HsaINT0090849 @ hg19
Intron Retention
Gene
ENSG00000139624 | LASS5
Description
ceramide synthase 5 [Source:HGNC Symbol;Acc:23749]
Coordinates
chr12:50529724-50531603:-
Coord C1 exon
chr12:50531511-50531603
Coord A exon
chr12:50529853-50531510
Coord C2 exon
chr12:50529724-50529852
Length
1658 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
CTATTTCCATTCCTTCCTAGGAC
3' ss Score
10.09
Exon sequences
Seq C1 exon
CCTCTTTCAAGTGGGCTTTATCACTATTATATCATGGAATTGGCCTTCTATTGGTCCCTTATGTTTTCTCAGTTTACAGACATTAAAAGAAAG
Seq A exon
GTAAGGACGTTGGCTCCCTCAATTCCCCAACTTATTACATCCTCCTTTCTAGCAGCTTCCATGACTGCCATTACGATGTATTATCTTCCCTGAGACTGCAAAAGGAGAAACTGGGTTTGATGGACTCTTAGCTTGTCGTAATGTTCCCAGAAATGAGACTGAATTAATGATGAAGTATATTTAAGACATTCAGGGAAGCCCCAGGATGAGAACAATTAACCAGCTAAGAAGCATACTTTTTTCCATATTCTTCTTTAAGCTTCTTACATATCTAAAGCTCAGGAAACTAGTCAGAATTGGGGGATAGCAATGCCTTATTCAGAAAAAATGTCTGATTCCAGAAAAGCTGGATATGGCTTTCACATGGCATTAGGGACCCTTGCTCTCTCTGTTCTCCCTTTCTGGTTACCCCACTTACTCAAAGAAAGTCAATTGGAAGGGGTTTTGCTCTCTTCCTGCTATTGTTTAGGAAGCAAAGATTGAGAGAAGTGAGCTGACTTGCCCAGATAGTGACAGAGTTGGAAATGACTTAAGTTTTACACAACTTAAGTCATTTAAAGGCAGAATCTTTACCTTTTTATTAGTGTCTACCTGAAATAATGTGGTTCTAGCAGCTCTAACCCTAATCTGTCACTAACTCAGGGTTATCTTTGATGAAGAAAACCAGGGTTAGCATTTATGGGAATGAATTAAAACTTACCCAGGTTGTTAGTGTTATCTAACATAGAAACTTGATACTCAATTTTTATGCCTTTTACTCTCCTATGGTCAGAAGACACAGGTCACTTTATTAAAATTTTATTTTAATTGTGATACATATAAGAAAGTTTGAAATACATATTTAAGTTTTAAAAATAATAAACTGAGAAGTATTTAATAGATGTGTCTGATAACTCAAGTATTTAGAGACTTCCCCAGGTCTAACTTGACATTTGAACCCAAGAGGAAATTAGAGCCACAAACCTCTCCCTTCCATTAGGTCCTTGTGGTTGACGTTTCTCTCATTAAAGCAGAAGAGTCATAGAATCTCAGGGAACTCTAAGGCTTGTATGTCTTACTGGGATGTTATCCCCAAGTGTCAGCTTAGCATCCATGCTATACGTATTCTGCAGTTACCAAAGGAAATTTTTACTTTCTGGCCTCTGAGCTGCATTAACATAGAGTATGGGTCAGTCACTGATGTAGGGAGTGTTCAGTTAAATGCTAGGTAGCCAAGGGAGAGTCTAAGCAGAATGGAAACTTTTTTTTTTTTTTTGAGACGGAATCTCAGTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCAGCTCACTGCAACCTCTACCTCCCAGGTTTGAGCAATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCACATGCCACCAAGCCCGGCTTATTTTTGTATTTTTAGTAGAGACGGGGCTTCCCCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGACCACCTTGCCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCTCGCCCGGCCAATGGAAACTATTCTATATGGGGTGGGGTAAGATTCTTAGAGAATAATGCAGGACGTTGGGTTGGCTGGTGTTTCTAGGGCCCAGCTTTTACCTCCCTCTTCTATTTCCATTCCTTCCTAG
Seq C2 exon
GACTTCCTGATCATGTTTGTGCATCACTTGGTCACCATTGGGCTTATCTCCTTCTCCTACATCAACAATATGGTTCGAGTGGGAACTCTGATCATGTGTCTACATGATGTCTCAGACTTCTTGCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139624-LASS5:NM_147190:6
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:
PF0379811=TRAM_LAG1_CLN8=FE(15.5=100)
A:
NA
C2:
PF0379811=TRAM_LAG1_CLN8=PU(30.8=96.0)
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:
CCTCTTTCAAGTGGGCTTTATCACT
R:
CTCCAGCAAGAAGTCTGAGACA
Band lengths:
222-1880
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)