HsaINT0067759 @ hg19
Intron Retention
Gene
ENSG00000136895 | GARNL3
Description
GTPase activating Rap/RanGAP domain-like 3 [Source:HGNC Symbol;Acc:25425]
Coordinates
chr9:130116125-130116689:+
Coord C1 exon
chr9:130116125-130116223
Coord A exon
chr9:130116224-130116572
Coord C2 exon
chr9:130116573-130116689
Length
349 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGTA
5' ss Score
-0.15
3' ss Seq
TGTCTTTTTTATGTCACCAGGAA
3' ss Score
9.75
Exon sequences
Seq C1 exon
ATGACCTTCCATCAGTGCCCGTGTTTGACAGAACTCTGCCAGTGAAGCAAATGCATGTGCTTGAGACCCTGGACCTTCTGGTTCTCAGAGCAGACAAAG
Seq A exon
GTGGTATTCCCTGCCGGGTGGCATGCTGTGGAGGAAGGAAAACAGTTGCCTTCTGCGGCCCACACCACAGGTCGCCAGGGTCTGACTGCATAAGTTCTGCCAGCTGTTTCCTTTCCTGATGCTCAGTGCTTGGGATCCCTCAGTGGCCCCTTTGTTCTCTGGGGAGGGAAGCCGTTGGGGGAAAGGGGTGCATACGTAATTGCATTGTCAGGTTAAAGTGGTGTGGGGTGCCTCCTGAATTCCAGAACACCTCCAATCCTAGTTTTTCTACACAGTCTGCCCCTGGAGGCCCTCCAGGTTACCTTACTTTTCCATTTAATCTCCTCCTCTGTCTTTTTTATGTCACCAG
Seq C2 exon
GAAAAGATGCTCGCCTCTTTGTCTTCAGGCTAAGTGCTCTGCAAAAGGGCCTTGAGGGGAAGCAGGCTGGGAAGAGCAGGTCTGACTGCAGAGAAAACAAGTTGGAGAAAACAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136895-GARNL3:NM_032293:18
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=0.207
Domain overlap (PFAM):
C1:
PF0078017=CNH=FE(10.8=100)
A:
NA
C2:
PF0078017=CNH=FE(12.8=100)
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:
ATGACCTTCCATCAGTGCCCG
R:
TTTGTTTTCTCCAACTTGTTTTCTCT
Band lengths:
214-563
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)