GgaINT0126303 @ galGal4
Intron Retention
Gene
ENSGALG00000000936 | LMX1B
Description
LIM/homeobox protein LMX-1.2 [Source:RefSeq peptide;Acc:NP_990689]
Coordinates
chr17:10148029-10149190:+
Coord C1 exon
chr17:10148029-10148207
Coord A exon
chr17:10148208-10149112
Coord C2 exon
chr17:10149113-10149190
Length
905 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TTAAACATTTCCTCCTCTAGGTC
3' ss Score
11.7
Exon sequences
Seq C1 exon
TTAAAAGCGATGATGAAGATGGAGATGTTAAGCCCACCAAAGGACAAGTAACACAAGGAAAAGGAAGTGATGATGGGAAGGACCCAAGGAGACCTAAACGACCAAGGACAATACTCACTACGCAGCAGAGACGAGCATTCAAAGCATCCTTTGAAGTGTCTTCCAAGCCCTGTAGGAAG
Seq A exon
GTAGGTGCTTCAGTAGGGACCTACATTCAGTTCTGACACCAGGCGGTGCACAAAGTGAGAGCGTCAGGTCAAAAAGGCCCCTGCCCCTTCCTGGGCCAGCAGCAGGCACTTGGGGGTGAATGCAGAAACCAGAAAGCATCTTGGGACCCGTTCTGTATCTATGTCATTTTTGATTATTCATTACGTAGAGCAGCTGTGTGAGTGATTCCCACGGAGCAACATATTTGCTTGTTGCAAAACACGGTCACGGACTTTCAGGGCCTGGGTAAAGTGACTTCATGCCCTTCTCCTTCCCACCACAGAGAGATTCACTCTCTGAGGAGATGGGTGCACAGCCCTGGTCCTACCACTTGTCCTTCCAGTCCTGTTTTTTTAAGCAAGTTAATCATGGTGTTGTCTCATTTATAACAGCTAAGGAAAGGTATGATGAAGCTGGTGAAAATGAAATCTTTGTGAAAACTAATCTAGATAATTATTTAAACCCAAGTTTGTCTGGAAAAAAAATGGAGTTGTATCACAAAATTTGTCTTTGTTGCAAAAAGTGACACTGTGCTGCAGGTGTACGAAGTACGTCTCCTGGGACAATGCAGTGTGCCCTGTCGCCAAAAGCATAAACACAGTCCGTAGCTCAGTCTGTAATTTTTCATTCAGAACTGGTTTATTGGTAAACTAAAAATCATGAAATGATTTAGTAACATTTTACACTGCTCAGAATATTTTTTTATTATTTATGAAACTAGTGATGTGAAGGGCAGAACTTGCACAAACTGTGCAAAAATATGAGGAATTAAAAAAAAATTCTGCGTGTGCAGTATTTATTGTAAATGCAAGTATCTTCCTCAGAATGTAACTTGCTAGATGTGGAAAAAAAAAAAAAATACAGCTTTAAACATTTCCTCCTCTAG
Seq C2 exon
GTCAGAGAAACTCTAGCAGCTGAAACAGGACTCAGTGTGCGAGTTGTCCAGGTTTGGTTTCAAAACCAAAGAGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000936:ENSGALT00000001376:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.192
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(47.4=45.0)
A:
NA
C2:
PF0004624=Homeobox=FE(43.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTAAAAGCGATGATGAAGATGGAGA
R:
AACCAAACCTGGACAACTCGC
Band lengths:
238-1143
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]