RnoINT0085891 @ rn6
Intron Retention
Gene
ENSRNOG00000017019 | Lmx1b
Description
LIM homeobox transcription factor 1 beta [Source:RGD Symbol;Acc:620843]
Coordinates
chr3:12611932-12612391:-
Coord C1 exon
chr3:12612210-12612391
Coord A exon
chr3:12612010-12612209
Coord C2 exon
chr3:12611932-12612009
Length
200 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TCTCTCTTCCCCCGGGTCAGGTC
3' ss Score
8.22
Exon sequences
Seq C1 exon
TGAAGAGTGAGGATGAAGATGGAGACATGAAGCCAGCCAAGGGGCAGGGCAGCCAGAATAAGGGCAGTGGGGATGACGGGAAGGACCCGAGAAGGCCCAAACGGCCCCGGACCATCCTCACCACACAGCAGCGAAGAGCTTTCAAGGCTTCGTTTGAGGTCTCCTCCAAGCCCTGTCGGAAG
Seq A exon
GTGAGGAGTTCTGGGTGGAGGGTCTGGGGCCAACGCCCCTCTTTTGCTTATTGAGGACCCGTTCCTCCACGACCCTCCTCCATGACCCACTTCTATCACTGGGGGGGAGTAGGAGTCCCCCTCTCACCACTCAACCCCACTGCCGCCTTCCAGCTGCCACCGACACAGACTTGACTCGTCTCTCTCTTCCCCCGGGTCAG
Seq C2 exon
GTCCGAGAGACACTAGCCGCAGAGACAGGCCTCAGTGTGCGTGTGGTCCAGGTCTGGTTTCAGAACCAAAGAGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017019:ENSRNOT00000022953:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.754 A=NA C2=0.192
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(47.4=44.3)
A:
NA
C2:
PF0004624=Homeobox=FE(43.9=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:
TGAAGAGTGAGGATGAAGATGGAGA
R:
AGACCTGGACCACACGCA
Band lengths:
237-437
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]