HsaINT0067735 @ hg19
Intron Retention
Gene
ENSG00000165219 | GAPVD1
Description
GTPase activating protein and VPS9 domains 1 [Source:HGNC Symbol;Acc:23375]
Coordinates
chr9:128121699-128123004:+
Coord C1 exon
chr9:128121699-128121771
Coord A exon
chr9:128121772-128122806
Coord C2 exon
chr9:128122807-128123004
Length
1035 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATA
5' ss Score
7.96
3' ss Seq
TTGTCTATGGTCTCACTTAGGTT
3' ss Score
7.64
Exon sequences
Seq C1 exon
GGTTCTTCATGAACATATCCAGAGATTGTCTAAAGTAGTGACTGCAAATCACAGAGCTCTTCAGATACCAGAG
Seq A exon
GTAATACAGGTTTATATAGCATGGGTAATGTTAACTAAATGCTGCGTGTTATTATACCATATAATGTTACCACGTGTTCAAGGAACTGAAATGTGATAAAATATAAAACATCATTTTCACTCTATGTAATTCAGTCTAACTGCGAAGTTCCTGAAGATGCTTTCAGGGATTAAAATTCCCTGGTATGAAATAGTAGAAAGCCAGTTGTGAGGAGCCCTTCCTTGATGCCACTTCTCAAGTCAGCCCTGCTCTCAGGGGCAGTACCTCTCCATCAGTGCTTTTATAGTCAGGTTTCTACAGAAATGTTTTGAAGAAGTGGGAGGCTGATAGCACTCCAAAGAGTGAGATATGCTGTCTCAGGAGAGGTCATTGAGTCTGCATGTGATCTCAGATTACCTTTTAGTCATTGATATTAGCATTTTTACCTGTCCTACATCTCTTAGAAAATAAGAAAACATGAAAATTTCAGGTATTTGAGCTTTCTGTTTGTTTTTGTTACAACCCCCACTAATGAGACATGAATTAGCATAAAATTTTAAATTATCTTTAGTTTTTTGAATCTGTTATTTCTGGAATTACTGCAACAATGGTACATATTTTTAAATTAACCTCTTTTATCACATGTGATAAATCTAGTTCCTGTGTAGAGCCAGTTTAAGCTAGTTTTAAGGAAAAGTCCTCTTTTAGTAGTTTGTACTTCTGGAATCAGCTACTAAATGTAGAGAAGTTCCATTCTAGCTATTTAAGAAAGAGAATGGTTTGAAATTTTGTGAATTCTAGCTTCTGTGCTGTTGAATGCCCTTTTTCTATTAATGGATATCTGGTTTGCTGTATTTTAAAATTCAGAGCAACTTATTTAAAAGTTCTAAAGTTACAATCTTTAGTGAAGGGGAAAGGGGCCTGCAATATGGTTTTACCAAAGAGAGGAAAAAGCAACCACATTATCCTCTGCCTCCTGACACGGAGGTTGCAGTAGTCACTGCGCAGGGTTGCCACTGGATTCAGAATCTGTATATTGTCTATGGTCTCACTTAG
Seq C2 exon
GTTTATCTTCGAGAAGCACCATGGCCATCTGCACAATCAGAAATCAGGACAATAAGTGCTTATAAAACCCCCCGGGACAAAGTGCAGTGCATCCTGAGAATGTGCTCTACGATTATGAACCTCCTGAGCCTGGCCAATGAGGACTCTGTCCCTGGAGCGGATGACTTTGTTCCTGTGTTGGTGTTTGTGTTGATAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165219-GAPVD1:NM_015635:25
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:
NO
A:
NA
C2:
PF0220413=VPS9=PU(56.3=87.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTTCATGAACATATCCAGAGATTGT
R:
TCAACACAAACACCAACACAGGA
Band lengths:
263-1298
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)