DreINT0089791 @ danRer10
Intron Retention
Gene
ENSDARG00000068365 | lmx1bb
Description
LIM homeobox transcription factor 1, beta b [Source:ZFIN;Acc:ZDB-GENE-050114-2]
Coordinates
chr8:33370956-33372198:-
Coord C1 exon
chr8:33372083-33372198
Coord A exon
chr8:33371143-33372082
Coord C2 exon
chr8:33370956-33371142
Length
940 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
ATGATGCATTTACCCTTCAGGGA
3' ss Score
7.67
Exon sequences
Seq C1 exon
GTCTAGGACGGCGCTTCCTTGCAGGTAACATTGGGAATATTTAAAGATGTTGGACGGTATAAAAATCGAAGATCATCCGCTGCGGTCGGGACAAGCAACACTTGGAGTTATGCTCG
Seq A exon
GTAAGTCCTTCAACATTTGTAGTATTTGTCTTTAAAAGCAAGCCTGTAAATGCTCGCAAATACTAAAGTAATTCTGGGAATTTTTATAATGCTGTTTCTGTTAAGATAGATAGAGATCTACAGTACAGCTGGAACTGTAGCAGTCGGGCCATGCAGTCGGCTGGGATGCACCCGCATGTGTCATGCATTTGACCGGCCGGCCGCATTCATCTGTTGAATAATCAAAACTATTTCCCATAGAAAATAATCCAAATACACGAGTGGTGTATTTAAATAATAAAATAATTTCTCTCATATTTACTGCGCAACGCAATGCAATTATTTCCATGCTCTCATGTTGTTGTTGTTTTAGGCTATATAAACTGCACGTATTTCCCATTCAAACAGCTGCACCATTACATCTTATTATGTTTGCTTAATTCTAACAAATAACTGTAACGTTTGAATGGTAGATGGACAGAAATAAAAAAATAGGTAAAAATGAATAATAAGAAGAAAATCTGCACAATTAGGCTATATATTTTCTTTTCTCTTACCCCATTAGGCTATTTATTCTTTGGACCGGAGATTTTGTTTACACATGATCTTGAAGGGTACATAAATACAATTGCAAATATTTAATTGGCAGTTTTTTGAGCATAGGCTAATAGTGTCAATTTTAGATTTGCCAGATATTGTGCAACGTTTTAATTTTTGTGCGTATGTAATAATAATAATAATAATAATAATAATAATAACAATAATAATAAAATAATAATAATAAGAAGAAGATATAATAAACAATTAATATCACACGTAATATTATTCGGACGCCTTTTTTCACAATGTCATATTGGTTTATGAGTATCTAGAATACAGAATTATATTACTAACACTTGTTCAATAATTACCCATTTATGTAAAATATTTATTTTATAAAAATGATGCATTTACCCTTCAG
Seq C2 exon
GGACGGAGTGCCATCACCAGGCGGTGTGTGAGGGGTGCCAGCGGCCGATATCCGACCGCTTTCTGATGCGCGTCAACGAGTCTTCATGGCACGAGGAGTGTTTGCAATGCGCCGTGTGTCAACAACCGCTCACCACCAGCTGCTACTTCCGGGAGAGGAAACTTTACTGCAAATATGACTACCAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000068365:ENSDART00000076420:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0041217=LIM=PU(94.6=84.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTAGGACGGCGCTTCCTTG
R:
TGTTGGTAGTCATATTTGCAGTAAA
Band lengths:
302-1242
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]