HsaINT0136383 @ hg19
Intron Retention
Gene
ENSG00000011454 | RABGAP1
Description
RAB GTPase activating protein 1 [Source:HGNC Symbol;Acc:17155]
Coordinates
chr9:125836564-125838565:+
Coord C1 exon
chr9:125836564-125836707
Coord A exon
chr9:125836708-125838523
Coord C2 exon
chr9:125838524-125838565
Length
1816 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGT
5' ss Score
9.81
3' ss Seq
TTTTGTCTGTTCTCTTTCAGGGA
3' ss Score
13.36
Exon sequences
Seq C1 exon
GAATACATTCCTGACCTGTACAACCACTTCCTGGATATAAGCCTTGAAGCACACATGTATGCCTCCCAGTGGTTTCTTACTCTTTTCACTGCAAAATTCCCTCTCTACATGGTCTTCCATATCATCGACCTGCTTTTATGTGAG
Seq A exon
GTATGTATCAGAGGCCACAGCACTTTGGCTTTTGTTTGCAGTGTACTTGAGGAGAACAGATTCTGTTTTGAGTGTCAGCTCTGTCAAAACAGAATTGGTCTCTTTAATTATTTTATTTTATTGCTAGGAAATCTAGGTTTAAGTGACTTCCTTGGACTAAAGCTAATGATCGTATTTGTTAAAGGTGTACTCTGAAAAGACGTACTGAATTAGACATTTGTATTAGTTCATATTAGTTTTGGCTGTATTGAATGAAGAAACCCAAAGTAACAGTGATTTTAAAAAATAGCTTTTTGCTCTCTTGTGAAAAAAAGTCAATGTTGGCAGTAGCGTGCCTTCCCCTCACTCTGGCTGTTAGCCGTATGGAGGAGTAGCACACCAGCCATTATATCATATTCAAGCCAGGAGGATTAGAGGATGGGAGAGGGTGCCTCCTCTGTTTTCAAAAGAGACTTCCTGGAAGTTCCATCCAGTATTTCCACTTTATGGTCAGAACTTAGTTACATGACCACACCTAGCTGCAAGGGAGACTTTTTAAAAAATAAGCTGAGCAGGAATTTGCTAAAAATTAGAGATTTATTACTAAAGAGAAAATAAGATATTAGAGTAAATAACAGTCTTTGCCATGACGTAATTTTGGATTTTGTGTGGTGTGTTTAAGAAAAACATAATTATAAAAATAATATATGTTTATAGAAAATATAAGTAAAAATAATTTAAAATACTACAAATCCCACTGTCTATAGGTTACCTCCTTTAACAGTTTGGTTAAAAGCAGTATCCTTTCAGCCTTTTTTATGTGTTCATATATGTGTATGTATAATTACTATACAGAATAGTATGGTTTCCATATGGATGGAACACTATATATATTATGGTTCTCCTATGTGTATATTTAAAAATATGATTGTTATTTATACTCTTTGGTATCCTCTTTTTAAATTTCATATACTTGAACATACACATCTGTACTATCCTTTTTAATTATGCTATATTCAAAACATACAAAAATTCATAAAGAATTTGTATCTACCACTCAGCTTGAAATATTCTAAGAAACAGAAGAAATAAATATTACCAAATATGCCGTTTTTCTTAGTTGCTGCCAAGTATCCCATTATTTGGATGTGCTATACTTTATGTAACCAATTTCTAATCACAAACCTTTAAATTGTTTCTAGCTTTTTAGTAGTATAAACAACCATCTGTTAAGTAGCTACTAAAGGCCAGGTGGCATGCTAAGTAATTTACATAAACTTTTCAGCTAATTATCTCAGAAAACCCATAGGAGAGTATTAGTTATGGAAACTGAGGCCCAGCAGCTTAAGCAGTTTAACTTGATCAACAGATGTTAGTGCTTCCTCTCCTTTGTTCTTAGCCCCAGGATTTGCAGAATGGAGGGAGCCTTGAGCAGATTCAGTTCTGGAATATAGGGCTTATCGACAGAGTGGTTGCTGTGCATGGATTGGGACAGCACAAGATAAAGGAAAAGTTCCCCAGGAGTTATTTCCTGAGAGATCACAACTTTATGACTGATCTTTTGGTTTGGAAGCATGGAATGCTTTGGAAAAGCATTTCTTATTATTGAATATGAGAACAGGGCAAGAAAAGCTCTTCTCTCAGAAAAAGGGGAAGCTAGGTCTTTAAGCAGCTTTTCAATGGCCCTTTAGTTTTTATTTTTCAAGGTAGTTCTGAGATAATGCATTTCCTTCCTTAAGTTTTCACAATTTCTTTAAAAATGTGGGGTATAAGGACAAATAGCATAATAGTCGAGATATAAAAACTGACAGTGTTCTTTTTGTCTGTTCTCTTTCAG
Seq C2 exon
GGAATAAGTGTTATTTTTAATGTCGCCCTTGGATTATTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000011454-RABGAP1:NM_012197:17
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:
PF0056613=RabGAP-TBC=FE(23.0=100)
A:
NA
C2:
PF0056613=RabGAP-TBC=FE(11.7=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:
ACATTCCTGACCTGTACAACCAC
R:
CTTTAATAATCCAAGGGCGACATT
Band lengths:
182-1998
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)