GgaINT1014913 @ galGal4
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
minor histocompatibility protein HA-1 [Source:RefSeq peptide;Acc:NP_001026108]
Coordinates
chr28:2847015-2847566:+
Coord C1 exon
chr28:2847015-2847152
Coord A exon
chr28:2847153-2847375
Coord C2 exon
chr28:2847376-2847566
Length
223 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
GTCCCCGTTGTTTTTTTTAGGCC
3' ss Score
10.78
Exon sequences
Seq C1 exon
GCAGAAGAGGCCATGGCCACCTACCGGACCTGCGTGGCGGATGCCAACACGCAGAAGCAGGAGCTGGAGGACACCAAGGTGAACTCCCTGCGCCAGATCCATGAGCTGATCAAGCAGAGCGACCAGGTCATCAAGCTG
Seq A exon
GTGAGTTGGGACTGCTGGGGGGGCTGGGGGCCGTGCCACAGCCGGGGGGGGGGGGTGGGGGATCCAGAGCTGCTCAGCCCCATGCATGGGGGAGCCAAGGGCAGGGCTGCAGCCCCAGCCCCACTCAGCGCTCTGATTCTCCACCTGGCAGCTCCGTGCCTCTCCTCCCCCCGCGTCACCCCATCACTCCAACCCTGACTTTCGTCCCCGTTGTTTTTTTTAG
Seq C2 exon
GCCACCATTGCCTTCTATCAGATCATGCACATGCAGACAGCGCCGCTGCCCGTTTACTTCCAAACGCTGTGCGAGAGCAGCAAGCTGTACGACCCCGGGCAGCAGTACGCCTCGCACGTCAAGCAGCTGCAGAGAGGGGATGAGCCCGACACGCAGTACGACTTCGAGCCTTACGTGTCCCACAGCGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.413 A=NA C2=0.344
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:
CCATGGCCACCTACCGGA
R:
GACACGTAAGGCTCGAAGTCG
Band lengths:
307-530
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]