GgaINT0124507 @ galGal4
Intron Retention
Gene
ENSGALG00000001347 | LHX6
Description
LIM homeobox 6 [Source:HGNC Symbol;Acc:HGNC:21735]
Coordinates
chr17:8724589-8725717:-
Coord C1 exon
chr17:8725622-8725717
Coord A exon
chr17:8724781-8725621
Coord C2 exon
chr17:8724589-8724780
Length
841 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
GTTCGCTGCTTTCGTTGCAGGTT
3' ss Score
10.18
Exon sequences
Seq C1 exon
GTCATGCAGGCACAGTTTGCTCAGGACAACAACCCCGATGCACAAACGCTTCAGAAACTCGCAGACATGACGGGGCTGAGTCGGAGAGTCATTCAG
Seq A exon
GTGAGGGGCGGCCGTGGGCGAGCATGCAGGATGCAGTGTGTGGGATGCAGGCATGGGATGCAGGTGGATGCAGCGTGTGGGATGCAGCATGTAGGATACAGGTGTGAGATGCAGGTATGGGATGCAGATGTGGGACACGGGGTTTGGGATGCAGGTGTGGGATGAAGGCAAAGTGTGGGCACCATCCAGAGTTGTTTTACCAAAGACACATTTCAGTTTCTAACGTGTAAAAACCTGGCTAAGGCCTCAGTTATTGAGACTCTTCATTCAGCAAGGGATCAAGTAGCCCACGTGCAGGGCGATTCCTCATGGGCTGTTTTTTGGAGGTGCTTTGAGCAGGAAGCGATTTGTCAAACGCTTGTGGCTGTTTCCTTGCTGTGGCCGTTGTGTGGCCTCAGGGCACTGCTCTGAGCTGTGACTCGTGGAAGGATTTCACTCCCAGTTTTCCTTCAGAAATAAAAGCATGAGAAAGAAAACACCACGATCATGGAAAAACCTCCACTCGTGTTTTAGTTCTGGGGTGTAATCCCCCAACCACTGCTTTAATTAAGAGCAGTGAGACACAGTCATGGCTGCCGGTGGGACGGAGCAGGGCTGTGTCCTGCAGCACCGGCATTTCTCAGCTGTAACGGAACGCTGTGGGACCAGCGATGCTGTCGTGGTATTTGTGTGGGCATTTCCACACACGGTTCCTTTTGTGACTCCTCAGTGGTGGGTCTGTGTGTGAGGGGTGATGGGTCCCTGTGGGAGGTGATGGGTCCCTGTGGGAGGTGATGGCTCCCTGTGCATGAGCACAGCTCAGCCCCCTGCCCTCCCTCAGCGTTCGCTGCTTTCGTTGCAG
Seq C2 exon
GTTTGGTTCCAAAACTGCCGAGCCCGCCATAAAAAACACACTCCCCAGCACACGGTGCCGCCCTCGGGGCCTCCCCCGCCCCGCATCCCCTCCTCCCTCGCCGAGGACATCCACTATTCGCCCTTCAGCAGCCCGGAGAGGGCCCGCATGGTGACGCTGCATGGATACATTGAGAGTGAGTGCGGGGCTGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001347:ENSGALT00000002057:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.656 A=NA C2=0.609
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(54.4=100)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=17.2)
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:
GTCATGCAGGCACAGTTTG
R:
CAGCCCCGCACTCACTCTC
Band lengths:
286-1127
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]