DreINT0089072 @ danRer10
Intron Retention
Gene
ENSDARG00000006896 | lhx6
Description
LIM homeobox 6 [Source:ZFIN;Acc:ZDB-GENE-041025-1]
Coordinates
chr10:9556920-9557281:+
Coord C1 exon
chr10:9556920-9557015
Coord A exon
chr10:9557016-9557106
Coord C2 exon
chr10:9557107-9557281
Length
91 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACC
5' ss Score
6.54
3' ss Seq
TCAGTTGCCTTTTTTCACAGGTC
3' ss Score
9.49
Exon sequences
Seq C1 exon
GTAATGCAGGCTCAGTTTGCACAGGACAACAACCCTGATGCTCAAACCCTGCAGAAACTGGCGGACATGACAGGACTGAGCAGAAGAGTCATACAG
Seq A exon
GTGACCACACATAAATCTTTTCATGCTTCATTTCTTCCATTAGAGTAAATAGAGAATTCGTATCCTTACAGTCAGTTGCCTTTTTTCACAG
Seq C2 exon
GTCTGGTTTCAAAACTGCCGAGCGAGACATAAAAAGCACACTCCTCAGCACAACGGCCCTCCTCAAGCTCATCCACAGGCTCGAATGCCACCCTCGCTGCCTGACGAGCTGCATTACTCTCCATTCGGTAGTCCTGAGAGAGCACGCATGGTGGCCCTGCACGGATACATCGACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000006896:ENSDART00000021100:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.656 A=NA C2=0.678
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(54.4=100)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=18.6)
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:
GGCTCAGTTTGCACAGGACAA
R:
GAGCCTGTGGATGAGCTTGAG
Band lengths:
170-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]