HsaINT0090845 @ hg19
Intron Retention
Gene
ENSG00000139624 | LASS5
Description
ceramide synthase 5 [Source:HGNC Symbol;Acc:23749]
Coordinates
chr12:50536857-50537840:-
Coord C1 exon
chr12:50537735-50537840
Coord A exon
chr12:50536988-50537734
Coord C2 exon
chr12:50536857-50536987
Length
747 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
CTCTGGTTATACATTCACAGTAT
3' ss Score
4.03
Exon sequences
Seq C1 exon
ATTTATTGCCAAACCCTGTGCACTCTGTATTGGCATCGAGGACAGTGGTCCTTATCAGGCCCAACCCAATGCCATCCTTGAAAAGGTGTTCATATCTATTACCAAG
Seq A exon
GTAAGTGGGCAAAGAAACAGAGAGGAATATTCACATAAGGCGTTGCTCCATGGGGCAGGGGAGGATAGAGAGCACGTACCTCTAAGGGTAAGGATAGGATGGGATGGTCCTTCATATTTGAGTAGTCCATGTAGCTATATGGAGAGCTTTATCCCCTCAGGGAAAACCTTTGGGCCCTACGTATGTCAAGTTTACGTACGTAGTAGGTTTGAGTTTTAGGCCCAGCAGCCACCCTTACCCCTCTTTCCCCAGACACATACCATATCTGGTTTTTGTTTTTCCTTGTTCCAGTTTCTGTCACTGCCTAGTTGTGTGATCGAGATGGAGACAGTACTGATAGCCTTTGCAGTTTGGGTTTTTTGTTTTTTGGAGAGACAAGGTTTTGCCATGTTGCCCAGGCTGGTCTCGGACTCCTGGGCTCAAGCCATCCTTCGGCCCTCAGCCTTCAAAAATCCCAGGATTACAGGCATGAGCCACCATGCCTGGCCTGCAATTTGGGTTTTTAATATCCTTTTTTACTCAGCTTGGGCTGGAGGAAGAGACAAAAGGATATGTATAGGTGAGCAGTACAGGTCCTTGATATGTAAGATAAAATTTCTTACTAAAAATGACTTTGGGATAAAACTTGGAAAGATAAACATCACTTGAGCCACTTATGGCTATCATACCTTGTCGCTCAGCTAGTCAATGGGATTGAAGGAGGGGTATGAGGAGACGGGTGTTCTGACTCTGGTTATACATTCACAG
Seq C2 exon
TATCCTGATAAGAAAAGGCTGGAGGGCCTGTCAAAGCAGCTGGATTGGAATGTCCGAAAAATCCAATGCTGGTTTCGCCATCGGAGGAATCAGGACAAGCCCCCAACGCTTACTAAATTCTGTGAAAGCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139624-LASS5:NM_147190:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(34.0=50.0)
A:
NA
C2:
PF0004624=Homeobox=PD(62.3=75.0),PF0379811=TRAM_LAG1_CLN8=PU(2.6=11.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TATTGCCAAACCCTGTGCACT
R:
TGCTTTCACAGAATTTAGTAAGCGT
Band lengths:
233-980
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)