GgaINT0044046 @ galGal3
Intron Retention
Gene
ENSGALG00000013090 | LOXL4
Description
NA
Coordinates
chr6:23680723-23681513:+
Coord C1 exon
chr6:23680723-23680934
Coord A exon
chr6:23680935-23681381
Coord C2 exon
chr6:23681382-23681513
Length
447 bp
Sequences
Splice sites
5' ss Seq
CCGGTAGGG
5' ss Score
7.63
3' ss Seq
CCTGGCTCTGCTCCTTGCAGGAA
3' ss Score
10.56
Exon sequences
Seq C1 exon
GGGCCAGGGCTGAGCTTGGAGGAGGTGCGGATCAAACCCATCCTGGCTTGGGCTAAGCTGAGCATGCCAGTGGTGGAGGGAGCAGTGGAGGTGAAGTACAACGGGCGCTGGAGACAGGTGTGCGACGCTGGCTGGACCCAGAATAACAGCCGTGTAGTGTGTGGGACGCTGGGCTTCCCCCGCGAGAAGCGTGTCAACACCAGCTTCTACCG
Seq A exon
GTAGGGATGGATGGATGTGCCATGGGATAGGGATGGATGGATGTGCTACGGGGATTTGGGGTATGGTGAAGAGAGGCTGCTAGTGAAGGGGTGCAGATGTAGCTAGGGGCATGGGGCACGTGTCCATGCCTGTGTCCCCTTCCTTGGGGCCTCAGCTTGAGCTCAGCAGCAGCCAGGGACTGCGGGATGCTCCCCTGCTTTGCTCTGTGCAGCATGGGTATAGGCACAGGAGAGCCGAGCCTTGTGCTGGGCTATAAATACAGCCCATAATGAGTCCCTGCCGGTGCCAGGCGTCTTGTCATCCCTGCTGGGCATGCAGTACAGCAGGATTTGGCACAAGATTGTCACTGAGGAGAGAACCCTACCGTGCAATGGGGTGCCAGGGAAGGCAGGGATAGGGGCGCAGTGGTGCTGAACCCCCAAACCTCCTGGCTCTGCTCCTTGCAG
Seq C2 exon
GAAGCTCTGGAACATGAAGCTGAAGGACCCCAGCTCCAGGTATGGCTCAGCCCTGGGCAGGGGGCACCAGCGCAGGAGCCCTCCCCCAGAAAAAACTTACACTTCTTCCCGCAGCTCTCCTCTGGCAGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013090:ENSGALT00000021368:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.711
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PU(43.1=70.4)
A:
NA
C2:
PF0053013=SRCR=FE(37.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAGGGCTGAGCTTGGAG
R:
CAGGCTGCCAGAGGAGAGC
Band lengths:
342-789
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]