HsaINT1021940 @ hg38
Intron Retention
Gene
ENSG00000136944 | LMX1B
Description
LIM homeobox transcription factor 1 beta [Source:HGNC Symbol;Acc:HGNC:6654]
Coordinates
chr9:126695839-126696451:+
Coord C1 exon
chr9:126695839-126695982
Coord A exon
chr9:126695983-126696293
Coord C2 exon
chr9:126696294-126696451
Length
311 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACC
5' ss Score
6.54
3' ss Seq
ACACCCCTTCTGCCCCCCAGGGA
3' ss Score
9.25
Exon sequences
Seq C1 exon
AGGTCCTGTCCAGCCGCATGGAGGGCATGATGGCTTCCTACACGCCGCTGGCCCCACCACAGCAGCAGATCGTGGCCATGGAACAGAGCCCCTACGGCAGCAGCGACCCCTTCCAGCAGGGCCTCACGCCGCCCCAAATGCCAG
Seq A exon
GTGACCACATGAACCCCTATGGTAAGCCGCCCTACCCCCACCCGCCCGCCCCAGCACAGCCCCTGCCCCCTGCCAGGCCAGGCAGGCCTGGGGCCAGGACAGCCACCTGCTGCCCTAGGGCTCAGGCAGCATGGCCAGCACAGCCCTCCTGCCCCTGCTGACAGGAAGGGCCCCAGTCCTTCTTGGCCGGCACTAGTCAGCAGGCCATCCTGTCTCTCCCTGGCCTCCAGTCACACAGCCTACAGGGCAAACAGGGGGCCCCCAGGAGCCCCAGCCTGTACCCCGGTCCTGACACCCCTTCTGCCCCCCAG
Seq C2 exon
GGAACGACTCCATCTTCCATGACATCGACAGCGATACCTCCTTAACCAGCCTCAGCGACTGCTTCCTCGGCTCCTCAGACGTGGGCTCCCTGCAGGCCCGCGTGGGGAACCCCATCGACCGGCTCTACTCCATGCAGAGTTCCTACTTCGCCTCCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136944:ENST00000526117:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.962 A=NA C2=0.237
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCTGTCCAGCCGCATG
R:
AGGCGAAGTAGGAACTCTGCA
Band lengths:
295-606
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains