GgaINT0145366 @ galGal3
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
NA
Coordinates
chr28:2389949-2390223:+
Coord C1 exon
chr28:2389949-2390059
Coord A exon
chr28:2390060-2390139
Coord C2 exon
chr28:2390140-2390223
Length
80 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
AGCTGCACCATTTGCTTCCGCAG
3' ss Score
-6.39
Exon sequences
Seq C1 exon
ACCAGCATGCCCTTCCTGTCCATCTACCTGCTGGCATTGGAGCAGGACATGGAGTACGGCACGTCGGTCCTGCAGACCGTCACCACGCTGCAGCACCAGACCTTCCTGCAG
Seq A exon
GTGAGCGGGCGGTGCGGGGTGCAGCTCCTGCCAGGGCTCCATGCAGGGCTGTGCTTTGCCAGCTGCACCATTTGCTTCCG
Seq C2 exon
CAGCCGCTGACTGTGAGGCGCCTGGAGCACGAGAAGAGAAGGAAGGAGATCAAGGAGCAGTGGCACCGCGCACAGAGGAAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:6
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=0.559
Domain overlap (PFAM):
C1:
PF0061118=FCH=PD(35.2=86.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCCTTCCTGTCCATCTACCT
R:
GTGCCACTGCTCCTTGATCTC
Band lengths:
169-249
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]