RnoINT0085175 @ rn6
Intron Retention
Gene
ENSRNOG00000003595 | Lhx4
Description
LIM homeobox 4 [Source:RGD Symbol;Acc:1308044]
Coordinates
chr13:73351844-73353890:-
Coord C1 exon
chr13:73353855-73353890
Coord A exon
chr13:73352016-73353854
Coord C2 exon
chr13:73351844-73352015
Length
1839 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACC
5' ss Score
6.54
3' ss Seq
TTCCCTTTGCTTTGTGGCAGGTT
3' ss Score
9.83
Exon sequences
Seq C1 exon
TCCTCCGAGACAGGCCTGGACATGAGAGTGGTACAG
Seq A exon
GTGACCCAGTCTCCACCCGCTTTGCCCCTGAGTGATCCAGGCCTGAGGCAGGTCTGTGTCTCTCTCCCGCTGAGGGACAACTGGGACATGAGTGACACCTGGTGAGCGGTGGCGCTAGTGTACAGGGAGCTGAGTTCTGGGGTGTGGGGCTCAGGCGACGGGGAGACGGCCACCCCTGTACTTAGCGCTCTGGCGCATTACCGAAAGCTTTGGCCACATTTTCCAGGGGCTTTGGGTGCCGCCTGAGTGTTATTCCTGTGGCGTCTGGCGTCTTTAGGTAAACCCTCTGAATCGTGTATCCCTTTGCTTGTGGCAGGCATTTGGTTCTTTCAGAACAGAAGGGCCAAGGAGAAGAGGCTGAAGAAGGACGCGCGGGCGGCGCATCGTTCTGGGGGCACGTTCTAACAAGAGCGTCAAGAGGAGCCCGGGAGGCGCAAGCAGGCAGAGCGAAGCCGTCAGCAGAGGACTGCTGCGGGTTAGGTGACAGTGACCAACATGACGCTTCCCCGCAGGCTGAGCAGGGCTGGACGGCGGTGNNNNNNNNNNNNNNNNNNNNNNNNNTAAAATTTTTAAATTATAATAGCACCGAATGTTATAATAACAGCAAATAGTTCCCATAATCACATGAGAAAGTCCGTGCCAATGGCCAGTGGGGCTTGGGCAACCAAGGGCCCTGTACGGGCAACGGGCATGGGCTGCACGGAAATGCTTTCTAGTTTCACACGGCCCAGCTTTCGCTGAAACTAAGTGAGTCTTAGGAACTGGGTTCCTCCCCTGCCACAAGCTACAAACATACCTGACAACACACACACACACACACACACACACACACATACACACACACACCTGCCACACACACACACACCTGCAACAACACATACCCTGCCATACAACACACACCTGCCATACAACACACACACACACACACACCGTGCCACCACACACATACCATGCCATACACAACACACCTGCCATACACACACCACACCATTGCATACACACCCAACACACACACACACCTGCTATACACCACCATACACACCCTGCCCACATACACACACCCTGCCATACACACACACACTGGCCATACACACACACACTGATACACACACTGGACACACATACCACTGACCTCACATTCTCTCTCGCTCACACACATACACACCACACGGCATACACACATACACACACAATATACATACACACCCCAACATATACAACGACACCACTGCCACACAATACACATATAGCCACCACACACAACATATGTCCTGCCATGTACACACACACACAATCCTGACCACACATACCCTGACACACACCACCACACACACCACCACACACACACACACTGTTTCTTTTGAAGAAGGGATCTTGCTGTGTTGTCACAGCTGGGCCTCAAACACTTGAGCCTCAGTGATTATCCAATCCGCACAAAATCAGCCAAATAACCAAATAAAAGTAGCTGGAACTATCTAGCATAGCTTTCTTTCTTTTTTTTTTTCTCCTCCGAGACAGGCCTGGACATGAGAGTGGTACAGGTGAGCCAGTCTCCACCGCTTTGCCCCTGAGTGATCCAGGCCTGAGGCAGGTCTGTGTCTCCCGCCTGAGGGACAACTGGGACATGAGTGACACCTGGTGAGCGGTGGCGCTAGTGTACAGGGAGCTGAGTTCTGGGGTGTGGGGCTCAGGCGAGGGGACGGCACCCTGTACTTAGCTCTGGCGCATTACCAAAGCTTTGGCCCATTTTCCAGGGGCTTTGGGTGCCGCCTGAGTGTTATTCCTGTGGGTCTGGGTCTTTAGGTAACCCCTGAATGTGTTCCCTTTGCTTTGTGGCAG
Seq C2 exon
GTTTGGTTTCAGAACAGAAGGGCCAAGGAGAAAAGGCTGAAGAAGGACGCGGGGCGGCATCGTTGGGGGCAGTTCTACAAGAGCGTCAAGAGGAGCCGGGGAGGCAGCAAGCAGGAGAAGGAGAGCTCAGCAGAGGACTGTGGGGTTAGTGACAGTGAGCTGAGCTTCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003595:ENSRNOT00000067253:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.194 A=NA C2=0.500
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(45.8=84.6)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=19.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCGAGACAGGCCTGGAC
R:
CTCGGAAGCTCAGCTCACTGT
Band lengths:
206-2045
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]