HsaINT0067765 @ hg19
Intron Retention
Gene
ENSG00000136895 | GARNL3
Description
GTPase activating Rap/RanGAP domain-like 3 [Source:HGNC Symbol;Acc:25425]
Coordinates
chr9:130145717-130147424:+
Coord C1 exon
chr9:130145717-130145824
Coord A exon
chr9:130145825-130147305
Coord C2 exon
chr9:130147306-130147424
Length
1481 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
ACACTCCCGTTCCCTTGCAGTCT
3' ss Score
9.8
Exon sequences
Seq C1 exon
ACAGTTGCATCTATAAAAAGGTTTGCCCCTTTAATGGTGGCTCTTTTTTGGTTCAACCTTCTGCGTCAGATTTCCAGTTCTGTTGGAACCAGGCTCCCTATGCAATTG
Seq A exon
GTAAGAAAAGTCTTTATCATAATGCTTTTCTCCTTCATGGATATGTCTGAACTATTGTAAGCAAATCCTATGTAAGCAAATCACTGGCTTACTGCGAAATTGCTATAAATTATACGCGTATGATGAATATTCACAGCGTTCTTTTTCTTTTTCTTTTATTTTTGTTCCCCTTTTGGGACTATCGTCTTCTACTGTTCTTCCTAGTTTCTCTCAGTGCCTGAGCATGTATGCATTTGAGAGCAATTAAATGTCATTTTTCAGTACTTGGTTATCATTTCAGCACCTCAGTTCATTTCTGGGCCTCACTTTCCTTTTTCTAAAATTCAAGTGTAAGGTCTCCAGCCTCAAAATGCTGACTGACCTCGGGGAGAAGCACAGTGCTTTCAGGGCCATTGGTATATGTTTCATAGAAATTCAGGTACCTGCCTGCCACTAAAATGTCAGGACATGAGCGGCGATGCTTTGTGTTTGTGATTCAAGATCCACAACTGGCCATTGCCTTTTGGAAGTCAGATCAGAGCCAAGAATGTTCCAGTTCATTCTTTTGTCCTCACAATAAAACTGTGTGTTAATAGGTCCACAGGACAGCATTTTGAGAGGAAGGCAGAGGGACCAACCTAAGATCCTGGGAGGACCAGTTAGACTTGATGACAGATTAGATCTGGTAGACAGGAAAGGGAGATTTTGAACCACGTTGCTGGAGGGGCTTGAAAGTCATGGCTGGAGGCATAGATGTGGTAGGCACAGTCACCAGGAAAGCCAGGAGAGCAGATGCGCTCATCCATGGAAAGAGTGCAGAGAGAGCCAGTGCGAAGAAGGGGACAACACGAAGTGCCAGGAAGAAAGAGGTGTGCCCCAGGGCAGCCAGGGCAGGCACAGTGCCTGGAAGCCAGTGTGTCATCCAAATCATTTCAAGCAGAGGGGCCAGCCCTTAACAAATAACTCAGCAAACCCCTTGATGCCGAGGGACACTGCGAGGGCCAGTGAGGAATAAGATGCAGCCCCGGCTCAGACGTGCAGCTGGAGGAGCACATGGGAGGAGCGAGGAGCACTGAGGGACACCAGGGCTGGGCCTTGAAGAGCGACCAAAGGGAAGGGTCCCAGGCAGGATGGCCTGGGCCTGCAGACAGAATGTCAGGCTGGCGTCTGAACAACAGAAGGGACTCCCCACAGGACTATGGCAAGTGAGCTGCCTCGCTGGAAGATCAGGCAGTGGGGTTTCCATGGGGGAAAATGGCAGCAAGCATGGTGACAGTGCACACCTCCTGGGAGGCGCAGTGTGGCAACCGAGGGGAGGCTGTCTTGGGAACCCAGGCTACCTTAGGATCAGGGTGACTTGCACATGTGAAGGAAGGAGAGAAGCAGCCAGAGGAATGAGAGATGGAAGTTTCTAGAGAAGTGAGTGTGACTATGACACAGTCACAGCCCCTTCGCGGCCACCAAGCCAGCAGCTGGGAGGTGACACTCCCGTTCCCTTGCAG
Seq C2 exon
TCTGTGCTTTCCCGTATCTCCTGGCCTTCACCACCGACTCCATGGAGATCCGCCTGGTGGTGAACGGGAACCTGGTCCACACTGCAGTCGTGCCGCAGCTGCAGCTGGTGGCCTCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136895-GARNL3:NM_032293:23
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:
PF0078017=CNH=FE(11.8=100)
A:
NA
C2:
PF0078017=CNH=FE(12.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTTGCATCTATAAAAAGGTTTGCCC
R:
CACGACTGCAGTGTGGACC
Band lengths:
198-1679
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)