DreINT0089065 @ danRer10
Intron Retention
Gene
ENSDARG00000039458 | lhx4
Description
LIM homeobox 4 [Source:ZFIN;Acc:ZDB-GENE-060728-1]
Coordinates
chr8:14416228-14421132:-
Coord C1 exon
chr8:14420961-14421132
Coord A exon
chr8:14417901-14420960
Coord C2 exon
chr8:14416228-14417900
Length
3060 bp
Sequences
Splice sites
5' ss Seq
GAGGTCCGT
5' ss Score
4.55
3' ss Seq
TTGTGTTTTCTTTCTAACAGATG
3' ss Score
11.77
Exon sequences
Seq C1 exon
GTGTGGTTTCAGAACAGACGGGCAAAAGAAAAACGGCTGAAGAAAGACGCGGGCCGGCATCGGTGGGGTCAGTTCTACAAAAGCGTCAAACGCAACAGAGGCTCCAGTAAAACAGAGAAGGAAAGCTCAGCCGACGATGCAGGACTCAGTGACAGTGAGCTCAGTTTCAGAG
Seq A exon
GTCCGTCTCTTTACATCTGCCACCACTCTAAGACTTATTATTCTTGTCAAAACCTTCATAAATTCATTTCCTTTCCCTTTCATTTAGAAAAACACACCATTTGATGAATGGTTTGTAATATTCAAATGAGGTTCATTTTATGATTATTCTTTTTTTTTTTTTTTTGTCGGCCCGTTTTGAGAACTCATAAAAGTCTAGAGCTGCTTTCAAATGGAGGTCGTGTTTACGAGAAATGAAAGCAGCGATGCGCAAACTCTATAAAAATGGTGAAGCTTTTAGTCAATTAGAGAGGCAGCATGCAGTGGCTTTGTAGTTGTTTGAAAGAACAGAGTAAGGTTTGTGCTCCTGTGTGTTTGGAGAGTAAATCACAAATACTGCATATCTGATCTTTACAGGTGTTACTAAACCTCTTTTTAAATTCCCTTTCATAGAAAATCTGTTCACTCAGTGGCCATATTTACAATGCCATCATGCAGCTGCTTAAGTGCTGTGTATATGAGTCATGAAATCCCAATAACTGCTTGATAAACTGCCATTTAAAATCAGGAACAAAATCTGACATGAGTAGAGATGAGATGAGTTGAGATGAGATGAGATAAGATGAGCTGAGATGAGATGAGTTGAGATGAAATTAGTTGAGATGAGGTTGAGATGAGATTAGATGAGATGAGTTTAGATGATATGAGATGAGTTGAGATGAAATTAGCTGAGATGAGATCAGATCAGATGAGTTGAGTTTAGATGAGTTGAGTTGAGATGACATGAGTTGAGTTGAAATAAGATGAGATTAGATTAAATGAGATGAGTTAAGATGAGATCAGATAAATTGAGTTGAGATGAGTTGAGATCAGATGGTAGAGTTTAGATGAGTTGAGTTGAGATGACATGAGTTGAGTTGAAATAAGATGAGATTAGATTAAATGAGATGAGTTAAGATGAGATCAGATAAATTGAGTTGAGATGAGATCAGATGAGTTGAGTTTAGATGAGTTGAGATGAAATGAGTTGAGTTGAAAAAAAGATGAGATTAGATTAAATGAGATAAGTTAAGATGAGATCAGATAAATTGAGTTTAGATGAGTTGAGATCAGATGGTAGAGTTTAGATGAGTTGAGTTGAGATGACATGAGATGAGATGAGTTGAGATCAGATGAGCTGAGTTGAGATCAGATGAGATGAGCTGAGTTGAGATGAGATTAGATGAGTTGAGATAAGATGACATGACATGAGTTGAGATGAGATGAGTAAGTTGAGATTAGATGAGCTGAGATCAGATGAGATCAGATTAGTTGAGATGAGATGAGATTAGATGAGCTGAGATCAGATGAGTTGAGATGAGATGAGATTAGATGAGCTGAGATAAGATGAGATCAGATGAGTTGAGATTAGATGAGATCAGATGAGTTGAGATGAGATTAGATGAGTTGAGATGAGATTAGATGAGTTGAGATGAGATCAGATGAGCTGAGATGAGTTGACTTGAGTTGAGATGAATTGAGATGAGATTAGATGAGTTGAAATGAGATCAGATGAGTTGAGTTGAGATGAGATGAGATGGGATGACATGAGATGAGTTGAGATGAGATTAGATGAGCTGAGATCAGATGAGATTAGATGAGTTGAGATGAGATCAGATGAGTTGAGATGAGATTAGATGAGCTGAGATCAGATGAGATCAGATGAGTTGAGATGAGATCAGATGAGTTGAGATGAGATGAGATCAGATGAGTTGAGATAAGATCAGATGAGTTGAGATAAGATCAGATGACTTGAGATGAGATCAGATGAGCTGAGATGAGATGGGATGACATGAGATGAGTTGAGATGAGATTAGATGAGCTGAGATCAGATGAGATTAGATGAGTTGAGATGAGATTAGATGAGCTGAGATCAGATGAGATTAGATGAGTTGAGATGAGATCAGATGAGTTGAGATGAGATGAGATTAGATGAGCTGAGATCAGATGAGATCAGATGAGTTGAGATGAGATCAGATGAGTTGAGATGAGATCAGATGAGTTGAGATAAGATCAGATGAGTTGAGATAAGATCAGATGAGTTGAGATGAGATCAGATGAGCTGAGATGAGATGAGTTGAGTTGAGATTAATTGAGATGAGATTAGATGAGTTGAAATGAGATCAGATGAGTTGAGATGAGATGAGATCAGATGAGTTGAAATGAGATCAGATGAGTTGAGATGAGATGAGATCAGATGAGTTGAAATGAGATCAGATAAGTTGAGATGAGATGAGATCAGATGAGTTGAGATGAGATCAGATGAGTTGAGATGAGACAAGATGAGTTGAGATGAGATTAGATGAGTGAGATGAGATCAGATGAGTTGAGATGAGATCAAATGAGTTGAGATGAGATTAGATGAATTGAGATTACTTTAATCTTACTATGTAATGGTAAACCGAACACAGATGACACTGTACTGAAAAACAAAACAAAAAATAAATAAATAAATGTAATGGCTGTAATTTTGATAAAGTTTCAAAAGTGTTGACAGTTTTGCTTCATGGGCAAATTTGAATAGTACACTCTTAGAAATCATGGTTCTTTATTGGCATTGAGGGTTCCATATAGAATCGTTATATTCCCGGACAGGGTCTTCGAGATAGGGATAGGTTCTTTCGATTCCTTAAACTAAGAAAAAATGGTCCTTTTAAGTGTTCACTGACGGATTTTTTTGGGATCCTACAAAAATGTGTCAAATGTGTACTGTCTTGAAGGGGGTGGGGCATGTCAAATACAGGAGAGCATTTGATTAGTTACAATTTGACAAGAAACTGAAGTATGAGATGACGTGAATAAAATTGTTGATCCATTTAGGCGGAAGTGACAAACTACAAGCTTTACATGTTCATATCAGTTTTAAATCTCCTAAATGGTCACTGTTTTGGAGCACACTGACTTATAGATATTCTAAAACTAACAATACTGATACTAAACATCTAAAAACTTTATTTTAGTTTCATGAGACTTTTAGGAGCTGTTGTATTGTGTATTATGAGTGAAACGTTTTGAAACTGATGTTGTGTTTTCTTTCTAACAG
Seq C2 exon
ATGATCAGATCCTGTCAGACTTGGGTCATGCTAACGGCCTGTACGGAAGTGTCGGCGACGTCTCTAATGGTAACATGCTCAACGGGAGCTTCTCTTTGGATGGAGGCGGGCAGCCTTACCATGACCTGCGGGCAGGGAGTCCCTATGGCCTGCCTCAGTCGCCCTCGTCCATCACTTCCCTGCCAGGCCACACTCCTCTACTCAACAACTTAGGCTTCAGCATGGACGGCCTCATGGGTCAGGCCGGTCAGCCCAGTGTGGGTCAAGCTCTGAGAGCCATGGCCGGAGGCCCCACCTCTGACCTATCCACAGGAAGCAGCACGGGATACCCAGACTTCCCCACCAGCCCGGCCTCATGGCTCGATGAAATGGACCACTCTCAGTTCTGAGGTCAGACACTATGAGGGAAAGTGCGCTACTATGGACAACATTTTATCGACGTAATTCCCAGAACTGGCCACGATTGACAGTGTTCGGTGTGGGCAAACCCCCATGGAATGCCTGCACTGTATCATTTTGTAACTCGTATTTTTTCATCGTTCTCAAAACTGGATTGGAGGATTTCCAGCATGAGAACCCCCCAGGCCACCCTGGAAAATTAATCACGATCCAACGCGTTTTTGAGAACAGGAGGGTTCCATGCATGTTTCCGAATGAGGAGGAAAATCGTCCACATTCAAAATGCCGACGCACTTTAATGTATGTTCCTCCTCGACTGAATACTGGAAACAGAGGAGCGCACCGAGCAAGGAGAGATATTTAAACAAGTGGCACAAGTGTATCTTTCCTATTTACAAGGGGTTGGGATTTTAATGGTTGACACTTTCTAAACGGCTCTACTAGAGACGGTCCTTCTCGTCAACAGGCCTGAAGAACAGAAAAAGGTTATTTTTTAATAAGGACGAATCCGCATGCACTGCTCTGAGTTTTAAAATCTCTGTGTCAATGCTTCTTTTTGGTCATATCCAGGAAGATAGATTGAAATTAAGGTTATTATTTATTTATTTTTTGGTATTACCACATTGAAATGTGTTTTCGTTCCTAGTCATTGCTCCATGAGCAAAACTTTATATATTTCAATGCATTTGGATGTTATTTATTTCAGAGCAGATGACAGTAGTGGATTTCCATTACACAGACACAAGTACCTTTATGGCCTGATCAGTTATTATCAAGCAAACCAAGTGAAAGGGAAACTTACTCTGCTATTTTCTTTCTTATTAGACACGTTTAAGCAACAACTGTGAGGATTTCATGTTATTTATTTCTATTTTGGGTACCAGTGTCAGTATTATGAAGGGTTGAGTTATGGGGAAGACTACAGTGATGTTATAAACACAAGGAGAATCATTTTCAGTTCGATACTGCAAAATTGGACCCACACACTGGTAAAAGGGATGTTATGCTGAAAAAGTGAACATAAGCTAATAAGAGCAACATGGAGGAAAACAAGAAGAAAAATAACCATGTTTTTGTTGAGTCTTAATGGCTGTAAATTTTGTAAAGTCTCAAAAAGTGTCGACAGTCTTGTTTCATGAGCACTATTTATTGCTATGGATCTTTGGAAAAAAAAAAGAGCACTGAATTTAGTCCTATATGCCTTCTGTCCAATGGTATGAATTGTGTACAGTCAAATCTATATGGAGAAATAAAGTCGAATCGTCTTTGGGTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000039458:ENSDART00000057644:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.552 A=NA C2=0.736
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=19.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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]