GgaINT0038981 @ galGal4
Intron Retention
Gene
ENSGALG00000011369 | LHX8
Description
LIM/homeobox protein Lhx8 [Source:RefSeq peptide;Acc:NP_001035556]
Coordinates
chr8:28617246-28618820:+
Coord C1 exon
chr8:28617246-28617429
Coord A exon
chr8:28617430-28618218
Coord C2 exon
chr8:28618219-28618820
Length
789 bp
Sequences
Splice sites
5' ss Seq
ATGGTAGGT
5' ss Score
8.6
3' ss Seq
AAATCTTTCTGTTTTTGTAGCTC
3' ss Score
7.48
Exon sequences
Seq C1 exon
GTGTGGTTTCAGAATTGCAGAGCACGTCATAAGAAACATGTTAGTCCTAATCATTCCTCTACTGCTCCAGTCACAGCAGCTCAGCCCTCCAGGCTGTCTCCACCCATGTTAGAAGAAATGGCATATTCAGCATATGTACCCCAAGATGGGACTATGTTAACTGCCCTGCATAGTTATATGGATG
Seq A exon
GTAGGTACAACTTTGCATATCTAAGTAATATCACTCTTGACTGTAGCAAGAACAGTTTACCAGGCTCCCATTAAAGAAGCTTACCAGATTTCTTGTTTTAGGCTTTATAGAATATCTTAATGCAGTATTTGCTCTCCGTGTCTTGTTAAGAAGTGCACCGCTTCTATCAGTAGCACTTCACTGTAGTAGCTTAGCTGAAGATCTGGGTATGAAGACTACTTTCTGTACTTCCTCCAAACCATGAGTATTAGTAGTAAGCATTCAAACACTTGTTTTTGTAGCATTCATGCTGTATTTTCTACAATATCTAATTTTAATGAAAACTGTTGACCAGACACTCCCTGACCCTACAAACTGTAGGTGTACTGCAAGCTTAAGCTTCTGTCACAGTAACACATAATGGGAGGAGCTTTGTTTTCAAAAAACATCATTGTGTGTTATTTGAGCCCAACTTGTTCACTTATCAGGTCAAACTCATGGTTTGGAGACACTGACAAATTTGGGAGGCCTGGACTCTCAGCTGCAGGTGTGGCCTAAGCCCCTTCTTCTCCAGAGTGGTGTGTGAGGTGGGCTGTGGTTGGAGGCAAATGAGCACCGGGCCTGAAGTATGGGGTTGGTGGAAGCACTTGTAATACCACTTAGTACCTCCTGGCATCAGGCTTGTTTAGAAAAATAGTGCCTGATTAGGTGGTTGGGACCAGTGAACATTTATTTACCCAGTGGGATTTTACTAGTTTATGTTTTTCTACTTCCAGTGAAGTTGACAAGTAAATCTTTCTGTTTTTGTAG
Seq C2 exon
CTCATTCACCTACAGCTCTTGGACTCCAGCCTTTGCTACCCCATTCAATGACACAACTGCCAATAAGTCATACCTAATTTCTTTCTGTCAGGGATATAAGCTATTAAGGATGTAAGCTTAAGTCACTTACTGTGTATGAAAGTTATCATTGGAAAGATATTAATGTTAACTTTTTATTTAACATCTAAAGCATTCTCAAGAACATTTTTGCTGCCCAGGTATATGTAAGTATACATTTAGCCTACAAGACACTTCTATGGATTCTGCATAATTACATATTACATTGTTTACAAGCCTTATTGAACACCTTTTTGTATTGTCTGGAAGTAGATCACTCTAGTTACGTATTTGTTAATTTATTTGTCATCAAAAGAGCACTTTGCCTAAAAGAAAGGACTGACAGTTGTGCAAAATGTTTACAATTCTTTGTGAGTTTGTAGTTTATCATTAGTTTGTATTGGTAAGTTATTGCTAAAAGTATTACTTGTATTTGAGTTGTATACAGCCTATATGTTAAAGCTTATTTCTGTGAATTTGCAAAAATAAATTTTGGTTGCAAATATTTTCAAAATGAACTAAATAAAGTTTTTGCTGTAGCATGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011369:ENSGALT00000018546:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.476 A=NA C2=0.341
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=17.7)
A:
NA
C2:
NO
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:
TCTACTGCTCCAGTCACAGCA
R:
ACCTGGGCAGCAAAAATGTTC
Band lengths:
347-1136
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]