DreINT0091305 @ danRer10
Intron Retention
Gene
ENSDARG00000060683 | lrsam1
Description
leucine rich repeat and sterile alpha motif containing 1 [Source:ZFIN;Acc:ZDB-GENE-060526-97]
Coordinates
chr5:32267209-32267539:-
Coord C1 exon
chr5:32267470-32267539
Coord A exon
chr5:32267376-32267469
Coord C2 exon
chr5:32267209-32267375
Length
94 bp
Sequences
Splice sites
5' ss Seq
ATCGTAAGA
5' ss Score
6.29
3' ss Seq
TGTCATCTTTTTCTCTTTAGCTT
3' ss Score
10.25
Exon sequences
Seq C1 exon
TTGGGGATCAACGAGGTTGGCGTGCAGAAAGCTCTTCTCCACTGGGCCAGAGATCGAACTCTGTCTGATC
Seq A exon
GTAAGAATCATCTTGAGGACATCATATTTTTTAATAGGTGACATTTGTGAATTCTGTTCGGTGACTGAGAGCATTGTCATCTTTTTCTCTTTAG
Seq C2 exon
CTTTGCCGAAAACACTGAAAGAGATGGAGGAAGCTGGTCCATTCGCTCAGAGTGTTCCACTTCCACATCAGCTCACTCCTCCACTGACCCCCAGTGCACCTCTAACCCCCACGACCCCAAATCCTGACCGCTTCAACTCTGAGTGTGTTGTCTGCATGGAGCTTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060683:ENSDART00000085769:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.042 A=NA C2=0.536
Domain overlap (PFAM):
C1:
PF0053625=SAM_1=PD(28.8=70.8)
A:
NA
C2:
PF139201=zf-C3HC4_3=PU(22.2=17.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAAGCTCTTCTCCACTGGGC
R:
TTGAAGCGGTCAGGATTTGGG
Band lengths:
180-274
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]