GgaINT0138720 @ galGal3
Intron Retention
Gene
ENSGALG00000021273 | E1C8L4_CHICK
Description
NA
Coordinates
chr24:5536744-5537462:-
Coord C1 exon
chr24:5537189-5537462
Coord A exon
chr24:5536867-5537188
Coord C2 exon
chr24:5536744-5536866
Length
322 bp
Sequences
Splice sites
5' ss Seq
TGTGTGAGT
5' ss Score
5.84
3' ss Seq
CAGCACGCGCTCGTCCCCAGTTA
3' ss Score
3.6
Exon sequences
Seq C1 exon
CTCCCGGAGAGGGGATGGAAGGAGAAAATGCATCCGTGTGCTCGCTGCCGGCAGAGGGGTGGTGTTCCCTGGGGGTGTGAGGGGAGAGCGGCACACGCTGAGGTCCAGGACGGGGTCTGGGTGCCTCGAGGAGGCTGTGCTCCCCCTGACTCAGCCCCTGTCCGGCTGCCAGGATCCTCCATGTTCAGAGCTCCCTGCATGAGCCAGCGGCGGCTCGCGCTCATCTTCTGCGTCTCCGTCCTCATCGTGCTGATCGTCGCCCTCATCCTGCTGT
Seq A exon
GTGAGTGCCGGGTCCGTCCCGCTGCGTGAGGGCCGGGCGGGGGGCAGGGGGCCGGGAGGACGGCTGCCGGGCTGGCACCCTGCAGGGGAGGGCCGGAAGGCGGAGCAGAGATGAGCGCTTCCTATTTTCTGCGTTTTCCTGACATCTGGTGGACGGGAGGGCGTAGGGAGATGCTCGGTGCCCCCAGCCCTGCCCTGGCTCAGCGGCCCTTCGGGATCCTAACCCTGCAGCCAAGCTGCGGGGGGGTGGGGGTTGGGGGGGGTGGTGGCGTCCGTGGCAGACCTCTGGACGCAGCCTCACCGCAGCACGCGCTCGTCCCCAG
Seq C2 exon
TTATGTTCTGGCGGTCGCAGACCGGCATCGTGTACAAGGAGCCCGCAGAGACCTGCAAGGACGACCCCGTGCGCTGTGACGGCGTGGTGGACTGCTCCCAGAGGAGCGACGAGCTGGGCTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000021273:ENSGALT00000011876:1
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=64.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAAATGCATCCGTGTGCTCG
R:
CTCTGGGAGCAGTCCACCA
Band lengths:
354-676
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]