GgaINT0000227 @ galGal3
Intron Retention
Gene
ENSGALG00000013254 | LOXL3
Description
NA
Coordinates
chr4_random:115561-116442:+
Coord C1 exon
chr4_random:115561-115804
Coord A exon
chr4_random:115805-116312
Coord C2 exon
chr4_random:116313-116442
Length
508 bp
Sequences
Splice sites
5' ss Seq
CCGGTGCGT
5' ss Score
9.74
3' ss Seq
CGCTGTGGGCTCTCTCGCAGGCA
3' ss Score
8.35
Exon sequences
Seq C1 exon
CTGCCTCTGACCTGCTGCTGCACGCCCCGCTGGTGCAGGAGACGGCATACATCGAGGACCGCCCGCTGCACATGCTGTACTGCGCCGCCGAGGAGAATTGTCTGTCCAGCTCAGCCCGCCACGCCAACTGGCCTTACGGGCACCGCCGTCTGCTCCGCTTCTCCTCCCAGATCCACAACAACGGCCGCGCTGACTTTCGCCCCCAGGCTGGGCGGCACTCCTGGGTCTGGCACGAGTGTCACCG
Seq A exon
GTGCGTGCGTGGCATGGGCAGGGACAGGGAGGAGGGTCGGGAACAGCCTGGGCTGGGTCTGATGGTGCTGGGCTGGGCTTGGTGAGGGCGACATCGGCTGAGGGTGATGTTGCTGGATGAGAGCAGTGCCACGGGGTGAGGGTGATGCTGGGTCACAGTGGCACTGTGCAAGGCACGGAGCCTGGGTGAGGGCCCTGATGCTGTTCTCCCCAGTTTGGCTCAGGGCTTCCCCTGGAGGAGTGGTGCTGAGGCTGGGCTGCAGGCTTCGCCCTGGGGAAGACTCCCCTGCCCGGGCTGCCCGACTGGGGACAGCCGTATCCCATCCCTGGGTGAGGCTGAGCTCTGCCTCGGCCTTGCTGCACTGTGTCCAAGCAGGGGCTATGCAGACCTTCCTGAGCAGTGGGGATGGGCACGTGGCTCTGTGGGTTCCCTCCATCATCCCCTCCGTCCCTCTGCCTTCCCTGAGGGGCTGGCTCTAGGGCAGCGGGCGCTGTGGGCTCTCTCGCAG
Seq C2 exon
GCACTATCACAGCATGGACATCTTCACCCACTACGACATCCTGACTCCCAACGGCACCAAGGTGGCTGAGGGCCACAAAGCCAGCTTCTGCCTTGAGGACACCGAGTGTGAGGAAGGTAGGACTGTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013254:ENSGALT00000021647:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0118612=Lysyl_oxidase=PU(66.9=96.3)
A:
NA
C2:
PF0118612=Lysyl_oxidase=FE(32.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTGACCTGCTGCTGCAC
R:
GTGTCCTCAAGGCAGAAGCTG
Band lengths:
342-850
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]