GgaINT0000526 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:367491-368075:+
Coord C1 exon
chr8_random:367491-367628
Coord A exon
chr8_random:367629-367953
Coord C2 exon
chr8_random:367954-368075
Length
325 bp
Sequences
Splice sites
5' ss Seq
CTGGTTGTT
5' ss Score
-3.89
3' ss Seq
CATGCTCTTAAAATTCACAGGAG
3' ss Score
5.78
Exon sequences
Seq C1 exon
GTCCAGCGCTGAGAAAGCTTGTTTCTATTCTGAGCCCAGTCTATTGGACAACTGCAAAAGAAGTTGGAGAAGCAATGAATGGGTTTACGCTCACTGACGCGATCTTCAAGAGAGAAACCCAAGTGGAATTTGCAACTG
Seq A exon
GTTGTTACCTGTGATGCACCATCTCTTTCCAGCAAGCATGATATATACTGCATCCCTTTAAAAGGATCACATCACCAGTGCTGAATTTTGAATCTTAATGACTATGCTGCTATTTTCTGAGTGTCTGTGGCTTTCAGAGTTTTAAATACAGCTTTTAGAGTTTTGATTGGGAACACATAATGCTTATGTTATAGGCATGATACCATGCTTTATAAAAATATTAGCATGAAATAAGTGGTCAAGTGATCCAATTCAGATAGTCCTTGGCTTACAGGAGTCCCTGGTTAGGATGTTTTATAAATCTGCATGCTCTTAAAATTCACAG
Seq C2 exon
GAGAGGTTCTGCGAATGACTCACATTGCCCGGGGGTTGGATTCTGATGGAGCCTTACTGCTGGATGTTGTTGTGAATGGCCATGTTCTTCAGCTGCAGCCACTAGCTAATGTTAACATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:95
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=0.000
Domain overlap (PFAM):
C1:
PF074747=G2F=FE(24.5=100)
A:
NA
C2:
PF074747=G2F=FE(21.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGCTTGTTTCTATTCTGAGCCCA
R:
CTTCATGTTAACATTAGCTAGTGGCT
Band lengths:
246-571
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]