RnoINT0085174 @ rn6
Intron Retention
Gene
ENSRNOG00000003595 | Lhx4
Description
LIM homeobox 4 [Source:RGD Symbol;Acc:1308044]
Coordinates
chr13:73353980-73357111:-
Coord C1 exon
chr13:73356909-73357111
Coord A exon
chr13:73354009-73356908
Coord C2 exon
chr13:73353980-73354008
Length
2900 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGC
5' ss Score
9.89
3' ss Seq
AAGGTGGTTTCCACTAGCAGATG
3' ss Score
3.81
Exon sequences
Seq C1 exon
GCGCTTTGGCACAAAATGCACAGCGTGCCAGCAGGGCATCCCCCCGACCCAGGTGGTTCGCAAGGCTCAGGACTTCGTCTATCACCTGCACTGCTTTGCCTGCATCATCTGCAACCGGCAGCTGGCCACGGGGGACGAGTTCTACCTTATGGAGGATGGCCGGCTAGTGTGCAAGGAAGACTACGAGACAGCCAAGCAGAACG
Seq A exon
GTAAGCGGAGTGGCCCTGCTCACATGCCTCCAGCGCTTTGCAGACTGTGAGCTACGCACTGAGGTGCCTGCCTCTCTCCATCCTTCCTGTCCAGCCCTCTGGGCCCCGCGGATACTCAGCCTAGTCCGAGAATTGTAACCAGAGCTCTACAGTGAGATTCCGTTCTGAGCAACCCCCAAACCCTCAGACCTTGCTGGCTTTGTGAAAGCATTAATAAAGCTGTGGTTATTAGAGTTGCTAAGGTCCTTATGAAGTTGTGAGCTCAGTGGTCTCCTTGCCTGGAGCACAGCTGGGAGCTTGATTGATGGGGGTGAGGGGTATATTTGGGGCATACACCTCCTTCATCATCTCATTCCTCACAGGACTTGCAGGGCTGGCTTGTTTTCAGCTGTCTCTTCCCTCTCCTCAGACTGTGGGCTCAGGGGAACTGACTCTTGAGTGCCCAAAGCCCCAACCAATTTTATGTATTTCTTTCTAGGTCTTTCCTGGACTCAGTTACCCATGTTATCTGGGTCTAATACATGGAGAAATTAGGTTTTCATGGTGTGGAGCAGGCTGAGGCAAATCTTCAGGGCCCCATGTGATTCAGTGGAGCCAACCTTGGCTTTGGCTTGTGGCAAGATGGGGCAGGAGCCTTCTCTCTCTTGGGGACTCCTAGCTCTGGCCTCTCCTGGTGGACCAAGGACATTGGTCTTCTTCTCTCAGGGACCAGAGACCTCTCTAGATCCCACCCAAACCTTAATGTGCTCAATCGCTCTGGTTCAAGGGTTCTGAACCTTCCCAATGCTGTGACCCCTTAATACCGTTCCTCATGTTATGGTGACCCCAACCATAAAATTATTTTTGTTGCTACTTTGTAACTGTAATTTCGTCACTGTAAAATGACTCATACTATAGATCCCTGTGTTTTCCAGTTGTCTTAGGTGACTCCCAAAGGGGTTGAAACCCACAGGTTGACAACCACTTCTCTAGTTCCTAAAGCTCCATGCTGTTGCTCCAGGGTGTCACAGAAGGGTGTCAACACAGAGATAGCAAGGCCATCAGAACTCTGTCACCTCTACCAGACCTTCATGAAAGCAATACCTCTCCTGGGCCTGTCCTGGCTTGAATTGTCAAGGACCTCATGTTGACCTGTGTGTTCTCTGCCCAGAACCTCTTGGTTCTGTGGGTGATTCCAGAGGGGAGGGAGGCTGTCAGGAGTGTCACCTGGGAGGCCAGAATGACATCACAGGTCTTGTCATCTTCTGGGAGGAGTTCGGGTATCTCATTGCAGCCTTCTGTAGGACACGGGTCTTGGCACCCAAGGCTGTGTGGGCAGCTTACAGGCTTGGAGCTTCTCTGGCAAGTTGTATGACAGGCTGAGTCTCGGCCTTGTCACACTGGGGTGTTTCCTGGGACTGACAGGAAGTTGCTTATAAAGGGGAATACTAAACAAGAACAAGGGCCTAGCAGAGAGAAATGTAGACAGGAAGTGAAGTACGCTAAAGGATTAAAAACAGCCTAAGGTCCTTGTTCCTGGTTCCCAGGTATCCCTTGCTTCCAGCCGTCAGACAGGCTGGGGCCCTCCCTCCTATGCAGGAACCCTTGACATGGTAGGGGACGTTTGGCTCTTTTTAGCTGTCATTCCTTCTCGTTTCTCTAAACCTTCTTCGGGACTCATAATAACCTGCCTGGAGCTGAACAAAGGGTCTTATATCAGCGATTTGCATCGTGGTGGGAATGGCTTTGTTCATTCATCTCACCTCCTTTGATATTTATATTTTCAATACGACGACACTGCATTTTATGCCAGGGACAGGTTTCAGGAGACACTGCATAATTCAAAATGAACATATGTTAAGGCTAATTTTCCACGGGGATTAACGCTGTAAGTGTGTGTTGCGGGGAGGTATTTCGCAGTCTCACACCAATCCATAACCAAACTGTAGGTCGCCCTAATGCTACTTTCTATTTCCTCAGCATTATCTCCAGTACCTTGCTGAATGCTCTCTCCTAAATTAACAGCCCAGGGTGTCATGGTCTCGCTTGGCCTCCCTCATAGTGTTTTTTTTTATCACATTTAACTTCCGCACCAAAGTTATTGATTTTTGGGTACATTTTTCAGCATGAGCACTGCCACCACCACTTAATGAACACTTGGATGACATTGTTATAGGATAGTGGCGACGTGCCGATGACACACACACACTGATACACACACCACTGACACACATACCTGCACACTACTTCTCTCTCTCATCACACACCATAGCACAGCCACCTGGGCACACGCATGACACACATACAGCCACACGACATATACCACTACACGACCCACATATACAGCACACCTGGCCACACATACAACAGTAATACCACCTGCAACACACAGCACATATGTCGCTTGCCATGTACAGACACCACACACAATCCTGACAGCACATACCCTGTGAGCACACACCAGTCACATCACACACACAACACACACACACACACACAGCACACACACTGTTTCTTTTGAAGAAAGGGATTTTTTTGCTGCTGTGTTGTCCACAGCCTGGGCCTCAAACACTTGAGCTCAAGTGATCCTCTCGCCTCAGCCTCTAGAGTCAGCTGGAACTATCTAGATAGGCTTTCCTTCTTTTTTTTTTTTCATTTTTTTTCTGTTTTCATGATTTGAAAGTTTTTACATGAAGGCCATCTGCATATTTTGAAAGCACATACTTTGTTTATGATCAATAATTTAGATTCTGCATCATCAAACACGTGAGCTCACCAGTGTCAGTGTCCCTGGGTATGGGTACTTCCCCACGATGATGCCCTATTCTTCCCTGGAGGTTGTCTGAGGAAGGAAGTGGCGGCAGAGGAGGCCTGGCTACTTCCACTCAGCTGATCCCCATTAAGGTGGTTTCCACTAGCAG
Seq C2 exon
ATGACTCGGAGGCTGGGCGAAGCGGCCGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003595:ENSRNOT00000067253:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.022 A=NA C2=0.971
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.6=2.9),PF036609=PHF5=PD(72.6=88.4),PF0041217=LIM=WD(100=87.0)
A:
NA
C2:
PF0004624=Homeobox=PU(5.3=30.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
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]