DreINT0089070 @ danRer10
Intron Retention
Gene
ENSDARG00000006896 | lhx6
Description
LIM homeobox 6 [Source:ZFIN;Acc:ZDB-GENE-041025-1]
Coordinates
chr10:9555053-9555455:+
Coord C1 exon
chr10:9555053-9555273
Coord A exon
chr10:9555274-9555354
Coord C2 exon
chr10:9555355-9555455
Length
81 bp
Sequences
Splice sites
5' ss Seq
GTGGTGCGT
5' ss Score
6.46
3' ss Seq
CAGTTTTGTGTTTCGTACAGGAA
3' ss Score
7.23
Exon sequences
Seq C1 exon
TAGGTTTGGTACAAAGTGTGCCCGCTGTGGCCGGCAGATCTACGCCAGCGACTGGGTCAGACGAGCCAGAGGAAACGCTTATCATCTGGCCTGCTTCGCCTGCTTCTCCTGCAAACGGCAGCTGTCCACCGGAGAAGAGTTCGGACTGGTGGAGGAAAAAGTGCTCTGTCGGATTCACTACGACACTATGGTGGAGAACCTGAAACGGGCCGCTGAGAGTG
Seq A exon
GTGCGTATGTTTCAGACGCGGGTTATGGCTTCGTGTCATTGATCTTGAAGGATTTGCTAAGCAGTTTTGTGTTTCGTACAG
Seq C2 exon
GAAGTGGACTCACTTTGGAGGGGGCGGTGCCGTCGGAACAGGACAGTCAACCAAAACCAGCCAAAAGAGCACGAACTTCCTTCACTGCTGAACAACTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000006896:ENSDART00000021100:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.735
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.4=2.7),PF0041217=LIM=WD(100=78.7)
A:
NA
C2:
PF0004624=Homeobox=PU(21.1=35.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTTCGGACTGGTGGAGGAAA
R:
GCAGTGAAGGAAGTTCGTGCT
Band lengths:
172-253
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]