GgaINT0145368 @ galGal4
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
minor histocompatibility protein HA-1 [Source:RefSeq peptide;Acc:NP_001026108]
Coordinates
chr28:2846646-2847152:+
Coord C1 exon
chr28:2846646-2846825
Coord A exon
chr28:2846826-2847014
Coord C2 exon
chr28:2847015-2847152
Length
189 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGA
5' ss Score
6.03
3' ss Seq
ACCTCCCCTCTCCTCTCCAGGCA
3' ss Score
10.78
Exon sequences
Seq C1 exon
CAAGACGCGGAGGTGAACCTGCGGAAGGCCAAGCAGGTGTACATGCAGCGCAGCGAGGAGCACGATAAGGCCAAATATGTGACAGTGAAAGCAGAGGAGGAGCAGCAGAGCACCGCCAGCAGCATCACCACCAAAACCCTGGACAAGAAGAGGCGGCTGGAGGAGGAGGCCAAGAACAAG
Seq A exon
GTGGGAGCCCAGCAGCTCCGAGCACTGCTTTGCAGGGACCTTCTTGCTCCTTGGTGTCCCAGCATAGGGCAGCCCAGAACCACGGGGGCTTAAAGCTGACCTCACACACAGAGCGGGTCCAGCACAGGGGGGCGGCTCCCATCTGATTCCACACCTCTGAGCAGCTTCCACCTCCCCTCTCCTCTCCAG
Seq C2 exon
GCAGAAGAGGCCATGGCCACCTACCGGACCTGCGTGGCGGATGCCAACACGCAGAAGCAGGAGCTGGAGGACACCAAGGTGAACTCCCTGCGCCAGATCCATGAGCTGATCAAGCAGAGCGACCAGGTCATCAAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.600 A=NA C2=0.413
Domain overlap (PFAM):
C1:
NO
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:
GAAGGCCAAGCAGGTGTACAT
R:
AGTTCACCTTGGTGTCCTCCA
Band lengths:
242-431
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]