GgaINT1014999 @ galGal4
Intron Retention
Gene
ENSGALG00000028128 | HOXD8
Description
Homeobox protein Hox-D8 [Source:UniProtKB/Swiss-Prot;Acc:P23459]
Coordinates
chr7:15793835-15794437:-
Coord C1 exon
chr7:15794223-15794437
Coord A exon
chr7:15793983-15794222
Coord C2 exon
chr7:15793835-15793982
Length
240 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
ACGGATACGATAACTTACAGAGA
3' ss Score
1.44
Exon sequences
Seq C1 exon
NNNNNNNNNGGGAGAGCAGCGGAGAGGCACCGGCGGCGGCACCGGGAGCAGCGCCCCGCGCCCGCTCCCCGCCCGCCGCTGCCCCCTCCCCGATGAGCTCCTACTTTGTCAACCCGCTCTACTCCAAGTACAAGGCGGCGGCTGCGGCTGCGGCGGCGGTGGCGGCGGGGGAGCCTCTGCCCGCCCCGTACTACGACTGTCACTTCGCGCCCGAG
Seq A exon
GTGAGCGGCCGCCACGCCGCCGCCGCCGCCGCTCTGCTCTACGGGACCGGCTTCCCGCAGCCCGGCGGGGCGGGGGGCGGCGGCGGCGGCGCGGACTTTTACCATCCGGCCGGGGGGAGCCCCGCGGCCGCCTACCAGCCGCCTCCTCCTCCCCCCGCCGCGCCTCCGCCTCCTGCCCCCTGCAGCGGGGTTACCTGTCACGGGGAGCCCGCTAAATTTTACGGATACGATAACTTACAG
Seq C2 exon
AGACAGCAGATTTTTACGACACAGCAAGAGGCCGAGCTGGTACAATATCCTGACTGTAAATCGTCCAGTGCTAATATTGGCGAGGAACCAGACCACTTAAATCAGAGCTCGTCTCCCGCTCAAATGTTTCCCTGGATGAGACCGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000028128:ENSGALT00000038689:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.580
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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:
GAGAGCAGCGGAGAGGCA
R:
TGGTCTGGTTCCTCGCCAATA
Band lengths:
299-539
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]