DreINT0089786 @ danRer10
Intron Retention
Gene
ENSDARG00000077915 | lmx1al
Description
LIM homeobox transcription factor 1, alpha-like [Source:ZFIN;Acc:ZDB-GENE-131213-1]
Coordinates
chr3:52621115-52621438:+
Coord C1 exon
chr3:52621115-52621278
Coord A exon
chr3:52621279-52621360
Coord C2 exon
chr3:52621361-52621438
Length
82 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
TATATACGCTGTGTCTGCAGGTC
3' ss Score
9.09
Exon sequences
Seq C1 exon
TAAAGAGTGAGGATGAGGAGGGTGGTGGTGTCTCTGTCGGAGGAAAGGCTGGGGATGATGGAAAGGAGCACAAGAGATCCAAGAGGCCCCGGACCATCCTGACCACACAACAGCGGCGCGCCTTCAAGGCTTCCTTCGAAGTGTCTTCCAAACCCTGCCGAAAG
Seq A exon
GTCAGTGATGGTCAGAGGGCATCTGTGCTGGTTTTATTTGTGAGATTGGGACTTATCTGATGTATATACGCTGTGTCTGCAG
Seq C2 exon
GTCAGAGAAACTCTGGCAGCTGAGACTGGACTGACGGTCAGGGTCGTGCAGGTGTGGTTCCAGAATCAGAGGGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077915:ENSDART00000168151:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.673 A=NA C2=0.115
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(47.4=49.1)
A:
NA
C2:
PF0004624=Homeobox=FE(43.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACAAGAGATCCAAGAGGCC
R:
TGCCCTCTGATTCTGGAACCA
Band lengths:
172-254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]