GgaINT0042573 @ galGal4
Intron Retention
Gene
ENSGALG00000023415 | HMX3
Description
homeobox protein HMX3 [Source:RefSeq peptide;Acc:NP_001007986]
Coordinates
chr6:31013803-31014912:+
Coord C1 exon
chr6:31013803-31014118
Coord A exon
chr6:31014119-31014301
Coord C2 exon
chr6:31014302-31014912
Length
183 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCG
5' ss Score
9.67
3' ss Seq
GTCCCTCTGTCCCCGTTCAGCCG
3' ss Score
8.42
Exon sequences
Seq C1 exon
ATGCCGGAGACCGGGCAGGAGCCGCCCAGCGCCCCGCCGCCGCCGCCCCCTCCCAAGGAGTCCTTCTACATCAAGAACCTGCTCAACGGAGACCCCCCCAAAGCGGCCCCCAAGCAGCCGAGGGCTCTGTTCGCCCCTTCGGGCAAAGCGGACGGCTCCGGCTTCGCCCTCTCGCAGGTGGGAGATCTCTCCTTTCCCCGCTTCGAGATCCCGGCGCCGCGCTTCGCTCTGAGCGCGCACTGCCTGGAGCGAGCCCAGACCTGGTGGTACCCCTACGCGCTGACGCCGGCCGGAGCCCACCTGCCCCGCACCGAAG
Seq A exon
GTACCGCTCCCTCCGACCCTCCGTCCCTCCTTCCTTCCATCCGTCCCTCCGTCCTCCCATCCGTCCCCTCCATCTGTCCATCCCCGACGGGACGGGGGTGGCACCGCGGGCGGGCGGCGGCGGCCCGTCGGGGGGCAGCGCAGGGCTGAAGGTGTCTCTTTGTGTCCCTCTGTCCCCGTTCAG
Seq C2 exon
CCGCGGAGAAATCCCTCCTGCGGGACTCGTCCCCCGCGTCGGGCACCGACAGGGACTCCCCGGAGCCGCTGCTCCAGGGGGGGGACGCGGAACAGAAGGAGCGGGACCCCAAGAGCCCCGCCGAGATCGTGCTGGAGGAGAGCGACTCGGAGGAGGGGAAGAAGGAGGGCGGCGCGGAGGACTGGAAGAAGCGGGAGGAGAGCCCCGAGAAGAAGCCGTGCCGCAAGAAGAAGACGCGCACGGTGTTCAGCCGCAGCCAGGTCTTCCAGCTCGAGTCCACCTTCGACATGAAGCGCTACCTGAGCAGCTCGGAGCGGGCCGGCCTGGCCGCTTCGCTGCACCTCACAGAGACCCAGGTGAAGATCTGGTTCCAGAACCGCCGCAACAAGTGGAAGCGGCAGCTGGCGGCCGAGCTGGAGGCGGCCAACCTCAGCCACGCGGCCGCGCAGCGCATCGTGCGCGTCCCCATCCTCTACCACGAGAACTCGGGCGCGGAGAGCAGCGCGGCGGGAGGCGGCGGCCCCGGCCCGCAGCCTCTGCTCACCTTCCCCCACCCCGTTTATTACTCCCACCCCGTGGTCACCTCCGTACCGCTCCTGCGGCCCGTCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000023415:ENSGALT00000011810:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.642 A=NA C2=0.463
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=27.9)
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:
GAGATCTCTCCTTTCCCCGCT
R:
GGTCCCGCTCCTTCTGTTCC
Band lengths:
243-426
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]