GgaINT0145372 @ galGal4
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
minor histocompatibility protein HA-1 [Source:RefSeq peptide;Acc:NP_001026108]
Coordinates
chr28:2849112-2849587:+
Coord C1 exon
chr28:2849112-2849275
Coord A exon
chr28:2849276-2849398
Coord C2 exon
chr28:2849399-2849587
Length
123 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATG
5' ss Score
8.73
3' ss Seq
AGCCCTTCCCTGTCCCCCAGTGC
3' ss Score
8.84
Exon sequences
Seq C1 exon
GCATCAATGGGATCACCCCGGAGATGACGGCTCCCACGGGGCCCTTCCGGAACGTGGGCCTGTCCAGGGCAGCTCAGACCCACCGGCTGAGGAAGCTGAGGGCCCCCTCCAAGTGCCGGGAGTGCAACAGCTACGTGTACTTCCAGGGGGCAGAATGTGAGGAG
Seq A exon
GTAATGCTGGGGATGTGGGAGGAGGAAGAGGTGGGGGGGGGACCACCCTGTGCCCACAGCGCTGCCACGTGTGCCCTCCCAGCCCCGCTGCCCCCCACCTCCGAGCCCTTCCCTGTCCCCCAG
Seq C2 exon
TGCTACCTGGCGTGCCACAAGAAGTGCTTGGAGACCTTGGCCATCCAATGCGGGCACAAGAAGCTCCAGGGGAAGCTGCAGCTTTTCGGGCAGGACTTCCTGAAGGCGTCCCAGGGCAGCGCGGACGGCATCCCCTTCATTGTGAAGAAATGCATCTCTGAGATTGAGAAGCGGGCGCTGAAAACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.436 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0013017=C1_1=PU(57.1=50.9)
A:
NA
C2:
PF0013017=C1_1=PD(38.8=30.2),PF0062022=RhoGAP=PU(18.6=28.6)
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:
CTGTCCAGGGCAGCTCAGA
R:
TTCACAATGAAGGGGATGCCG
Band lengths:
251-374
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]