HsaINT0067768 @ hg19
Intron Retention
Gene
ENSG00000136895 | GARNL3
Description
GTPase activating Rap/RanGAP domain-like 3 [Source:HGNC Symbol;Acc:25425]
Coordinates
chr9:130151183-130153046:+
Coord C1 exon
chr9:130151183-130151398
Coord A exon
chr9:130151399-130152919
Coord C2 exon
chr9:130152920-130153046
Length
1521 bp
Sequences
Splice sites
5' ss Seq
TGGGTAATG
5' ss Score
5.68
3' ss Seq
ACCTATGATTCTCAATCCAGGCC
3' ss Score
7.36
Exon sequences
Seq C1 exon
GTGAAATTCAATCAAAAAATCTGTACAAGATTCCACTTAGAAACCTCGTGGGCAGAAGCATCGAACGACCTCTGAAGTCACCCTTAGTCTCCAAGGTCATCACCCCACCCACTCCCATCAGTGTGGGCCTTGCTGCCATTCCAGTCACGCACTCCTTGTCCCTGTCTCGCATGGAGATCAAAGAAATAGCAAGCAGGACCCGCAGGGAACTACTGG
Seq A exon
GTAATGGTTCTCAATCCTGGTTTCCACTGTCTGTGAACAGACCAGCTGGTTTTATCTTTGGATATGAATTGTCCTCAGAAACAATGAGTTTAAAAGGAAAGTTTCCTTTTAAGAAGGGATTTTTAAGTAAGTTCTAATACCTCTATACCAAGGAATACACTATAATGTAGCCACCAACAGTGATGTTGTTGATCTATATTTATTGGTGTGGAAAGCTGCTCAAGCCATGTGAAGGGGGGAAATGGGCAGTTTATAAAACACTATGTCTAGTCTGATACCATTTTTAAAAATAAAAGTACCAATCTATGTATGATTTCCTAGAAAGGTGTCTAGAAGGATTTATATCCCACAGTCCTCAGACAACATTTTATGTTGGTATGTCCCAAAGTGGAAATGTACCATGTTTTTACACGTGTGTGTTCAGTTCCCTTATTACTTCTCCCAGCCCTAGACAGTGGGGGCAGGTCTGTGGATAGAACAGATGCAAGATATGTGTTGAGCTCATTTCTCTCAGTATAACTATGGGACTGGGCTCACACCTGTTATCTCAGCATTTTGGGAGAGGCTGAGGCAGGCAGATCACTTGAGTGCAGGAGTTCAAGACCAGCCTGGGTAACATGGTGAAACCCCATCTCTATAAAAAATAAAAAAATTAGCCAGCCATGGTGGCATGTGCCTATAGTCCCAGCTACTCAAGAAGCTGAGGCAAGAGAATCGATTGAGTCCGGGAGGTCAAGGCTACAGGGACCCATGATTACACCACTGCACTCCAGCCTGGGTGACAGAGTGACACCCTGTCTTTAAAAAAAAAAAAAAAAAAAAAAAAAAGATGAGAGGCCAAATCAGAGAAACATAAAGCCCCTGATAAGTGTGAAAAGGTTAGACTGTTAGAAACCTTTTTGTTCAGATTTGTGGAAACAAAATAAGGAAATATGGAAGTGACATGTTAAACCAGGAGAAACTGGTTTGAAAACTTAGACTGGGACCTGCATGAACGTTGGCCTGGGCACACCCCTGCCCTGCAGTAATATTCCCTGAACAACTGCAGGAGGGGATTCAGGCCACCTGACAGGGCAGGACTAGACACTAACAAAGTCCATTGGTTTTTCAAGTTGGTGCCTTCTACTGTGTTTTGAAAATAAATGTATTGCTATTTTTAATGCAGCCTTCCATATCAAAGCTTGATCTGCCCACCACTGTTTACAAACCACTGAGCTTTTGCAAAACGGAACCTCTGAATTGGAGAATTACAGGGTTATCAACGGTAGGACTGTAAATCATCTGTCCTCATTAGGCTCTTTGAGTCTAATTTTTTTGCAAAGTGTGTATACTTTATAATCAGAAAAGAAAAACCTTCTACCAACCAGAAAACCAATAATTTGAAAATATATATTCTATCATCTTTCTTCCTGACTCTAGCACAACAATGCACCAGTTCCCAACCAAGAAAAAATAAGGGTCTTTTCTGTCTCCGTGGCAGCCCTGTGGTAGTGACCCTCTGACCTATGATTCTCAATCCAG
Seq C2 exon
GCCTCTCGGATGAAGGTGGACCCAAGTCAGAAGGAGCGCCAAAGGCCAAATCAAAACCCCGGAAGCGGTTAGAAGAAAGCCAAGGAGGCCCCAAGCCAGGGGCAGTGAGGTCATCTAGCAGTGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136895-GARNL3:NM_032293:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.320 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0078017=CNH=PD(0.1=0.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAAGATTCCACTTAGAAACCTCGT
R:
TGTCACTGCTAGATGACCTCACT
Band lengths:
318-1839
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)