DreINT0089071 @ danRer10
Intron Retention
Gene
ENSDARG00000006896 | lhx6
Description
LIM homeobox 6 [Source:ZFIN;Acc:ZDB-GENE-041025-1]
Coordinates
chr10:9555355-9557015:+
Coord C1 exon
chr10:9555355-9555455
Coord A exon
chr10:9555456-9556919
Coord C2 exon
chr10:9556920-9557015
Length
1464 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
AATCTATAAACTCTACACAGGTA
3' ss Score
5.66
Exon sequences
Seq C1 exon
GAAGTGGACTCACTTTGGAGGGGGCGGTGCCGTCGGAACAGGACAGTCAACCAAAACCAGCCAAAAGAGCACGAACTTCCTTCACTGCTGAACAACTGCAG
Seq A exon
GTGAGACAGCAGAACACACATCGGCTTTTTGATTTGAATTTTTTTCAATGTTATTTATAATTTATTTGTTTGTTTGTTTGTTTTAAAATGAATATGGAAAATAATTTTATCGTTCACAGTAATTCGCAAGTAAATGCTAAGGTATTAAAATATAATAGCAATGCTAAATAATATTAATGTTACAATATATAATTATATTTTTTTATGATTTTTTATGCTAAACAAACCTTCATTCCTTTGATCAAACATACAGTAAACTGTAATATTGTGAAATATTTTAGTGCTGGGCAAAAAAAATCTAAATTTTTATAGTTGCATCCTAAATAAACGTTTGGTTTGCCATATGTGTGTGGTGTATATATTTATTATCTATGTATAAAAACACACATACATGCATATAATTGGGAAAGTGTTTATATACGTATAAAATATATATGTATAAGATACAAACTATATATAAATGCCAATATCTATGTAACAAAATTGTTTTGTATAGTTTTTTTTTCTTTGTATGTGTTTGTATCATATATATAAATATTTTTTTCAAGACACTTCTATACAGCTTAAGGTGACATTTAAAAGCTTAACTAGGTTAATTAGGTTAACTAGGCAGTTTAGGGTAATTAGGCAAGTTATTGTATACCGATGGTTTGTTCTGTAGACTATCGAAATAATATAGCTTAAAGGGGCAAATGATATTGACCTTAAAATAGTTTAAAAAAAATGTAAAACTGCTTTTATTCTAGTCAAAATAAATCAAATAAGACTTTCTACAGAAGTAAAAAAAAATATTATTAGACATACTGTGTAAATTTCCTTGCTTTGTTAAACATAATTTAGGAAATATTTAAGAAAGAAAAAAACAAATCAAAGGGGGGCTCATAATTCTGTGTGTGTGTGTGTGTGTGTGTATAGCTATATATATATATATATATATATATATATATGGTCCCACTTTATATTAAGTGGCCTTAACTAATATGTACTTACACAGGATTTAATAGTTTGTTACAATGTACTTACTGTGTAAATACATGTATTTACTGTGTACCTAAGCTTGAATAAATACATGTATGTAATTACATCTGTAATTTACTTTTGTAATTACATTTGTAAATACACTGTTGACCATCCTATACACCTTAACCCACCCTTAAACCTACCCATGCCACTAAACCTGTACATAACCCAACCTCTATCCCAACTCAAAAGCACCACAAGTGTTCTCAAATACATTATCAACACAGTAAGTACGTTGTATTTATTTTTTGATGTAAGTACATAGTAGTTAAGGACACTAATAGAAAGTGGGACCATAAATATATATATATATATATATATATATATATTCACATAGAAAACAGTTATTCAAAACTGTAATAATATTTCACAATACTTCCCATTTCATTTTAATATATCACTTTGAACATACCCTATGATTTAAAATCTATAAACTCTACACAG
Seq C2 exon
GTAATGCAGGCTCAGTTTGCACAGGACAACAACCCTGATGCTCAAACCCTGCAGAAACTGGCGGACATGACAGGACTGAGCAGAAGAGTCATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000006896:ENSDART00000021100:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.735 A=NA C2=0.656
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(21.1=35.3)
A:
NA
C2:
PF0004624=Homeobox=FE(54.4=100)
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:
GTGGACTCACTTTGGAGGGGG
R:
ATGACTCTTCTGCTCAGTCCTGT
Band lengths:
190-1654
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]