RnoINT0085892 @ rn6
Intron Retention
Gene
ENSRNOG00000017019 | Lmx1b
Description
LIM homeobox transcription factor 1 beta [Source:RGD Symbol;Acc:620843]
Coordinates
chr3:12611722-12612009:-
Coord C1 exon
chr3:12611932-12612009
Coord A exon
chr3:12611789-12611931
Coord C2 exon
chr3:12611722-12611788
Length
143 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CCTGGACTGTCCCTCTGCAGATG
3' ss Score
10.56
Exon sequences
Seq C1 exon
GTCCGAGAGACACTAGCCGCAGAGACAGGCCTCAGTGTGCGTGTGGTCCAGGTCTGGTTTCAGAACCAAAGAGCAAAG
Seq A exon
GTGAGAGGTCACTGCTAATCCAGTGCTCCAGGGCAGACCTGGGAGATGGGGAGAGCAAGAGAGAGGGGGTAGGGGGAGGAGGCAGAGAGCAGGCCTTGCATTTGGACTGAAACTGAGTGGGCGCCTGGACTGTCCCTCTGCAG
Seq C2 exon
ATGAAGAAGCTGGCCCGGAGGCACCAGCAACAGCAAGAGCAGCAGAACTCCCAGCGGCTGGGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017019:ENSRNOT00000022953:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.192 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(43.9=100)
A:
NA
C2:
PF0004624=Homeobox=PD(3.5=8.7)
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:
GTCCGAGAGACACTAGCCGC
R:
CAGCCGCTGGGAGTTCTG
Band lengths:
138-281
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]