DreINT0089066 @ danRer10
Intron Retention
Gene
ENSDARG00000006896 | lhx6
Description
LIM homeobox 6 [Source:ZFIN;Acc:ZDB-GENE-041025-1]
Coordinates
chr10:9539143-9540186:+
Coord C1 exon
chr10:9539143-9539520
Coord A exon
chr10:9539521-9540114
Coord C2 exon
chr10:9540115-9540186
Length
594 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
GTGGCTTGACTGTGTTGTAGGTG
3' ss Score
6.55
Exon sequences
Seq C1 exon
ACTCAAGCAACTGCATCCCAAAAGAGGGAAAAAGTAGGAAATATCCTGCAAACGGTTCTAAATAAGGCGTCCCGACGAACCGCTCGCGTTTGGCGTGTCCGCTGTCGGTTAACTGAGCTACCACGAATGTGAAGACGTTTGTATAGAGATTATTGACTGACTTACACCGAAGGAAACGACGAATTAAAACGACGAATTGCTGTTATATCAAACCGAATTTATCCGAAAAAGGCGCATGGGATGAACATTTTGCAAAAAACACTTGATGCAGCTTAAAAACATCTGAAGTTACGCCGTCAAATGTATTGGAAAAATGAAGCTCTGGCCCCTCTTTCAGAGGGAAATCAGTTTCTATCCGAAGGAATTCCCTCAAAACAG
Seq A exon
GTAAGACATTTATAAACCGTTTATGCTTGTTAGCTATTATCTATTTAATTGCATGCAACAAAAAAAGTAAGAAGTCGCCAACATGTTGCTGGATGTGAAAGTCCTCTGTGCATCTCCTGCAGCCTGTAACATCTTCACCTTAAAGTGATGTCATGAGAATCAGGATCTCTTCTGAATAGTGTGATTTGCGGTCCATCCTCTTCACATGCCAAGTCTGCAGAGGAAAAATTAGATTTTAATTACTGCCATTAAAAATCAAATTTGCAATTCTTTGGGTGGCCCGTTGCTTTCCCTGATTGGCAGTTGAAATTGACACTCTGGGGTCCTCTTATCGCGAGCATTTCAAGCTATTTGTAATTGCAGGTAGTTTATTTTTTTCAGCTCCCTGGATTGCGTGGAAATACGATTATGGGAAGAGGCACGGGTTAAGTGTGGGGAAAAAATCAATCCAAATTGAAATCGCTTCATTAAAAACAGGGGCTTTTGTCGCGAGGCTCTCAATACACAGTTAAAAGCGCTTTTATTGTTTTTGGACGCATATATAGAACCGAGAACGTGCCTGATATGGAGCACTGTGGCTTGACTGTGTTGTAG
Seq C2 exon
GTGATCTCTCCAGATTCGCACAGCACACCGGGAGCATCACGCTGCGTGGACGGACAACACGGACAAGCGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000006896:ENSDART00000021100:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.577 A=NA C2=0.958
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGTTCTAAATAAGGCGTCCCG
R:
GTGCTGTGCGAATCTGGAGAG
Band lengths:
352-946
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]