCAAGTAGGAGGGCTCTATGGAAGGAGAAAAAAAGACAACACGAGAAAAATTAGTATTTTCTACCTTCCGAAATTAATGGCCATGAGTTCGTATATGGTGAACTCTAAGTATGTGGATCCCAAATTTCCTCCTTGCGAGGAATATTTGCAGAGCAGCTACCTAGGCGAGCAGGGGGCCGAGTATTACGGGGCCTCGCAGGGCTCCGATTTCCAGCACCAGGGGCTCTACCCACGGTCAAACTACAGCGAGCAGCCCTTTGGCTGCGCCGGTGCCCAGGGCTCCGCCGTGCAGCCGCGGGGTCACGGACAGGAGCAGTCCGCCCCTCCGAGCCACTTCCCCGGCCAAGCCGAGCATTGTCCTCCGCCTCCAATGTCCAACTCCCGAGCCTGCGGCCAGCAGCCAGCCCTCAAAGCCCCCCACGGGTCAGCAGTTAAGCAGCCAGCAGTAGTTTATCCCTGGATGAAGAAAGTCCATGTTAACTCGG
Seq A exon
TGAACCCCAATTACAGCGGAGGGGAACCTAAGCGCTCCCGAACAGCTTACACCAGGCAGCAAGTCCTAGAACTGGAAAAAGAATTTCATTTTAACAG
Seq C2 exon
GTACCTGACCCGGCGCCGCCGTATCGAGATAGCGCACACTTTGTGTCTCTCTGAGCGCCAGATCAAGATCTGGTTTCAGAACAGAAGAATGAAGTGGAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000023419-2-2,2-1,2-0-2/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.489 A=NA C2=0.545
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=55.9)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATTGTCCTCCGCCTCCAATG
R:
GTGTGCGCTATCTCGATACGG
Band lengths:
172-269
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]