GgaINT1014923 @ galGal4
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
minor histocompatibility protein HA-1 [Source:RefSeq peptide;Acc:NP_001026108]
Coordinates
chr28:2845013-2845482:+
Coord C1 exon
chr28:2845013-2845091
Coord A exon
chr28:2845092-2845344
Coord C2 exon
chr28:2845345-2845482
Length
253 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CCTCCATTCCCACATCACAGTCC
3' ss Score
5.93
Exon sequences
Seq C1 exon
TCTATGGAGAGCCTCTATGGGGGGATCCCTGGGCCTGGAGGGGATGGTGTGCCCTCGGGCATGGAGAGCTATGACACAG
Seq A exon
GTGAGCAAGCAGTCACTGGAGTGGGACTTGGAGTGGTCAGACAGCAGAAATGGGCTCTGCCATCGCCACTTGGATACGTGGACAGCATCCTGGGCTGAGGTGCCCCTGGGGGCACAGCTGAGAGGAGATGGCAGAGCTGCTGCTGTGGGCATTGGGGTCTTCCTGGCTATGCTGGGGGTCCTGGGACCGGCCCAGCAATCAGCAGCAGCACGGATTGGGATCACTCCCCTTCCCCTCCATTCCCACATCACAG
Seq C2 exon
TCCGTCCGGCGGCTGAGGAGGTGGATGTGATGCTGCAGCGCTGCGAGGGAGGTGTGGATGCAGCCCTGCAGTATGCCAAGAACATCTCCAAGTACATGAAGGACCTCATCGGGTACCTGGAGAAAAGGACGGCGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.852 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0061118=FCH=PU(39.6=76.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTATGGAGAGCCTCTATGGGGG
R:
CGCCGTCCTTTTCTCCAGGTA
Band lengths:
212-465
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]