HsaINT0014165 @ hg19
Intron Retention
Gene
ENSG00000198513 | ATL1
Description
atlastin GTPase 1 [Source:HGNC Symbol;Acc:11231]
Coordinates
chr14:51057659-51058357:+
Coord C1 exon
chr14:51057659-51057793
Coord A exon
chr14:51057794-51058252
Coord C2 exon
chr14:51058253-51058357
Length
459 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
TGTACTCTTCTTGCCTGTAGGTT
3' ss Score
10.31
Exon sequences
Seq C1 exon
GAATCAGTTGATTGGGTTGGAGACTACAATGAACCATTGACTGGTTTTTCATGGAGAGGTGGATCTGAGCGAGAGACCACAGGAATTCAGATATGGAGTGAAATCTTCCTTATCAATAAACCTGATGGTAAAAAG
Seq A exon
GTATGATGCTAACTTCCTAAATAAAATTGAGTTTTCACTTATAACAGTTACTACTTTTTAGGATCCTTGAAGTTGCACTTTTGAAAATTAATTTTGACCATTTGACATGAAGCTTAAAGTGGGGTAGCATCCTATAGCATGATCTTTGTTTCCCTTTCTTGTGATCAGAGTAGGCGAAATTATAACGATGATAGAACAGCAGATCAGCAAGTAACATCTGTATTTTGTTTCACTGCTACATAAAGTTTCTGTTACGTTGGATTACTAGTAAAAATTACTTATAATAGTAATCAGCTGTTAATATTTTTATTTTCTGTGGCATTCATGGCATGTGTAAGAAATTATCTAAAATAGTATTGATTAATAATGGTTTGCTTTAGTTCTTATATTAATATTATGGTAACCCTAATGACCTAGATGTTCTATAAAATATCAATAATGTACTCTTCTTGCCTGTAG
Seq C2 exon
GTTGCAGTGTTATTGATGGATACTCAGGGAACCTTTGATAGTCAGTCAACTTTGAGAGATTCAGCCACAGTATTTGCCCTTAGCACAATGATCAGCTCAATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198513-ATL1:NM_181598:3
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:
PF0226314=GBP=FE(16.2=100)
A:
NA
C2:
PF0226314=GBP=PU(38.7=96.7)
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:
ATCAGTTGATTGGGTTGGAGACT
R:
CTGTATTGAGCTGATCATTGTGCT
Band lengths:
238-697
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)