DreINT0089779 @ danRer10
Intron Retention
Gene
ENSDARG00000020354 | lmx1a
Description
LIM homeobox transcription factor 1, alpha [Source:ZFIN;Acc:ZDB-GENE-041014-332]
Coordinates
chr20:34033775-34035865:+
Coord C1 exon
chr20:34033775-34033852
Coord A exon
chr20:34033853-34035777
Coord C2 exon
chr20:34035778-34035865
Length
1925 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACG
5' ss Score
10.19
3' ss Seq
GAATCGCATTGTCTCTGCAGATG
3' ss Score
7.83
Exon sequences
Seq C1 exon
GTGAGGGAGACTCTGGCAGCAGAGACAGGACTGAGCGTACGAGTCGTTCAGGTCTGGTTCCAGAACCAAAGAGCCAAG
Seq A exon
GTAACGTGATGCCCGCCGACACAGACAAACACACTCATTGAAAGAACATCAACTTATGCAATTGATAACAGACCTCTTTCTGCAGCACACCAGCTTGCCAATCAGGAAACAAGCTGTGTTATTGCCTCACGTAGGAAACCGATGACATATTATGTATAGATAACCTTAGATTAGACTTGGATTTCCTTTCAGGGTTAGCGCTGTGTGTTTTCAGCCTTCCTCTGCATTTTTTAAGGATATTTTCTCTTATTACTTACAGTGTTATGCAAACGTCATGCAAAAATGTGAAAAATGTACACAAAATAAGTGGTTTTTTATCAGTTACACTCCTGAGTAAGATAGATACACAATTATTTTTATTGTTTGCAACTCTGCAGTATTCACAATTGCAGTTAAAGATACAGAAAAACAGAACAGTGATAAAATAATTTATGACATGTATGTGAACGGGCAGACTTGACTCAAAAACTTACACTAAACTCAAACCCCCAAAAAGGTCATTGAAATGAATATTCACAAAACATCACGGATGTAATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATTCAAGATCATTAGATCATTAAACTATATCTAGCAGGCAGCAAAGTGACAAAGTAGCCACACAGCTTGAAGGTTGCAGGTACAAGTCCCAGCTCCAGGATGTGGAGGATGTGGAGTTTGCATGTTCTCCCCGTCTCCTCCTGTTTCCTTTACAGTCTAAAAACATGCAGTATAGGTGAATTCAGGTAAACTAAATGTCTGAATGAGAGTGTATATTTCCCAGCATTGAGGGTTTTCTCTAGTTTAACAAAATCAAAAAAAATGTATTTAACACACGATTTTCAATTTCATAAAATTAAACGTCTCGCCAAGTGTTACAAAAGCTACTATTTGGGAATGTTAGAGGGAGGGGAAAGTGCTGTGGTAGCTATTTTACATAAAATAGACTGGTGCAGTGGGTAGCGCTGTCACCTGACAGCAAGAACATCGTTAGTTCGAGTCTCAGCTGGGTCAGTTGGCATTTCTGTGTGGAGTTTTCCTGTTCTCCCCCTGTTTGCGTGCGTTTCCTCCGGGTGCTCCGGTTTCCCCCACAAGTCCAAAGACATGCACTATAGGTGAATTGGGCAAGCTAAATTGTCTGTAGTGTATGTGTGTGAATAAGTGTGTATGGGTGTTTCCCAGTACTGAGTTGCAGCTGGTAGGGCATCCGTTGCGGAAAACGTATGCTGGATAAGTTGGCAAACCCCATATTAATAAAGCGACTAAGCTGAAAAGAAAATGAATAAATGAATAGTTCACAAGACAAAAAAATAGCTTACTATTAAAATTAGTTTTTAAAAAAGGTTTTAATTCTGTGGCTGTTTACCTATGAATGATCTGTGGTTGTTGTTTGCTTCATAATGGTTGTTTTTTAAGTCTCTTGTTGCAGTTAAATTGGCTGCTCTTCTTCTATGTTCAGTAGATACATTTGCATACGTAAACCCTTTCTAGCAGTGACTGAATGAATCTGAGATTAGAATGCATTAGGATCTGACGGTGAAAAGTTTTTACATTTTGAAGTTTGTCCTCCGGGAAGCATTCAAGTGTCTTCTGTTGCTTCTGAAGAGCAGTGTTAAATGGAATCAAAAGTTGTATTTCAACAAAATAAGAAAAAACAATACAGTGTACTTTATGTAACATATCTGATGTAAAATATCTTACTCAGGACAGTACTAAATAAAAAAACATGCATTTTGTATAATCTTGTTTATTTGATAAAAAATTTCACATTTTCACAGCTTTTGCAAAAGGTTTCAAAACTTATGCATAACACTAAATATGTGATCCTGGATATTTTTTGTTATGGGAATCGCATTGTCTCTGCAG
Seq C2 exon
ATGAAAAAACTGGTGAGAAGACAACAGCAGCAGAAGCAAACTGTGTGCCCACAGGAGAAGAGGGAGAGTCCATCACAACAACATACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020354:ENSDART00000019059:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.978
Domain overlap (PFAM):
C1:
PF074236=DUF1510=FE(23.6=100),PF0004624=Homeobox=FE(43.9=100)
A:
NA
C2:
PF074236=DUF1510=PD(3.8=57.1),PF0004624=Homeobox=PD(3.5=28.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal3)
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]