RnoINT0085885 @ rn6
Intron Retention
Gene
ENSRNOG00000004642 | Lmx1a
Description
LIM homeobox transcription factor 1 alpha [Source:RGD Symbol;Acc:1304784]
Coordinates
chr13:86052375-86054050:+
Coord C1 exon
chr13:86052375-86052452
Coord A exon
chr13:86052453-86053980
Coord C2 exon
chr13:86053981-86054050
Length
1528 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATC
5' ss Score
7.46
3' ss Seq
TGTGGTCCTCTCCTCATCAGATG
3' ss Score
8.71
Exon sequences
Seq C1 exon
GTGAGGGAGACTCTGGCTGCGGAGACAGGGCTGAGTGTCCGTGTGGTTCAGGTGTGGTTCCAGAACCAGCGAGCCAAG
Seq A exon
GTAATCTGCTTCTCACCTTCATCTGTCTTTGTCTTACTGGTTTCTTCCACCAACAGCAGATGGGCATTGGACTTACTGTCAGCCTTTTTAAACTAACTTAGTGGGCTCTCTTGATTAAAAAGCAACAACCATCAGTGATTATTTCAGCCACAGCATCCCTGCAGAAGGTAGAAACAAAGTGTTTCTTAGTGAAACAGTTTTTGTCATGGCGGGTGGGATGTGTTCACTCCCAGCTTGCGGTGTCTGGCCTCTCTGACTCCAACCAAACCACCTTACTGTCCTAGGTAACAAACAGGTTCTGGGTTACTTATTTTCTTCCTAACTCTAAAAATATACATGTCCTGGCCATTGTCCCAGGATCTTGGTTTTTATTTATCCTTCTTTCTTTCATGTATGCTCATGTATAGGTGTGTGCATGGAAGTGTGTGCATTTACATGAAGGCCAGAGGTCTTCAGGATAGTAATTCACCTTGGTTTTCATTCTTTTGAAAAGAATGTCTCACTGGGATCTGGAATCCCTCAATTATGATAATTCTGGGGGCCAGGCAGCCCCCAGGACCCTCTTTGTCTCCATTTCTCAGCCCTTGAGTAATAGAGTGCACACCAATACCCCGACTTTTTGCCTGAGTTCTTAAACATTGAACTCAGAACGCTGTGCTTACTTAGCAGCACTTTGCAAACTGAGCTATCTTCCCAGTCCTTAGATGGTGATAAATTACCCTCTCAGTAGGTCACAATTCTGCAGCAGAATTCCTCAGATCAGGGCTGTTGTTGCTGTGTTGCTATTCCGTCGACAGAAGACTTCATGCTGCAGCGTCTGTTAGAGAGTTCACAAAGCCGGAGCACACTGCCAACTCCTGGGGGATTTTCTGGCAAAGGAATTCACTCTTCTAGTATATCACACATGCACACGTGTGCGCAAGCACATGCTAGTGCAGCAAATAGTAAGATCTCACTGAGTGCTAATGCTTCCCAGAACACAAGTTGGGTAAAAATACAAGTTGGGTGAAAGGGCTGCTTTGGTGGACGAGCTTCTGATCTAGAGGTATGGATCTCACAGGAAATGCCACAAACACGGGGCCAGCAGATAGGAAGGAGGAAAAAGAGTGTCTGGGCTCATCCCAAGTCTCACTCCCTGGGCAGTCCACACTTCACAACTATCTGAGACCATGAAACACATATCCACATACTTACTGCCCCACACGAGGCAGTTCCAGAGAAAACAGCATGTGGTCCTTACTGGGAAGAAGTCTGTTTCTGAGAAGCCAGGTTAAACTTTGCTGTATCTCTGCCAGCTGCAGTCCTAGGAGCTTCAAAACTAGGAGAGCCCTTGTCACTAAGCATCTGAGTTACGGTGCTGCACCTAATGTGTGTTTCCTGGATAGAGTCAAAGCTGAGGGATCGCTTCCTCTACTCTAGAAACAGTCCTTTCACCAAAGGGTAAAGGTCACACCCTTTCTGCTCTCCCTTGTCATATGGACCCAACCCAGGCCTCTGGCTTCTAATTCTGTGGTCCTCTCCTCATCAG
Seq C2 exon
ATGAAGAAGCTGGCCCGGCGACAGCAGCAACAGCAACAGGATCAACAGAACACCCAGAGGCTGAGTTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004642:ENSRNOT00000006163:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.077 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(43.9=100)
A:
NA
C2:
PF0004624=Homeobox=PD(3.5=8.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]