GgaINT0145368 @ galGal3
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
NA
Coordinates
chr28:2392741-2393296:+
Coord C1 exon
chr28:2392741-2392920
Coord A exon
chr28:2392921-2393109
Coord C2 exon
chr28:2393110-2393296
Length
189 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGA
5' ss Score
6.03
3' ss Seq
ACCTCCCCTCTCCTCTCCAGGCA
3' ss Score
10.78
Exon sequences
Seq C1 exon
CAAGACGCGGAGGTGAACCTGCGGAAGGCCAAGCAGGTGTACATGCAGCGCAGCGAGGAGCACGATAAGGCCAAATATGTGACAGTGAAAGCAGAGGAGGAGCAGCAGAGCACCGCCAGCAGCATCACCACCAAAACCCTGGACAAGAAGAGGCGGCTGGAGGAGGAGGCCAAGAACAAG
Seq A exon
GTGGGAGCCCAGCAGCTCCGAGCACTGCTTTGCAGGGACCTTCTTGCTCCTTGGTGTCCCAGCATAGGGCAGCCCAGAACCACGGGGGCTTAAAGCTGACCTCACACACAGAGCGGGTCCAGCACAGGGGGGCGGCTCCCATCTGATTCCACACCTCTGAGCAGCTTCCACCTCCCCTCTCCTCTCCAG
Seq C2 exon
GCAGAAGAGGCCATGGCCACCTACCGGACCTGCGTGGCGGATGCCAACACGCAGAAGCAGGAGCTGGAGGACACCAAGGTGAACTCCCTGCGCCAGATCCATGAGCTGATCAAGCAGAGCGACCAGGTCATCAAGCTGGTGAGTTGGGACTGCTGGGGGGGCTGGGGGCCGTGCCACAGCCGGGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=NA C2=0.460
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGAAAGCAGAGGAGGAGCA
R:
CAGTCCCAACTCACCAGCTTG
Band lengths:
249-438
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]