DreINT0013618 @ danRer10
Intron Retention
Gene
ENSDARG00000003803 | LHX3
Description
LIM homeobox 3 [Source:HGNC Symbol;Acc:HGNC:6595]
Coordinates
chr5:71038588-71040274:+
Coord C1 exon
chr5:71038588-71038759
Coord A exon
chr5:71038760-71040071
Coord C2 exon
chr5:71040072-71040274
Length
1312 bp
Sequences
Splice sites
5' ss Seq
CAAGTCAGT
5' ss Score
2.74
3' ss Seq
TGCCTGTGTTTTGTGAGCAGGAG
3' ss Score
6.72
Exon sequences
Seq C1 exon
ATATCCCGGTCTGTGCGGGCTGTAATCAGCACATCGTGGATCGTTTCATCCTGAAGGTTCTGGATCGCCACTGGCACAGCAAGTGTCTGAAATGCAGCGACTGTCAGTCTCAGCTGGCCGACAAATGCTTCAGCAGAGGAGACAGCGTGTACTGCAAAGACGACTTCTTCAA
Seq A exon
GTCAGTGCTCCTGCTCCCCCACACACCATAGCAGTGTTTCTCAACCACATTCCCGGAAGATCACCAGCACTGCATTGGATGTCTCCTTTCTCTGTCGCACCCATTCTTAATGAGCTGATGGCCTGAATCTGGTGTGTTTGGTTAAGGAGACATGGAAATGTGCAGAGCTGGTGCTCCGCCAGGAACGTGGTTGAGAAACACAGCCTTTAGGAGTGTCTACAGTAAAATACAGTTGTAGAACGCAGTGGTATACGCAGCATATGAGTGTTATCTATAGTAAAGTGTGCTGTAGTATACCTTACAAGTTACTACATCATATTAGAGTACTTAGATTGTTAATGTATCCAACAGTATGAAGAACTGTATGAAAAGTTGCCTGTGAAACAGAGTTGGTGAACAGTGTGCATTATAATGATTTAGAGTAACTGATCATTTTACCAAACACTCTGATTGGCTGAGTTATTGATTGCATCAAAAGTGAGATTCCAAAACATAACGTGTAAAATGTCCTTAAAATATTAATATACACAGCAAAAACTGCAAAGCTGATCATACATTCTGTATAATCTAGCTGGAGGAAATTGACTAGTAAGTGTGGCTTGCTTACATAAAGCAGTTACTTTCATTGTAATGTTCAAAAACACTACAGTAAATGAGCTCTGTTCTATACATTCAATAAAATCCGGGTTGTTTTACTCTGACCTTGATTCAAGCATGGACAAACTCAAAGTTGGGATATTTATAAACAATGTAAATAACCATATTAACCCAACACAGAGTCAAATACAGACAAACACAAAGTTTTTTATTATTATTAAATTTAAAATCACACTTTTAAATCCGACTTTTGTGCTTTTGGTCCCAGCGTTGGGTTAAAAAATAACCCAACACTACAGAATATGTATATGTTCTGTATACAATGAAAACAATTCTGGGTTGTTTCAACACAACGTTTTAAAGTCAAGTGTGGACAAACCATACGAAAAGTATTCGATTTAAACCATTTTAACCCAATGTTTGTGTCAAATTTAACCCATTTAAAGCGGTTGCCTTTAAAGCAACGAGTGGATTTTACTTTAAAAAGTCAGTGAATCCATTGACTTTTATTATTTTGCAGGCATATTTCACAATTATAAGGCAATGAGTGAACCAATCTATTTCTACAGTGCACTTTTAAACCCATGCTGTGTGTCTGTGCACATTTGACCCAGCGTTGGCTTGAAAACAACCCAACACCACAGTATTTTTCACGTGGGTCATCTTCTCGCTTCAGATCTCCCCTGACCAGGGTTTGCCTGTGTTTTGTGAGCAG
Seq C2 exon
GAGGTTTGGCACCAAGTGCGCGGCGTGTCAGCAGGGGATTCCGCCGACGCAGGTGGTCCGCAGGGCGCAGGATTTCGTCTATCACCTGCACTGCTTCGCCTGTATCGTGTGCAAGAGGCAGCTGGCCACCGGGGACGAGTACTACCTGATGGAGGACAGTCGGCTGGTGTGCAAAGCGGACTACGAGACGGCCAAACAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000003803:ENSDART00000171230:2
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=0.017
Domain overlap (PFAM):
C1:
PF0041217=LIM=PU(94.6=91.4),PF036609=PHF5=PU(15.8=20.7)
A:
NA
C2:
PF0041217=LIM=PD(3.6=2.9),PF036609=PHF5=PD(82.9=91.3),PF0041217=LIM=WD(100=87.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCACATCGTGGATCGTTTCA
R:
CTGTTTGGCCGTCTCGTAGTC
Band lengths:
344-1656
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]