HsaINT0067753 @ hg19
Intron Retention
Gene
ENSG00000136895 | GARNL3
Description
GTPase activating Rap/RanGAP domain-like 3 [Source:HGNC Symbol;Acc:25425]
Coordinates
chr9:130100395-130102030:+
Coord C1 exon
chr9:130100395-130100440
Coord A exon
chr9:130100441-130101923
Coord C2 exon
chr9:130101924-130102030
Length
1483 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
CTGCAATATTCTCTACTTAGGCT
3' ss Score
6.45
Exon sequences
Seq C1 exon
ATATTTTTGCCTTAGTGAGATACAATCAACAAAATGACAATTACAG
Seq A exon
GTAGGTAATGACTTTGTCTCGATTGCTTGTCCTAATTCTCATGCTTGTTAATTTAGCATTGATTTTTACAAGACTCTTGATATACATATTTCTTGATTGATTTAATATGAGTGCCTGCACCTTACAAAACTTTCTTCAAGGCCACCATCTCTTCAGGAAACATTTACTCCATCCAGTGTTGTTCCATGAAGGAGACCTAGGGGTCAGGGTTAGTTTGATATTTTATTGTACTTTACCATGGGAACAGGTTTGATATATTTGATCTTCATCCTTTCCTAGTCTACATTCTTGCCTGCTTATCTTTCTGTTCTCAAATATTAATCTGTTAAAAGGTATTATGTTGTAAAAAGAACCTGAACTTTGAGCCAAATAGATTTGAGTTCGAATCCCAGTTCTATCATTTATTTGAGGCTTTGAAAAAAATGTTTTATCTTCTTGAAGCCTCAGGCCTTCTGTGTAGAGTGAAGGTAATGACACTACCCCGGCAGGTGTAGTGACAATCAGAGGCAATACTGTATCTTAAAATACCAAGTATGCTGCCTGGTATGCAGCAGGTGCTCAGTGATGGCCATTGCTCTTCTTCCTGGGTACCTGGCTTGATGGGTTGGACCATGAAGGATTCAGGAAGACCTGGTCTCTATCCTCAAAGCACATTGACTAAGCTGGAGGGGAAAGCGAGGTAGTGGCCTCGGCCCTGGCAGACCAGAGAAGGCACTCCTGGCATGGAGCAAATATTCCTGACACATCCCATATGCAGCTGGATAAATGGAAGGACAGAATAGTGGTGTATTACTTCATTTTCATACTGCTAATAAAGACATACCCAAGACTGGGAAGAAAAAGAGGTTTAATTGGGCCTGGCGTGGTGGCTCATGCCTGTAATCCCAGCACTTTGGAAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGATGAAACCCCGTCTGTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCAGGTGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGTGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCCAGATCGCACCACTGCACTCTAGCCCGGGTGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAGAGGTTTAATTGTACTTACGGTTCCACATGGCTGGGGAGGCCTCAGAATTATGGTGGGAGGCAAAAGTCATGTCTTACATGGTGGCGGCAAGAGAAAATGAGGAGGAAACAAAAGCAGAAACCCCTGATAGGCCTATCAGATCTCATGAGACTTATTCACTATCACGAGAATAGCACGGGAAAGACTGGCCCCCATGATTCAGTTACCTCTCCCTGGGTCCCACCCATGGCATGTGGGAATTCTGGGAGATACAATTCAAGTGGCGATTTGGGTGGGGACACAGCCAAACCATATCAAGTGCTAATATTAATTCTGCAATATTCTCTACTTAG
Seq C2 exon
GCTGAAAATATTTTCAGAAGAGAGCGTACCACTCTTTGGCCCTCCCTTGCCAACTCCACCAGTGTTTACAGACCACCAGGAATTCAGGGACTTTTTGCTAGTGAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136895-GARNL3:NM_032293:12
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=0.081
Domain overlap (PFAM):
C1:
PF0214510=Rap_GAP=FE(8.0=100)
A:
NA
C2:
PF0214510=Rap_GAP=FE(19.1=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)