RnoINT0085176 @ rn6
Intron Retention
Gene
ENSRNOG00000003595 | Lhx4
Description
LIM homeobox 4 [Source:RGD Symbol;Acc:1308044]
Coordinates
chr13:73349369-73352015:-
Coord C1 exon
chr13:73351844-73352015
Coord A exon
chr13:73349761-73351843
Coord C2 exon
chr13:73349369-73349760
Length
2083 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CTCCGTTCTTTTGTCCACAGAAG
3' ss Score
10.27
Exon sequences
Seq C1 exon
GTTTGGTTTCAGAACAGAAGGGCCAAGGAGAAAAGGCTGAAGAAGGACGCGGGGCGGCATCGTTGGGGGCAGTTCTACAAGAGCGTCAAGAGGAGCCGGGGAGGCAGCAAGCAGGAGAAGGAGAGCTCAGCAGAGGACTGTGGGGTTAGTGACAGTGAGCTGAGCTTCCGAG
Seq A exon
GTGAGCAGGGCTGGAGGGGTGAGGCTGAGGCCCTAGGTGAGACACTAGGGGACGCTAATCCTTGCCAGCAGGAGGGATCTTTCTGTTGACAACCTCTTGGGCACAGGGTTTTCCTAGACTTTCACTAAAGGGTGGGAAGGGCGTTCGTGGCCCTTCCAGAAGGGGCGAGGAGTAAAGAGCAAGAGAACAGACAGCGGTTGCTGAGATACAAAGGCTGGGGTCCCGGGGACCCAGCCTAGCCCTGTCCTGGCCCAGAGGCCCCTCCCACTTTCCTGTTGCCAGAGATGCCCTCAGCAGCCCACACAGTTGTGAGCAGATGGCCATGTCTTTGCCCCAGCCCTCCTGCACCTCTCCCCTTTGCAGGGACACTGAGCTCCTCCCACGGTCCCCTAGAGTAAGCCGGTCCTCCAATCCTGGTGGAAGGAGGACATGCTCAACAGGCCTTTTCCTGGGAAATCAATAATGTGAGTGCATGACGGGGAACTGGCTGCGGTTCTGAGACCCCTCCCCCCACCACTCACTCCATCTGTCCTCTGCACACCAGCTTTGCAGCATGCGCTACGTTCAAATCTGTGCATCAGCAAAACTGCAGATTACCGCATGAGTGGGTCCTCAGGTTGTTTACAAATAGCCACGACTGTTCTTGGTCCCCGAGCCCGCAAATACAGATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTACTTTGGGTAGGGAGGGAAGAGTCCTATGCCGAGGGTCAGAGACCTGATGTCTAGGGTAGCTTTGCCAAAGCATCCGTTTCTCCCGAAACGGCTTTACCCGGGGATGTCGTCCTTACCCATCTCACAGAGTTGGCATCTGTGGACACACCCAGCTCTGGATGTGCTTGGGGAAAGATAAGCACACCTCTGTACATGAAGATAAATGGATGGCATGGCTGTTCCCATTGTAGCCTATCACAGGGACTGCAGGTACCAGGCGAAGGGCCAACTTAGCCATTTTACTGTGGAAGAGTCTAACCTCCGCCTTCCTGCTCCCTTTGAACGACACATGCTCCCTCTTTCTTAGTGTTTGGGAATCGGAGAGGCGAGGTTTTGAAGTCTAGTCACAGTGGCTGTTTGTGGACTGGTAGACACGGGGAAGGAGGACACGGAGTACTTGCTTACCATAAGCACAAAGCTGTGACGTCTCTGACCAGAGCCCAGGGCGCCACTGAGCCCAAATGCTTAGGACACAATGCTTAGGACCCAAGGAGGGCCAAGGAGATCTGTGCCATTCCCAGGCCTTTTGGCAAGATTGGGAAAACAGGTTAATCCCATCCGAGCTGCTCAAACCCATGCCTGGAACACAGAGGAACACTATCTCTCATGGTTTGTTTCTCTTGGGCACGGGCAGGCATCTGACAATAACGTGTTCTCTCTGGGAAATACTCAATCTTGTAATTCTTAAGACTAAACCTACTCACCTCTGTTGGAGAGAGAAATTCCTTCAGAAAATTCCATTAGATCCCCTTAATGAAATTCTTCAAGAAACCAGAAGGTCCATTTACCTTAATCGAGTCTTTCTTATCCTCAGTAAGTAGGTTATGGGATATAGAAAGGCACTGAGTTTATGATATTGAACTCCGTTTTGGGATGGATCAGGACTTTACCTACAAGTCTAAGAGTGGTCCTTAGCCACCTTTGTCAGATAGGCCTGTTTCTCAACCAGCCCAAACAAGTACTTTCCTTGGTTTGAAAACCTTCAAAGTGAACCAGATCAGCATGGTTTCCGTTTGTGAGGGAATGTGGTCCACCGACCCCTGGCAGGCATTCACTCTCCTCAGGGTGGCCAGAGGAGCTACTCTAGACCACCAAGCTCAGCAGCCACTTCCAGCCCCTGGGGCCTGGGGACTTGGCTACAGGCCTTCCTTATTTTCCCTTTGGTTGGTTGCTGTCTGGGTGGCAGGCTGACGTGTTGGTGTCTGATCCGGGCTTGGCAGGGAGGCAGCTGCTGTCCCTGGGCATCCTTCCTGGCCATTGTGTTGCTGGTTGTGAAAAGCAGGGGCCACAAGAGTCCTGGGCACTGACGATCAATCTCCGTTCTTTTGTCCACAG
Seq C2 exon
AAGATCAAATACTCTCAGAGCTTGGCCACACCAATAGGATTTATGGCAACGTGGGGGACGTTACAGGCGGACAGTTAATGAATGGGAGCTTCTCCATGGATGGGACAGGACAATCCTATCAGGACTTGAGGGATGGGAGCCCCTATGGAATCCCCCAGTCTCCATCCTCCATATCGTCCTTGCCATCCCATGCTCCTTTGCTCAGTGGGCTGGATTACACAGTGGACAGTAATCTGGGCGTCATTGCCCATCCAGGGCAGGGAGTAAGCCAGACACTGAGAGCCATGGCTGGGGGGCCCACCTCTGACCTCTCGACAGGAAGCAGTGTAGGCTACCCTGATTTTCCAACTAGCCCAGCCTCCTGGCTTGATGAAATGGACCATCCTCCTTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003595:ENSRNOT00000067253:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.658
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=19.0)
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:
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]