RnoINT0085890 @ rn6
Intron Retention
Gene
ENSRNOG00000017019 | Lmx1b
Description
LIM homeobox transcription factor 1 beta [Source:RGD Symbol;Acc:620843]
Coordinates
chr3:12612210-12614569:-
Coord C1 exon
chr3:12614337-12614569
Coord A exon
chr3:12612392-12614336
Coord C2 exon
chr3:12612210-12612391
Length
1945 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
TTGGCTTGTGTCTTTCACAGTGA
3' ss Score
8.81
Exon sequences
Seq C1 exon
GCTCTTCGCGGCAAAGTGCAGCGGCTGCATGGAGAAGATCGCACCCACTGAGTTCGTCATGCGGGCGCTCGAGTGTGTGTACCACCTGGGCTGTTTCTGCTGCTGTGTGTGCGAGAGGCAGCTGCGGAAGGGTGATGAGTTCGTGCTCAAGGAGGGCCAGCTGCTGTGCAAGGGTGACTACGAGAAGGAGAAAGACCTCCTCAGCTCCGTGAGCCCGGATGAGTCTGACTCTG
Seq A exon
GTGAGCCTGGGCTGGGACAGTTGCAGGTCATGGCTCAGGGGAACACTGGAGCAGGGCTTCTGAGGTCCACAGACCTGCACATCCATGCACATCCAGCCAGCACCAATGTGCCACATCCACCCTATCACTTATCTGAATGCCAGTCCTGAGGTACACACATCTGTGTACCACACATATACCCAGTGCCACAAAGACACCACCTCGTGTGCCCATATGTGAGGACATGTGCTTACACATCCAAACATGCAAAGCTCTTCCTATAAGCACACACATATATGTATATTCTTCATACTGCCACACCTGACCAGCACATGCATGATTTTATACACACTCACATGTGCTATACCCATGCATACGCTTGTTCTCTAGCAAAATCCTGAAGGGGGATTCCTTGTCACTCCTGAGTCTTGGGCAGGGAACATGTCAAGATGACCGGTCTGCCCTTTGAGGTACCCTAGACCCACACACATATCCTCTGCTCATGTTGGGAGTGTCTGCAGTTTCCAGGGCCCCAGTGTTTGGTCCTCAGTGTGACAGAGTCCTTGTGTATCTGCTGCTGGCCATCCCTGGGTTAGACACTGTGATGGTGTCCCTGTGGCCACCTGCACTCTCATGGAATGGAAGGCCACTGGCCCAGCTTACAGACATTGTAAAGTCACGGTTCTCCATAGGGCTAACCTCCAAAGAAAGTAAGACTCGGGAGGGGACAAGTTCCAGTGAGGGGTGTCAGAGCTCATGGTTGTTGGGAAACTTGGCCATGTACCTAGGTCTCTAAGGCCCAAACAAAACCCTGGGGTCATAGAAGTGCTGTGTATGTTGCTGACTGATGTGCACACATGCTTCTTCACACCACATGTGTCTTGGAATGTAAGTGTTCCTGCCTGTGGGTGTAGGCCTCTGTGAGTCTGCAATAGTAAATGTCTCTAAGTAACAGATTCAGGTGTGTGCACCCATCAGCGAGTCCATTGTGCGCGTGTGCCCGTGCCTGCATGTCCTGGTCCTAAGTCCTCCAGTGAGGATGTCTGGTCCTTCTGTCTTTGCCAGTTGTTAGTCCCTGGAGGCCTCAAGAAAAAAGGCTCCAGCCATTCCTCTCTTTTTCACCCTGGTCCCCAGGTAGCATGACACATGGACCCTCAGTGGCCAGCAGGAGAAGGTGGCTTTCAAATAAGATGAGGCAGGGAAGCCCAGGGCCTGTCTGGGCCATAGTCATCATATTACCTATTGCGGGAGGCTGCTGGCCTTCAGAGTCACACAAGAGCACATCTGCCCTTGTGTGCGAGTGCCGGAATGCTGCACACGCTCTAGTGTGTGTCTCTTTTGCTTATTGTGGGTCTGTTGCTCCTCCCCAACCCACTGCTATCACCAGGGGTTGAAGTATCCCTCCCACCCCTCAACCCGAGCCTTGTCACAGCCATGCATGTGGACCTGGGTACTGAGTCATGGGCTCCCTGAACCTGTAAGCACCTGAGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTTATACAGGAACCTGTGTGTCAGCAGCATTAGACCAACCCAGGGAAATGAGTGTATGCTGGGGTCAGGGGACATGGCAAGGAAGGCTCTATGGGGGCTGGAGAGATGGCTCAGCGGTTAAGAGCACCCGACTGCTCTTCCAGAGGTCATGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTGTAAAGAGATCCAATGCTTTCTTCTGGTGTATCTGAAGACAGATACAGTGTACTTATATATAATAAATAAATAAATCTTTAAAAAAAAAAAGAGTTCAAAAGGAAGGCTCTATGGGCCTAGGGAAGGCTCCATTTATCCTGCGGTCATTAGGGAGCTGTAATTATCAGCAGAGGGTGAGGGAAGTCTCAGCTACAGGTAAGCTCCCACTGACTGGTTGGCTTGTGTCTTTCACAG
Seq C2 exon
TGAAGAGTGAGGATGAAGATGGAGACATGAAGCCAGCCAAGGGGCAGGGCAGCCAGAATAAGGGCAGTGGGGATGACGGGAAGGACCCGAGAAGGCCCAAACGGCCCCGGACCATCCTCACCACACAGCAGCGAAGAGCTTTCAAGGCTTCGTTTGAGGTCTCCTCCAAGCCCTGTCGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017019:ENSRNOT00000022953:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.114 A=NA C2=0.754
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.6=2.5),PF0041217=LIM=WD(100=74.7)
A:
NA
C2:
PF0004624=Homeobox=PU(47.4=44.3)
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:
CACCCACTGAGTTCGTCATGC
R:
AGGAGACCTCAAACGAAGCCT
Band lengths:
357-2302
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]