GgaINT1014912 @ galGal4
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
minor histocompatibility protein HA-1 [Source:RefSeq peptide;Acc:NP_001026108]
Coordinates
chr28:2846063-2846825:+
Coord C1 exon
chr28:2846063-2846143
Coord A exon
chr28:2846144-2846645
Coord C2 exon
chr28:2846646-2846825
Length
502 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
CGCTGCTGCTCTGTTGGCAGCAA
3' ss Score
5.61
Exon sequences
Seq C1 exon
CCGCTGACTGTGAGGCGCCTGGAGCACGAGAAGAGAAGGAAGGAGATCAAGGAGCAGTGGCACCGCGCACAGAGGAAGCTG
Seq A exon
GTGAGGCTTGAAGGCATCCATCCATGCATGCATCCATCCAGAGATGCATCCATCCATGCATCCATCCATGCATGTTGTTCCTCATTGCCCATCCATCCATTCATCCATCAAATCCATAGATGCATCCATCCATGCATCCATGCATCCATCCATGCATGTCATTCCTCATTGTCCATCCATCCGTCCATCCATCCATAGATGCATCCATCCATGCATCCATCCATGCACGTCATTCCTCATTGCCCATCCATCCATCCATCCACAGATGCATCCATCCATGCATCCATCCATGCATGTCATTCCTCACTGTCTGTCCATCCATCCATAGATGCATCCATCCATGCATCCATCCATGCATGTCGTTCCTCATTGTCCGTCCATCCATCCATCCATCCATAGATGCATCCATCCATGCATCCATCTATCTACCCATCCCGGGCAGCTTCATGCAGGGTGACCCTTGCAGGGCTCAGCCCTCACCCCGCTGCTGCTCTGTTGGCAG
Seq C2 exon
CAAGACGCGGAGGTGAACCTGCGGAAGGCCAAGCAGGTGTACATGCAGCGCAGCGAGGAGCACGATAAGGCCAAATATGTGACAGTGAAAGCAGAGGAGGAGCAGCAGAGCACCGCCAGCAGCATCACCACCAAAACCCTGGACAAGAAGAGGCGGCTGGAGGAGGAGGCCAAGAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.519 A=NA C2=0.600
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:
CTGACTGTGAGGCGCCTG
R:
CTTGTTCTTGGCCTCCTCCTC
Band lengths:
258-760
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]