GgaINT0145366 @ galGal4
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
minor histocompatibility protein HA-1 [Source:RefSeq peptide;Acc:NP_001026108]
Coordinates
chr28:2845869-2846143:+
Coord C1 exon
chr28:2845869-2845979
Coord A exon
chr28:2845980-2846062
Coord C2 exon
chr28:2846063-2846143
Length
83 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGCACCATTTGCTTCCGCAGCCG
3' ss Score
8.29
Exon sequences
Seq C1 exon
ACCAGCATGCCCTTCCTGTCCATCTACCTGCTGGCATTGGAGCAGGACATGGAGTACGGCACGTCGGTCCTGCAGACCGTCACCACGCTGCAGCACCAGACCTTCCTGCAG
Seq A exon
GTGAGCGGGCGGTGCGGGGTGCAGCTCCTGCCAGGGCTCCATGCAGGGCTGTGCTTTGCCAGCTGCACCATTTGCTTCCGCAG
Seq C2 exon
CCGCTGACTGTGAGGCGCCTGGAGCACGAGAAGAGAAGGAAGGAGATCAAGGAGCAGTGGCACCGCGCACAGAGGAAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.519
Domain overlap (PFAM):
C1:
PF0061118=FCH=PD(35.2=86.5)
A:
NA
C2:
NO
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:
TGCCCTTCCTGTCCATCTACC
R:
GTGCCACTGCTCCTTGATCTC
Band lengths:
167-250
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]