GgaINT0135562 @ galGal4
Intron Retention
Gene
ENSGALG00000000402 | LOXL2
Description
lysyl oxidase-like 2 [Source:HGNC Symbol;Acc:HGNC:6666]
Coordinates
chr22:1212180-1214639:+
Coord C1 exon
chr22:1212180-1212531
Coord A exon
chr22:1212532-1214463
Coord C2 exon
chr22:1214464-1214639
Length
1932 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
CTATTTTCTTTCCCCTTCAGGGA
3' ss Score
12.26
Exon sequences
Seq C1 exon
ATGGAAGGATTCCTGGGCTTTAACCATAACCACTGTTTCATCGTGCTGTTCTTTGTCTCCCTGAGCCTTGCCCAGTATGAACACTGGCCCTACCTCCCCGGGTACCCTGAGCCACCCCCGCAAGTCTACCAGCCCCCCCGCAGGCCAGCAGACGTTCCCAAAATCCAACTACGGCTCGCAGGGCAGAAGAGAAAACACAATGAAGGCCGAGTTGAGGTGTTCTACAATGGCGAGTGGGGCACGGTGTGCGATGATGACTTCTCCATCCATGCCGCACATGTGATTTGCAGGGAGTTGGGCTACGTGGAGGCAGTGTCTTGGCTACCGAGCTCAAAATATGGGAAAGGAGAAG
Seq A exon
GTAAGGCGACCCCCTCCCCGTGCTTAGCTCTCTCTCTCCAACCCTAATTATTCTTGACTTGATGGCCAGATTTGAAGATGTAGGCCCAGACAAAGAGCTGAAGGAGCTGATCTTGGCATGTGAGCTCCAGCAGAGGATGAGGGTAGGAAGATCTCCAGCAGCCAGTAGGGCTACTGAAAAGGGAATCTGCAACCACAGATGTAATTTACGGGTAGTTATTTCCCTGTTCGTGCTTCCACTGACATACAGTGAGTCAAACAGGACCTCTGAACACTCTTTCCTCCTGTTCTTCTTTTCCCTGTGAGCTGTTTGAGCTCTAAATAGCTCTCTGTGATGCTGTACAATTCTTTTTCCTCCTGTCATCCTCTCTAGAGAGGTATACCTCATTCTGCAATGCTGAGTAGCCTGTAAAACCCCAAAGGAACGTCTGTGCTTTGTGTCCTATATAGGACTGTGTTTGGAATAATCTTTTGGGACTCTCCAAGCTGGTCCTGGTGAGGAAGAGCCATTCACCCCTAACCCAAACTGCTCTTTGCTTCTATTGTGATGTTTGAAATAGCACGTGAGGATTGCGTGGGCAATTACAACTTGGAAAGTTGGATCTTTCCTTTTTATAGGTAGTAATAAACTCTCAGAATAGCGATGCTTGAGGTAGAGTAGCTCTGTGAGAGTATGCAACTCAACAGCCTTGTTTAATTGTCTTTTACTATGCTGTTAGTTAAATACCGGCTGGCAGAGAGTTTCTTCCTCCAAACATTCAGGCCTGGTGCACTGTTGATGTAACCCACAGACAATTTCCACTCCAGCAGGGATAAACGTGCTGTATGTCTATTACTTAGCAGTGCTCGTTAGCTCTCACACCTATAAAATTGCCCATTAAGGACCAAGCAAGCCTTAACATTGCAGGTTTCATGTTTCACTCAAGTCAATGTTGTCCTAAGCTGTGGATTTTGGCTTTTGGGGTGGAGAAGATTTCCGAGAGAGAGAAAAGAGTCCATGACATTGGAAAACAAGCCAGAAAATCATTGCCATCTGGTTCAGCGGGTAAATCCTGAAGCAGAGAGCCTGTGTAGGGGGAATTGTGCCTTCCTAGATCAGGAAGGACTCAATAGACCTGATGTTTGGGGAGCAAGAGGAGGGCTGGCAGATCCATCAGCTGGCTGGTGTTGAACCAAGTGAGCATTAGGGCTGCTGGAACAAAGCTGGGAAAGCCAAGGGAAACAGCTCCAACTGCTTTTGCAAAATCTCCTTCTGGCTTTGAAAGTTGGGCAGTCCCTTCTACCCAAAGGGGAGATATCCTTCTTACAAGCAAGGCCTTGGGGACCCTAAAATAGGGGAATTGTTGGTTGTTGCTCCTTGGAGTTTAGGGGATAAATCATAGGGGAGTAACACATACCCAGCACATTTCCAAAGGGAACGTGAGCACTTGGTCAAGGGGAGTCTCAAAGGTGCTGTTGGTTCTTTGCTTGGAAAATATGACCTCAAGTTCTTGGAGTGGCACCTATGGATTTTTGTCCACCTGTCAGTCAGCTCCAAAGGACCTGATTTGTTTTAATACAACATACATGTGTGCACACGGATGAGCACACACTTTTTGCTGGGGGGAAAAAGAGTAACTACAGTCTGGAAAGTGGATCTGGTCATTGGTTTTCAAGGAGCACACAAATAACAGGAGGTTCCAATCAACAGTGGTTTGTTGAATCTTTTGCAAACGTTTGCCTTTAAAATGTTAGGACGTTTAATCAGAACTCGGAGCGCTCTCACAGAAGAGATTTAATGAGGGTTTGATGAGAAACGATGTAAAGTGAAGCCTTAAATACAGAGGGTGATTTGGTGTGATTAGAGGGCAGGGCCCAATCAGCCAAAGCCCTGATTAGCACAATCTAGATCTCCATCTTTCTGAGTCTCATCTCTATTTTCTTTCCCCTTCAG
Seq C2 exon
GGAAAATTTGGATGGACAACGTCCACTGCAACGGCAAGGAGGCCACGCTGGCAGCATGCACCTCCAATGGATGGGGAGTGACAGACTGCAAACACACCGAGGACGTGGGAGTGGTCTGCAGTGAGAAGAGAATCCCTGGCTTCAAGTTTGACAACTCGTTGCTCAACCAAATAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000402:ENSGALT00000000548:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.076 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PU(58.2=48.3)
A:
NA
C2:
PF0053013=SRCR=PD(40.8=67.8)
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:
ATGAACACTGGCCCTACCTCC
R:
ATCCATTGGAGGTGCATGCTG
Band lengths:
348-2280
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]