GgaINT0036062 @ galGal4
Intron Retention
Gene
ENSGALG00000003424 | LMX1A
Description
LIM homeobox transcription factor 1-alpha [Source:RefSeq peptide;Acc:NP_001244317]
Coordinates
chr8:5163884-5166718:+
Coord C1 exon
chr8:5163884-5164051
Coord A exon
chr8:5164052-5164564
Coord C2 exon
chr8:5164565-5166718
Length
513 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
CTCCTTCCTTTCTCCCCAAGGTG
3' ss Score
10
Exon sequences
Seq C1 exon
CCCAGCCGAACAGCAGTGGCCCTGGGGGGCTGGAGGGGCTTATGAACCCCTACACTGCTCTGCAACCCCCACAGCAGCTCCTGGGCATGGAGCAGGTCTACAGCTCCGACCCCTTCCGGCAAGGGCTCACCCCCCCACAGATGCCTGGAGACCACATGCACCCCTATG
Seq A exon
GTAAGGCTGTAGAGGGGGGCAGGCCACAAATCCCCTGGATTTGCGCTCTTGCTTGTCCTCACAGTGTCAAAGGGTGGGCTGCATGACGGGGGTGCAGCAAGTTATGGGAAGGCAGCAATCTCTGCTGCCGTAAATCCCCACAGTGCAGAACTGAGGGCACTAAGGTGGCCAGCACCATCAGGGCACCGCGCTGAGCAGCTGGACTCAAAGCCAAGGGGAGTAGGAAGCAGGAAGCCCTGGTAGGAAGGTTATGAGTGCCATCTCCTCCCTGATGGTGCCACCTCCCTCCTAATAGTTCCACCATCTCTCTGCTGATGCCATCCCAACATCTCTGATGGTGCCAACACCTTTCTGATGATGCTAATCCCTATGGGTTTAGCACCCTGGCATGGGACAACACCCCCAGAGCATCTCAGCAGGCTCTTGGTGTCCCAGTAGGAGCCGGCTGCAGGGGCTGGGAGCTGCAGCAGCACGCAGCATCCCTCCAGCACTGCTCCTTCCTTTCTCCCCAAG
Seq C2 exon
GTGCTGAGCCCCTCTTCCATGACATGGACAGCGACGATACCTCACTGAGCAACCTGGGTGACTGCTTCCTCGCCACAGCAGATGCGGGGCCACTGCAGACACGGGCGGGGAACCCCATCGACCACCTGTACTCCATGCAGAGCTCCTACTTCACCTCCTGAGCATGGCAGGGCCCTGCAACGGGACGTCGTCCCGCAACATTTTGTAGCTCGGGATGCCCAGGGACCCAATGAGTTTTGGGTTGCATAGTTTCATGTTTCTCTTAGGATCCTAGGGTTAGGGGCAGGTTGGGCAGCTGGCGGGTTGGATTCAGGTTGCCGTGCAGATGTAGAAGCCTGGAGACGTCTCCCCAGGATGTGGGGCTGGGTGTACGTGTGTGGCACATGTGTGTGCGGAGCCGTGCGGCTGTGTGCGGGGATGTCCCGCCAGATTGTATCCACAAAGTTTATTTCTAAGTCTATCAGAAATTTACTGTACAGCAAAAGTAACTTTATTTTCAGCGTGAACCATATTTAAGGAAATACTCAATGCACTTAAGTTATAAGATGAAATGATTTACTTTTTATAAACGTTATGTTTAGGTTGCAAAAGCCCAGCGGCAGGGAAGGAACACCTGCTTGTTTCAGGAGGTAGGTCTGGGTTTTGGGGTCGGTTCTTTTCGGTGCTCTCAGGTTACCCCACTTGTTTTGAGGTGGACTCCGCAGCAGGCTCCTCACCAGAAGGGCGGTGGGGACGGCAAGGTGACAGCATCCTGTCCTCACCACTCAGCATGGCTGGTGCTTGATGCTGGAGATGGAGAAATCCCCGCCTCTATCCTCCAGCACAGACCCATCCCATACCCAGAGGTGGGTGATGGGGTGGTGTGGAGTGATGTCCCGGCTCTGGGAGGCACCAGCCCATGCCGCCAGGAGGAAGGAGCCCTGCATCTCCCACCCTACGCACGGGTCCATCTCTGCAAGTTCTCCGGGTCGAGCTTTCAGCCGACCATCGCCTCATCCCCGTCTCGTTTTCATGCGTTGTGTCCTTTTGTGCTGCTGTTCCCAAACGATGTAAAGACATGCAATGAATGGCTGCAAGGCTCAGAACACTGGTTCATTGGCACAGCTTGATTTGACACTGAATGTAGCAGGGTCTGGAGGTGGCTGACCCGGCAGGAGATGCTGACACTCTGTCGGGTATCACGTAGCAAGGTGAAATTAAAAGACAACAAAATCCCCCCAAAAAACCAACCAACAGCCATGCCTGGTCTCTTCTTGTGTGGGGTGTCCTGTTGACTTGGGAGGGATGGGTTTGGATAATCTCCCGAGTCAGCAAGGAGTTGGGTATCTCTTCTTCTCATTGGGTATTAAATATCAGTGGAGGGTCAGGCTGGATATCAAGAAAAGGTTCTTCACTGGAGGGTGGTGGGGATAGGCTTCCCAGGGCAGTGGTCATGGCACAGAGCTGCCAGAGATCAACGAGCGTTTGGACAACGTTCTCTGTCACATGGTCTGAATTTTGGGTGGTCCTGTGTGGAGCCACGAGTTGGACTCCATGATCCTTATTGGTCCCTTCCAACTTGGGATTTCTATGGTTCTATGATCAAGTATTCTCTGTCCTGGGGCTGTGCTGAGTCTTGAGGGTCTCTGCAGCCAAGGAATGGAGGTGAGTGGCTCTAGAAGTGACACAGTGCCCACAACCCATGGGGATGGGGACTGCTCTGTCAACCTGACACAGGAAAATGGCTGGAATTTTCTGGTATGAACAGGATGGGAAATTACTGCTTGGGATTTTTCTGACACTTGGCTTAGTGGTCTTGGAGGAATGCTGGCTGGTGCTAGCAGGGTGGAGGGGATCTGGGCGAGGTGATATTCATCGTGGGATGAAAGTGAAGATGTGCTCTGCTTGTGGGAAGGGGGCTTTAGGAAGGATGGAGGAAGTGTGGCGTGGAGGAGCTGCCGTGAAGCCAGCATGAGCCTGATTTGTAGGATCCAGGTGTACATAATGGCTGGGTTAACACCACCCAGGCTTGCAGTAGAAAAATGGATGTTTCCACTCATGATTATTAAAATTGCCTTAAAAATTGCCTTGCTTGGATGTTTCTTAAAACATTGCATTTTACATTTTTTTTAAGAAAAAAAAAAAAAGCTTTAAAGATGAAAGGTTTGCTTTCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003424:ENSGALT00000005411:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.982 A=NA C2=0.679
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CAGATGCCTGGAGACCACATG
R:
ATCTGCACGGCAACCTGAATC
Band lengths:
358-871
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]