GgaINT0145374 @ galGal4
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
minor histocompatibility protein HA-1 [Source:RefSeq peptide;Acc:NP_001026108]
Coordinates
chr28:2849892-2851201:+
Coord C1 exon
chr28:2849892-2850029
Coord A exon
chr28:2850030-2851057
Coord C2 exon
chr28:2851058-2851201
Length
1028 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGG
5' ss Score
6.92
3' ss Seq
TCGCGCTGTTCTCCCTGCAGCTG
3' ss Score
11.54
Exon sequences
Seq C1 exon
GGCATCTATCGAGTGAACGGCGTGAAGACCCGCGTGGAGAAGCTCTGCCAGGCCTTTGAGAACGGGAAGGAGTTGGTGGAGCTGTCGCAGGCGTCCCCACACGACATCAGCAACGTGCTGAAGCTCTACCTGAGACAG
Seq A exon
GTGGGGGGGGGGGGGGGGTCAGGGTAGGGGTGATTCCAGAGCCAGGCCTGGTGCCAGCCGGGCGTCTGGAATGGGCAGTCCTGCTGCAAATCGGGCTGGCAGCTGCCTGCTGGTGACGGAGTGGGTCAGAACCCCCCGTGTCCAGGCTGGCCTGGTGGAGGTTTGTGCAGGAAGGGCTCTCCCCGAGCAGCAGTCTTACTGCGCACCCCAGGGCGGTTCCAGCTGTCTGCTCCCAGCTGCGGCAGCGAAGTCCCTGCCCACAGCAACACCACGCAAAGTGCTGGACCGTCCCTCCCCTTTGCAGCTGGGGAAGCGGCACGAGAAAGGGAAGTGGCCGTAAAGGTCGCCCCGCAGCAGTGCCGGGCTCGGCTCGCTTCTCGCAGCCCTCTGCCTGCAGCACCACCTCTGCCATCAGCTCACCGCTCCGGCACCGAAACTCAACCCCCGACCCACATCCTCAAACGGGGCAGGAGGAGAGGAAGCAGCTTCTCTCTGCAGCCCCGCGGCTTAACCCTTTGTGTCGGAGGCAGGGGGAGGCTTCTCCCCACATCCCCACGCAGCAGAGAGGGGCTGTGAGCTCCTGGACAGGGCGAGCAGAGCGCAAACAGAGGAGGAGAGCGGCCCTGCGCTGCGATCCGGGCTCGGTGCACTGCAGGGGAATCGGTTTAAAGTCCCCCTGCAGGAGCGCTGCTCCGCTGCAAAGCAATCCATCCCCAGCAGGCATCTGATGGAGGCACTTTGCAAACAGCGGCAGCGCTGCAGAACCTCCAGGCGGTGCACGAATGCGCTCCGGGTGCTGCGTGCAAACTTGAAAGCAAAGCGCTCCTCCTCGACAGCCCCGGCGCCGATTGCATCTCACCTCCTCCTCCACCCAGGGAACAATTAGCGCCGGCCTAATGAACGGCCTCTTATCTATGGGGAAACCACACACCCACCCCAGGACGGGGTTTTTCTGGGGAGGGGGGAGGAAATGGGCATTCTCCATCTGGAGACCCTCCAGGCTTCACCTCGCGCTGTTCTCCCTGCAG
Seq C2 exon
CTGCCGGAGCCCATCGTGCCGTTCCGAATGTACAACGCGCTGATGGGAGCGGCCAAAGAGAGCCTGCAGGGCGGCAGCGACGCCAAAGGGAGGAGTGGGAAGGGGGGTCCGGAGCTGATGGACAGAGGGGCCGACACCGACCGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:19
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=0.583
Domain overlap (PFAM):
C1:
PF0062022=RhoGAP=FE(46.4=100)
A:
NA
C2:
PF0062022=RhoGAP=PD(32.0=64.6)
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:
GGCATCTATCGAGTGAACGGC
R:
CGGCCCCTCTGTCCATCA
Band lengths:
271-1299
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]