RnoINT0085884 @ rn6
Intron Retention
Gene
ENSRNOG00000004642 | Lmx1a
Description
LIM homeobox transcription factor 1 alpha [Source:RGD Symbol;Acc:1304784]
Coordinates
chr13:86050119-86052452:+
Coord C1 exon
chr13:86050119-86050291
Coord A exon
chr13:86050292-86052374
Coord C2 exon
chr13:86052375-86052452
Length
2083 bp
Sequences
Splice sites
5' ss Seq
AAGGTATAA
5' ss Score
7.08
3' ss Seq
TGTGTTTAATTTTCTTCAAGGTG
3' ss Score
8.57
Exon sequences
Seq C1 exon
GCAAAAGTGATGATGAGGAGAGTCTTTGCAAGTCAGCCCACGGGGCAGGGAAAGGAGCATCAGAGGACGGCAAGGACCATAAGCGACCCAAACGTCCCAGAACCATCTTGACCACTCAGCAGAGGAGAGCATTCAAGGCCTCATTTGAAGTATCCTCCAAGCCCTGCAGAAAG
Seq A exon
GTATAAGAGGGGGGTGAAGTCAGGAGAAGGGATCACAGCTTGGCTATGTGCAGCTGGACTCATCTGGGATATTAACAGGCTGTGGGGGAGATGTCTGAGTGGGGAATGCTTCTCAGAGTCTGTGACAGTTATGAGCCCTGCAGGAGCTTTCAAAGATAGCTAAGATATAGTTTGGGAAGCAATAGAATCTCCCCCAACTTTCTACGCGCTTGCCAACTCCTGACTAACAAACACCTCCCATTTCATGAAGTGCAACAAGGAACCATAAATAGTAACTAAATCATTGTGTAATAAGTACTAGTTGTGATACAAGCCAGATACCTTAACAAAGATTACAAAAATACAGTAGCTTGCAATGTGTGCTTTTTATGGTCGGGTTTTGGCTTATTCTCCTTGGTGTGGTGACTTGGGGATTGCCTGGATAGAAATTCATTCCTTCCCACGATATTTTCAATGGAATGGATGTGTTCTGGTTTTTCAACTCACCTAATGATGGGGATTTGGGGTTGTGTTTTGTTGGGACTATTATGAATAGGGGGTCTTGTGAACATTTATAGAAAATTACTCATGCACTCAATGAAATAGTATTTTCTTTCCATGTCACATTTCAGAGGCGAGCAAGATAAGGCTGGGAGGGAAGTTCTGTTATCCACCACCTAGGTCCCAACAGTTGCTCCAGCTGTCCGCATTTTCCCAGCCACCATGGTGGGGACAGCAGAAGTAGTGAGTAAGCACCTGCCAGTTTGAGGACATTCCGGGGGTTCATGTCCACCCGTTTATGCATCTCCTGTCCACAGGGTAGGAGAAGAATTTGGTATTTGTTGAGCAGTAATATATTCTGATACAACTTTGATCTTGGAAAAGATTTACCCATAGACTCTTCTCTTGTCTTTGCCACTCCCTGCACTCTGTGGGAGGTACATGTAGGTAGTGAAATATCTGAAATAGGCTTACACATGGACCAATTACAGTGAGAAGGACACGAGTATACGCAAGTGTCACACAAGGGAGAAAGCTATAGCAACGTAACAGAGAGGCTGCCAGGAGCTATGGGGAAGGGGAAAGCTATTTCATCTGAGTATCTACCAGGCTTTATGGATCAAGTGGCTCCTGGTCTGAGGCTCTGGGGCATGGATAGGGTTTCAACAGGTGCAAGAGCCCCTGTGTCCACTTATGCTGACTTAGCTGATGTTCACGCCTCAGCTACCTACCCTACTCATCTTACTCCTGAGCTTCAGCCCAATTTCATGGTCATGGCGATGTGTTTCCTGCAGCCTCCATTTGGTCTACTCATTCAGGCTCTTTTAGTTCATCTTCCCTGGAGTCTGTCAGGTAGGGGTAGTGTCTTGGAGTCCCTCTCACTATCATACCAGTCCCTCACCATGTGCCCGGATGGCTTAAACAGCCAAACACGTCTCTTTGTTATCTGGATCCTAACTGTCCTCATCTCTATATGACCCCAGTGCATTTACCAGTATTAGAGTTGTTCACCTGGCACTGCTCGATTCCAGATAGCCCTCATGTTTTATATCCACCCACCCCGCCCCCAGAAGGACTTACTCAAAAAAATTAGTGAACATGAATATTCAGAAAACAAAGTTAGTTGGAAACAGACAAAGGTGAAAATTTAAGTCAATGAGAAGACAGGAGGACAAGAGAGAACCATCTGTTCTGCAAAGAGATTTTCACTTTAGTTTCCCTTAAGTCAATGAAAGCGTATGAAAGCCTACCACTGAAGAGAAGTCAACTCCAGTAGATCATATCAAGACATAACTTCAGAGTACAAGAAACCCAAAGTTCCTCCTGGGAATGGGCATCTAAATAAAGGAGCATCTCTTCCTTTTTCTAGCTTGTGAACGATGCCTTCTCTGCCAGAAAGAGAGCATAACCTTGTGTTTGAGTGTATTTGAACATCAATCATGAACTGGTCTCTACTTAGCAATGTGACCTATGCCCCCGCCTGATACCACTCAGGAAATGGTGTACCTCCTACTCTAAGAAGTCAGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTATACTTATGTGTTTAATTTTCTTCAAG
Seq C2 exon
GTGAGGGAGACTCTGGCTGCGGAGACAGGGCTGAGTGTCCGTGTGGTTCAGGTGTGGTTCCAGAACCAGCGAGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004642:ENSRNOT00000006163:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.552 A=NA C2=0.077
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(47.4=46.6)
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:
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]