RnoINT0085171 @ rn6
Intron Retention
Gene
ENSRNOG00000018427 | Lhx3
Description
LIM homeobox 3 [Source:RGD Symbol;Acc:71078]
Coordinates
chr3:3654755-3655934:-
Coord C1 exon
chr3:3655766-3655934
Coord A exon
chr3:3655174-3655765
Coord C2 exon
chr3:3654755-3655173
Length
592 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
AGCTCTCTTTTCTGTTGCAGATG
3' ss Score
11.54
Exon sequences
Seq C1 exon
GTGTGGTTCCAGAACCGCCGGGCCAAGGAAAAGAGACTGAAGAAAGACGCAGGCCGGCAGCGCTGGGGACAGTATTTCCGCAATATGAAGCGCTCCCGCGGCAGCTCCAAGTCCGACAAGGACAGCATCCAGGAGGGACAGGACAGCGACGCGGAAGTCTCCTTCACTG
Seq A exon
GTAAGTTGGTCGCGTTAACTCGGGCTGGCCTCCCGGCTCACTTCTCCAGCTGCCTCTCCGGGGAGGATCCATGTTGGCCCTCAGGCTTCATGTTCCTGAGGCGACCGGCTGCAACTCTGGAATTATACAACACGAAGCTTCCCGAAGGCAGAGAAGGTACTTCCATCCTCCGCTGAGGGACCCAACTCTTATTTTCTCTACCAGGATCGCCGCTCACATCCCTTAATACCCACTTCCGTTTGGGACCGTATTGTGACCTCGGTTACTAGTACAGCCTCTGGGCCCTTAAATTTTCTCATCTATGAAATGAGTCCCTCCCAGAATTGCCACATCCTGGGCACTGGCTGGGGTTGCAACCTCTCTGAGCAGAGATCAAAGCCTTCCTTGGAGGGGCAGAGGGTAGAGGAGTGAAAGGAGGAGGCTGAAAGCTGGCCTAAGTTGAGAGTGCTGAAGAGACTGCCGCTGACCCATTCGTTCTAGTGTATAAGACGGCCTCCTCTATTCAGTCAGAGTACTATTCAGACACTACAGGAACCCGTAGTCTCCTGGTAGAGGCATGAGCTTCTCAGCAGAGCTCTCTTTTCTGTTGCAG
Seq C2 exon
ATGAGCCGTCCATGGCTGACATGGGGACTGCTAATGGCCTGTACAGCAGCCTGGGAGAGCCTGCCCCTGCGTTGGGCCGGCCTGTAGGAGGCCTGGGCAGCTTTACATTGGAGCACGGAGGTTTGGCAGGTCCAGAGCAGTTTCGAGAGCTGCGTCCAGGCAGCCCCTATGGCATCCCACCATCTCCTGCGGCCCCACAGAGCCTTCCCGGCCCCCAGCCTCTCCTCTCCAGCCTGGTATACCCAGACACCAACTTGGGCCTTGTCCCTTCGGGGCCTCCAGGTGGGCCCCCACCCATGAGGGTGCTGGCTGGAAATGGACCCAGCTCTGACCTCTCCACAGAGAGCAGTGGTGGCTACCCAGACTTTCCTGCTAGCCCTGCCTCCTGGCTGGATGAAGTAGACCATGCTCAGTTCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018427:ENSRNOT00000025047:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=NA C2=0.978
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=19.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGGACAGTATTTCCGCAAT
R:
GGGTATACCAGGCTGGAGAGG
Band lengths:
350-942
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]