GgaINT0145375 @ galGal3
Intron Retention
Gene
ENSGALG00000002559 | HMHA1
Description
NA
Coordinates
chr28:2397127-2397732:+
Coord C1 exon
chr28:2397127-2397368
Coord A exon
chr28:2397369-2397494
Coord C2 exon
chr28:2397495-2397732
Length
126 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
AGCCTCCGCTCCTCCTCCAGGAT
3' ss Score
9.69
Exon sequences
Seq C1 exon
CTGCCGGAGCCCATCGTGCCGTTCCGAATGTACAACGCGCTGATGGGAGCGGCCAAAGAGAGCCTGCAGGGCGGCAGCGACGCCAAAGGGAGGAGTGGGAAGGGGGGTCCGGAGCTGATGGACAGAGGGGCCGACACCGACCGCGTGGTGGTGAACCTCGTGCTGAAACTGAAGGAGCTGCTGAAGGAGCTGCCGTGGGAGAACACGGCCACGCTGCGGTACCTCCTGCAGCACCTGCGGAG
Seq A exon
GTGAGGAGGGGGGGATCCGGGCTGGGGGACGTCCCTTTTGGCCCCACGGTGGGAAGGGGATGGCAAAGGAGCGCAGCGCCCATCGCGCCGCCGCCCGCTCTCACGGAGCCTCCGCTCCTCCTCCAG
Seq C2 exon
GATCGTGGAGGTGGAGCAGGACAACAAGATGACCTCCAGCAATCTGGGCATCGTCTTCGGGCCGACGCTGCTTCGGCCCCGGCCCACGGATGCCACCATCTCCCTGTCCTCGTTGGTGGATTACCCCCACCAGGCGCGCGTCATCGAGGCGCTCATCATCTTCTACCCCACCATCTTCGAGGACAAAGACAGCAAACTGACCGCCGAGGGCAGCGAATTCAGCGCGGATCGCGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002559:ENSGALT00000023142:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.291 A=NA C2=0.113
Domain overlap (PFAM):
C1:
PF0062022=RhoGAP=PD(32.0=63.3)
A:
NA
C2:
PF0062022=RhoGAP=PD(18.0=40.0)
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:
ATCGTGCCGTTCCGAATGTAC
R:
CTTGTTGTCCTGCTCCACCTC
Band lengths:
258-384
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]