GgaINT1014914 @ galGal4
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
minor histocompatibility protein HA-1 [Source:RefSeq peptide;Acc:NP_001026108]
Coordinates
chr28:2847376-2847934:+
Coord C1 exon
chr28:2847376-2847566
Coord A exon
chr28:2847567-2847785
Coord C2 exon
chr28:2847786-2847934
Length
219 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGA
5' ss Score
6.77
3' ss Seq
TCCTCCCTCCCCACCACCAGGTC
3' ss Score
9.74
Exon sequences
Seq C1 exon
GCCACCATTGCCTTCTATCAGATCATGCACATGCAGACAGCGCCGCTGCCCGTTTACTTCCAAACGCTGTGCGAGAGCAGCAAGCTGTACGACCCCGGGCAGCAGTACGCCTCGCACGTCAAGCAGCTGCAGAGAGGGGATGAGCCCGACACGCAGTACGACTTCGAGCCTTACGTGTCCCACAGCGCCTG
Seq A exon
GTAGGAGAGGAGGGGGAAATCACTGCTCCTTTGCGCCAACCTCTGCTGCAGCCTGAGAGCGCCCTGGAGGGGTCCTGCAGGCAGAGGCTGCATGGTGTTGGAGCAGAGGGCTTCCATCCCAGCTCCGGTGGAGAGCTGCTGCTTTTGGAGTGGCTTTTCTGGCATCCCTGTCCCCACGTCCTCTCGGACACGGCCCTTCTCCTCCCTCCCCACCACCAG
Seq C2 exon
GTCCCCCTTCACCCGCGCGCGGAAGGGCAGCTTCAACGCCAGCGACTTCTCCAGCAGCGGTGGCTCTGATGGGGCCGGACTGCCCAGGGATGGGAGCAGCACGGAGGGACCCAGAGAGACCCAGGGTGGGACGCTGGCAGAGCGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.344 A=NA C2=0.784
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:
GCCACCATTGCCTTCTATCAGA
R:
TGCTGCTCCCATCCCTGG
Band lengths:
292-511
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]