GgaINT1014918 @ galGal4
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
minor histocompatibility protein HA-1 [Source:RefSeq peptide;Acc:NP_001026108]
Coordinates
chr28:2842568-2844039:+
Coord C1 exon
chr28:2842568-2842892
Coord A exon
chr28:2842893-2843895
Coord C2 exon
chr28:2843896-2844039
Length
1003 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
TCACCCCCTTTCTCCTGCAGACC
3' ss Score
12.69
Exon sequences
Seq C1 exon
GATCTGTCCCGCAAGGACTGCCTGGAAGCTCCCAGCCCCGGGGAGCTGCCCCCCACCAGCGTCAAACTCAGCAGCAGTCCCAGTGCCGTGGGCACCCTGAAGCGCCCCACCAGCCTCAGCCGCCATGCCAGCGCCGCCGGCTTCCCCCTCACCTCTGCCGGCCCCCGGGCCGTCCCTAAGGGCCACAAGACCCCCACATCCTACAGCCCCATGGAGGGTGGGGAGGGCCTTTTCATCGACGTGGAGGACATCTCCCAGCTGCTGACCGACGTGGCGCGGTTCGCGGATGCCCTGGAGAACCTTCGGGACGTGGTGCTGCGCGATG
Seq A exon
GTGAGCGCTGGGCTGGGTGCCCCCCAGGTGGCCACAGTGGGGGAGTGGGACTGGGGGACCACAGAACCCCCACGGCATCGCCTGCTAACCCATGGCACGGGGCTGTGGGGCTCCAGGGACGAAGGCTCCAGCGGGTGCAGAACCACCCCATGCCTGGCCCCATGGGAGGGGGTCCCTGCTGTGGGGGCTGTGCAGAGCTGGGGGCCCAGGGGCAGAGGGCGGTGGGTGGCTGCTGGGAGCTCAGAGCCAGGATAACACTGCTTCCTGCCCGCGAGCTATTTTCATCCGCCCGCTTTCCTGTTTACAGCGTAGCGGTGCCAGCTGCCTGGCAGCAGCCCTGGACCCCATGGGGCACCAGCACAGCCCCTGCTCCTGTCCCCTGGCCCTCCCTTTGGGATGGGGATGATGATGCTCAGCGCAGGAGCGGGGCTGTGGGGCTGTGGTCCCCGGGTGTGCAGGAAGCAGCCGCTACGGTTGCTCCCCACGGTGAGGTGGGGCTGCTGGGATCACATGGTGCCCTGTTCTCAGCAAACATGTTGACGTATCCTCACTCACCGTGGAAAACAGCCGTGCCCAGCTGTGGGGAACGTGGTGTGGGAAATGAGAGAGGGAGCAGAGGAAACCCCTTCCCCACCTGGAGCTGGGGGCCAGGCTGCTGTCCTCGGTGCATCCCTATGGGATGCTGAGCGCTGCCCAAAGGGGCTGCCAGCAGCCTGCCCTGAGCCCACACACTGCTTCCCCTGGCCCTGGGTGCTGGGTGGGGGCTGTGACGTGGTGTCAGACCCCCCCGGGGCACAGCTGAGCCAACGGATGGGGCAGGATGGCGCGGCCAGCAGGGAGGAGGGGAGGAAATGGGGAGGAAGTTCCCAAACCTCTTCCAAAGGAAAAATTTACTGCTGAGGAAAAAATGCCTCCAAGGTGTGACTGCGCCACGGCAGGGGTGAGCGTGGTACCAGGGGTGGGCTGTATGCAGGGGCAGAAGTTCACCCCCTTTCTCCTGCAG
Seq C2 exon
ACCCCAAGGAGTCCCAGCGGCCTCAGGCCCACGAGTGCCTGGGCGAAACGCTGCGGGTGCTGCGCCAGGTGATCAACAAATACCCACTGCTCAACACGCTGGAGACCCTGACAGCAGCGGGGACCCTCATCTCCAAAGTGAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.706 A=NA C2=0.286
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCAAACTCAGCAGCAGTCCC
R:
ATTTGTTGATCACCTGGCGCA
Band lengths:
346-1349
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]