GgaINT0145364 @ galGal4
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
minor histocompatibility protein HA-1 [Source:RefSeq peptide;Acc:NP_001026108]
Coordinates
chr28:2845345-2845770:+
Coord C1 exon
chr28:2845345-2845482
Coord A exon
chr28:2845483-2845705
Coord C2 exon
chr28:2845706-2845770
Length
223 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGA
5' ss Score
6.04
3' ss Seq
TTCCAACCTTTCTCTTCCAGAAA
3' ss Score
10.22
Exon sequences
Seq C1 exon
TCCGTCCGGCGGCTGAGGAGGTGGATGTGATGCTGCAGCGCTGCGAGGGAGGTGTGGATGCAGCCCTGCAGTATGCCAAGAACATCTCCAAGTACATGAAGGACCTCATCGGGTACCTGGAGAAAAGGACGGCGCTGG
Seq A exon
GTGAGACGTGGGGGGGGGGGGAGGGGAGGGGTCTGTGCACTGTGGGGTGGCCCTGGGATGGGGGGATGGTTCTGAGAGCACTGCATGGGGCTGAGGGACTCAGAGCTGCTGGATCTGGAGGTGGGAGATTCCTGCAGCTCTTGGCTTGTGTTGAAGAAGGAACCCGACGAGCACAGAAACCCTTCTGCTTCGTCCCTCTTCACTTCCAACCTTTCTCTTCCAG
Seq C2 exon
AAATGGAGTTCGCCAAAGGGCTCCAGAAAATGGCAAACAGCTGCAAGCAAACCTTCACGCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.045
Domain overlap (PFAM):
C1:
PF0061118=FCH=PU(39.6=76.6)
A:
NA
C2:
PF0061118=FCH=FE(23.1=100)
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:
TGAGGAGGTGGATGTGATGCT
R:
CTCCTGCGTGAAGGTTTGCTT
Band lengths:
190-413
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]