GgaINT0138226 @ galGal3
Intron Retention
Gene
ENSGALG00000007406 | F1N9M8_CHICK
Description
NA
Coordinates
chr24:5556219-5556562:+
Coord C1 exon
chr24:5556219-5556294
Coord A exon
chr24:5556295-5556409
Coord C2 exon
chr24:5556410-5556562
Length
115 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGG
5' ss Score
6.74
3' ss Seq
AGCTCCCCGCTTCCCCCCAGTCA
3' ss Score
6.22
Exon sequences
Seq C1 exon
TCCTGGAAGCGCATCGGCATCCCCATCCTGGTGACCGTGCTCATCCTCGCCTGCCTGGCTGCGGTTGGGCTCTTGG
Seq A exon
GTGAGGCTCCTGCTCTGTTCTGAGCCTGCTCCTGCCCGGTGCTCGGCTGGGAGTGGCTGTACCACCACCATCCTGAGCCCCCCGGCCCCAAGCTGAGCTCCCCGCTTCCCCCCAG
Seq C2 exon
TCAAGGTTTATCTGGAGCACCACTACTTCATCTGCAAGCAGCCCCTGAAGCTGGTGCCGCTGGTGCAGGTTTGCAACGGGGAGGCGGACTGCCTGCACGGCGAGGATGAGACCAGCTGTCCCCAGCAGGTCCCTGAGGGGCCACAGGCTGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007406:ENSGALT00000011978:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.077
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=65.4)
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:
CTGGAAGCGCATCGGCATC
R:
CTCAGGGACCTGCTGGGG
Band lengths:
211-326
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]