GgaINT0145365 @ galGal4
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
minor histocompatibility protein HA-1 [Source:RefSeq peptide;Acc:NP_001026108]
Coordinates
chr28:2845706-2845979:+
Coord C1 exon
chr28:2845706-2845770
Coord A exon
chr28:2845771-2845868
Coord C2 exon
chr28:2845869-2845979
Length
98 bp
Sequences
Splice sites
5' ss Seq
GAGGTACGG
5' ss Score
9.4
3' ss Seq
CTGCTTTTGTCGTTCCTCAGACC
3' ss Score
9.76
Exon sequences
Seq C1 exon
AAATGGAGTTCGCCAAAGGGCTCCAGAAAATGGCAAACAGCTGCAAGCAAACCTTCACGCAGGAG
Seq A exon
GTACGGCCACAATAGAGCTCCCCGGCTCCGAGATGTCCCGGAGCTGACAGAATCAGCCTCGTGCTGAGCCTCAGGGTGCTGCTTTTGTCGTTCCTCAG
Seq C2 exon
ACCAGCATGCCCTTCCTGTCCATCTACCTGCTGGCATTGGAGCAGGACATGGAGTACGGCACGTCGGTCCTGCAGACCGTCACCACGCTGCAGCACCAGACCTTCCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.045 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061118=FCH=FE(23.1=100)
A:
NA
C2:
PF0061118=FCH=PD(35.2=86.5)
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:
AAATGGAGTTCGCCAAAGGG
R:
AGGAAGGTCTGGTGCTGCAG
Band lengths:
172-270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]