GgaINT0145361 @ galGal3
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
NA
Coordinates
chr28:2386164-2387354:+
Coord C1 exon
chr28:2386164-2386372
Coord A exon
chr28:2386373-2386866
Coord C2 exon
chr28:2386867-2387354
Length
494 bp
Sequences
Splice sites
5' ss Seq
ACGGTACGG
5' ss Score
9.91
3' ss Seq
GCTGTGCTGTGCTTCTGCAGGAT
3' ss Score
10.19
Exon sequences
Seq C1 exon
ATCCCCATCCCCTCCCCACGGCGCTCCCTGGCTGAGGGGTCTATGGGTGGGCGCAGCCTGCGGGCGCTGGGGCTGGCGGGATGCTCGGCCGGGCGGCGGGGCGGAACAGCTACAGCCCCTACGCTGCCGGGCGCCGCAGGACGGGGAAGGCCACCTCTCCAAAGCACTCCCTGGACTCGCTGCCCCGCTCGCCCTCCGTGCGGCTGACG
Seq A exon
GTACGGGGATGGTGGGAGGGAGCAGTGCCCACATCAGCTCTGCTCGGGGTGCTGCCATCTGCGTGGCCTCGCGTTGCCGGGCAGGATTGGAGGAAGGTGCTGCAACGTCTGCCCCGTTGGTGCCAAATCTGCTTCTGGCCCCAGCACGATTATGTCACGGCTGAGGCTGCGTGGGGCTGGAGGGGTGTGGGACACATCCCCATCAGTGATGGCTTTGGGGCATGGGGTCTCGGGAGGTGCTATCAGCCTCTCCCTCGGGGCGATTTCACCCCTAGAAATCAGGGCTCCGTGTGCCTGCAGCAATTCTGCATTGTCTGCTATTGGCGGCCCGGGAGGTGTCCCCATCCCTGCAGTGCTAAAGGACGTGCTGGACTTGGGGCAGGCAGAAAAAGAGGAAGGGATGTGTGGGGCCGCATCCCTCTGTCAATGGAGCCCGCCATCCTCGGGCAGTGCCATCCCCAGGGCAGTGCTCACGCTGTGCTGTGCTTCTGCAG
Seq C2 exon
GATCTGTCCCGCAAGGACTGCCTGGAAGCTCCCAGCCCCGGGGAGCTGCCCCCCACCAGCGTCAAACTCAGCAGCAGTCCCAGTGCCGTGGGCACCCTGAAGCGCCCCACCAGCCTCAGCCGCCATGCCAGCGCCGCCGGCTTCCCCCTCACCTCTGCCGGCCCCCGGGCCGTCCCTAAGGGCCACAAGACCCCCACATCCTACAGCCCCATGGAGGGTGGGGAGGGCCTTTTCATCGACGTGGAGGACATCTCCCAGCTGCTGACCGACGTGGCGCGGTTCGCGGATGCCCTGGAGAACCTTCGGGACGTGGTGCTGCGCGATGGTGAGCGCTGGGCTGGGTGCCCCCCAGGTGGCCACAGTGGGGGAGTGGGACTGGGGGACCACAGAACCCCCACGGCATCGCCTGCTAACCCATGGCACGGGGCTGTGGGGCTCCAGGGACGAAGGCTCCAGCGGGTGCAGAACCACCCCATGCCTGGCCCCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.779
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAACAGCTACAGCCCCTA
R:
CACGTCGATGAAAAGGCCCTC
Band lengths:
351-845
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]