GgaINT0124728 @ galGal3
Intron Retention
Gene
ENSGALG00000008819 | LRSAM1
Description
NA
Coordinates
chr17:1927784-1928790:-
Coord C1 exon
chr17:1928642-1928790
Coord A exon
chr17:1928374-1928641
Coord C2 exon
chr17:1927784-1928373
Length
268 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
TCTGCTCTCTCTTTCCACAGGCC
3' ss Score
14.16
Exon sequences
Seq C1 exon
AGCTGCTGAGGACGGAGGACGCTGAGATCCCTGCAGCTGCACAACCCAGTGCCCCTGAGGAGGAGGCCCCGAGTTCTGTGGTCCCCACCGCTCCCCTGCTGCAGTGGGATGAGAAGAAGTCAGAGTGCGTTGTCTGCATGGAGCAGGAG
Seq A exon
GTGAGAACCCAGCATGTGTGCTGCCAGAGCAGGGGTGAGTGAGGGCCAGCCGGGACGTGGCACTGGGCAGTGCTCTTCCTGAGGCCTGGTTTCACTGTGCATTCTTTGCACAGTGCAGGGGCTCAGGCTGCTGGCACTGTCTACCACTCTGACAGCTGTAGATGTTGCCCATCATCTCCAGCTTCCTCCTGTACTTTGTCTAAGTGTGGTGGTGCTGAGATTATGGCACAACAGTACTGTTCATGTCTTCTGCTCTCTCTTTCCACAG
Seq C2 exon
GCCCAGATGATTTTCCTGCCTTGTGGCCATGTGTGCTGCTGCCAGACCTGCTGCAAGCGGCTACAGACCTGTCCCCTGTGCCGCAGGGACATCACACAGCACGTCCGCATCTTCTACAGCAGCTAGGCGGGCTGGAGGAAGGCATGGCTGCCCAGCACCACCCTCATCACTCCGTCCCAGGGCAAGGCTCTTCTGTCAGTATTAAATACACTCGCACAGCATGACCAGCGCTGCCCTCACCCTGCATGCAGCCCTGGCTGGCTGCTGGCTGCACTCAGGGCTCTCAGCAGCCCTCCACCTTCCCGGTGGCTTTCCAGCCTTTGCCTTGGGTGCTTTCTTCATCTGCATCCACCATCCAGCCTGTTTGCCCAGCCTGAGAGCACTGGGTGATGGCACTGGGTATAATGGTGCTCGCTCTTCTCTGGCTGTATATTTGCCATCGGAATTGCCTGTTGCTCAGCAGGGATGCAGTTAGTGCCATTGCTTCTGAAGCCACTGGGACCCTGCAGCTGCTCTGTTGTGGCCACGGCACTGCCCTTCTGCTCTGGTGAATTCTCCACCAGGAGGACTTGGCCGGGGACTTGTTATGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008819:ENSGALT00000014334:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.340 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF139201=zf-C3HC4_3=PU(23.9=22.0)
A:
NA
C2:
PF139201=zf-C3HC4_3=PD(71.7=78.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
CCGAGTTCTGTGGTCCCCA
R:
GGTCATGCTGTGCGAGTGTAT
Band lengths:
307-575
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]