DreINT0091660 @ danRer10
Intron Retention
Gene
ENSDARG00000026281 | lyrm1
Description
LYR motif containing 1 [Source:ZFIN;Acc:ZDB-GENE-040718-210]
Coordinates
chr24:39626200-39626506:-
Coord C1 exon
chr24:39626348-39626506
Coord A exon
chr24:39626261-39626347
Coord C2 exon
chr24:39626200-39626260
Length
87 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGA
5' ss Score
7.75
3' ss Seq
TCTCCTCCACCCCTTTATAGATA
3' ss Score
9.75
Exon sequences
Seq C1 exon
AGGGTCCAGATGTCTCGTGCAAATGTGCTGTCTCTGTATCGGCGGGTTCTCCGCATTGCACGCAGCTGGAAGGCTCAGTCTTCAATACCAAAGGACACTGACACTGAGAAGAAATACATCACGCAGGAGGCTCGAACCCTTTTCAGACAGAACCAGCAG
Seq A exon
GTGCGACTGACTTCATATCATCCTGTGAGCTGTCATAGATCTCTTTTCTATCACATGTGTTCTTATCTCTCCTCCACCCCTTTATAG
Seq C2 exon
ATAACAGACCCAGAATCAATCCAGAGATGCATTGAAGAGTGTGAAGCTCGGATAGAAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026281:ENSDART00000031486:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.390 A=NA C2=0.032
Domain overlap (PFAM):
C1:
PF0226314=GBP=FE(57.8=100),PF0534710=Complex1_LYR=PU(68.7=86.8)
A:
NA
C2:
PF0226314=GBP=FE(22.2=100),PF0534710=Complex1_LYR=PD(28.4=90.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCTGTATCGGCGGGTTCTC
R:
TCCGAGCTTCACACTCTTCAA
Band lengths:
181-268
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]