GgaINT1014915 @ galGal4
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
minor histocompatibility protein HA-1 [Source:RefSeq peptide;Acc:NP_001026108]
Coordinates
chr28:2847786-2848133:+
Coord C1 exon
chr28:2847786-2847934
Coord A exon
chr28:2847935-2848058
Coord C2 exon
chr28:2848059-2848133
Length
124 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
AGCTCTTCCTCCCACAGCAGGGA
3' ss Score
4.91
Exon sequences
Seq C1 exon
GTCCCCCTTCACCCGCGCGCGGAAGGGCAGCTTCAACGCCAGCGACTTCTCCAGCAGCGGTGGCTCTGATGGGGCCGGACTGCCCAGGGATGGGAGCAGCACGGAGGGACCCAGAGAGACCCAGGGTGGGACGCTGGCAGAGCGCAGAG
Seq A exon
GTGAGAAAAGCCCGGCCCCGAGCACTGCCTGCAGCAAGCAAACGCTTCTGGCATCCGAGCTGCTCTGTGCGGCATCCCCGAGCACCGGGACAGCCCCAACGCAGAGCTCTTCCTCCCACAGCAG
Seq C2 exon
GGAGGGGACACCAGGTGCACAAATCCTGGCCGACCTCCACCTCCGAAGCCGACAGCAGCCTGGATTCCAGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.784 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAAGGGCAGCTTCAACG
R:
GAATCCAGGCTGCTGTCGG
Band lengths:
197-321
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]