RnoINT0085888 @ rn6
Intron Retention
Gene
ENSRNOG00000017019 | Lmx1b
Description
LIM homeobox transcription factor 1 beta [Source:RGD Symbol;Acc:620843]
Coordinates
chr3:12685779-12686869:-
Coord C1 exon
chr3:12686731-12686869
Coord A exon
chr3:12685966-12686730
Coord C2 exon
chr3:12685779-12685965
Length
765 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TCTCGCCCTGTGCGCTGCAGGCT
3' ss Score
7.91
Exon sequences
Seq C1 exon
ATGGATATAGCAACAGGTCCCGAGTCGCTGGAGAGGTGCTTCCCTCGCGGGCAGACGGACTGCGCCAAGATGTTGGACGGCATCAAGATGGAGGAGCACGCCCTACGCCCCGGGCCCGCCACCCTGGGTGTGCTGCTGG
Seq A exon
GTGAGTGCTGGGTCGCAATGCCCGAATAGTCCAGGTCAGGGAGTAGGGCTGTCCGTGGTGCCGCTGTGGACACCGGCGTGAGGGCCAAAGAATAAAGAAAATAGGTTTTCAGGACGTGGGGATGGGGTCCGGACCCCTGGAATGACCAGCAGAGGGGCAACAAGCACACCTAGACAGCTCCCTGAGGGGACAGCGTTCAGGGACGTCACCTAGACAGGGCACTGAACAGCCTCCGCCGTCACTCACACCATCCTCTCCCGGTCTGGGTTCTAGTACTGCTACACTGGACCGGGCTGGGGTGGGAAGGGGTTGGCGGAGATGCTGGAGAACCAAGTTGTCTCCTTAGAGCCCGGGAGAGATGCCAGGTCACTTGGGGGAAGGGGAACTTCTAGAAGAGAAAAATATCCCCGGGTCTATCCAAACCGCGGGTCTTAGGGCAGAAGGTTCCATCAGCATCGTGGGGCGTGTCAGCCAGCGAGTGTCCTGGCCTCACCTCGCTGGTTGGGTTCCAGCCGGCCACCCCGCGCGGAGCTCCTTCTCGTTGGTAATAACACCATACGCTGGATCTCCGCAAGCGGGGAGAGCGCAGCACCCAGCCAAGGCTGCAGGCCCTCGGCCTCTCGGCGCCCCGGCTTACGGAAAGGAACGTGCTGTCTAGGGCTGCCGGGTATTTGGCGCGCCGGCTGGGGTCCTCAGGCGACGGGTGGCGCTCCGGGGCTGGGCCAGGCGGCGCTGACGGCCCGGCTCTCGCCCTGTGCGCTGCAG
Seq C2 exon
GCTCCGACTGCCCGCATCCCGCCGTCTGCGAGGGCTGCCAGCGGCCCATCTCCGACCGCTTCCTGATGCGAGTCAACGAGTCGTCCTGGCACGAGGAGTGTTTGCAGTGCGCGGCATGTCAGCAAGCCCTCACCACCAGCTGCTACTTCCGGGATCGGAAACTGTACTGCAAACAAGACTACCAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017019:ENSRNOT00000022953:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.043 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0041217=LIM=PU(94.6=84.1)
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:
ATGGATATAGCAACAGGTCCCGA
R:
TGTTGGTAGTCTTGTTTGCAGT
Band lengths:
326-1091
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]