HsaINT0067767 @ hg19
Intron Retention
Gene
ENSG00000136895 | GARNL3
Description
GTPase activating Rap/RanGAP domain-like 3 [Source:HGNC Symbol;Acc:25425]
Coordinates
chr9:130149472-130151398:+
Coord C1 exon
chr9:130149472-130149610
Coord A exon
chr9:130149611-130151182
Coord C2 exon
chr9:130151183-130151398
Length
1572 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAG
5' ss Score
5.73
3' ss Seq
TTTTTGAAATCACATTTCAGGTG
3' ss Score
7.44
Exon sequences
Seq C1 exon
TCGGATATATACTTCACAGCAACTGCAGCTGTGAATGAGGTCTCATCTGGAGGCAGCTCCAAGGGGGCCAGTGCCCGAAATTCTCCTCAGACACCCCCGGGCCGAGATACTCCAGTATTTCCTTCTTCCCTGGGGGAAG
Seq A exon
GTGAAGTCCAAGTTTTACTGTTTTATTAATATTTGTAATTCACTCTAATTTCTCTAGTTTGTTGTCTAATATCTACATGTGATTACTGTTTAAAGAAGTTACTATTTAAAGCCATTAAAAAAAGAAACTAGCTGAGCGTGGTGGCTCACCCCTATAATCCCAGCACTTTGGGAAGCTGAGGCGGGCGGATCACCTAAGGCCAGGAGTTCAAGACCAGCCTGACCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCGGGTGTGGTGGCACACACCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGACCCTGGGAGGTGGATGTTGCAGTGAGCCGAGAGCACGCCATTGCACTCCAGCCTGGGCGATAGAGCGAGACTCTGTCTACAAAAAAAAAAAAAAAAAGAAAGAAATCTTGCAGTCTGAATACATGGTTGTGTTCTTAAGAAACCTGGTGATAACAACGACAAAACTCCATTATAAAAATAATAAATAAATAAATAAACTGGGCTAGGCGCTGTGGCTCACACTTGTAATCCCAGCACTTTGGCGGGCTGAGGCAGATGGATCGCTTGAGCCCAGCAGTTCAAGACCAGCTGGGCAACATGGCAAAACCCTGTCTCTAAAAAAAAATACAAAAACTAGCTGGGCATGGTAACATGTGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGTGGGAGGATCACCTGAGCAGCGGAGGTCAAGGCTGCATTGAGCCGGGATTGCACCTCTGCACTCCAGCCTGGGCAACAGAGTGAGAGACCCTGTCTCTACAAAAACTAAAATTAAATTAGCTGGCTGTGGTGGCATGCACCTGTGGTCCCAGCTACTCAGGAGACTGAGGTGGGAGGATCACTTGAGCCTGGGAGGTCAAGGCTGCAGTAAGTCATGATTGCATCATTGCACTCCAGCCTGAGCGACAGAACAAGACCTTGTCTCAAAAAAAAAAAAAAAAAAGTTTCAGTGGGGAGGAGGGAGTTAAAGGCTATAGAGTTTCCAACTTGCAACAGCAGTTATTTTTCCTTCAGGGCTGTTAACAGTAGTGGGTTTTGAAAGCTAAAAGAATAGAGTCATCAAGCCTAGACATTCCCCAGCACATGCAGTCTTTCACTCTATCTGGCTTTGCCCGCAAACCCCAGAGGCCTCTGCTGTGGTTACCTCATCGCTTTGAACACAGCGCTTTTCATAAATTCTTACCACATCACTCATCTTTATTGCACGCAGTTAAGATAAAGCACAGAATTCCCCAAGCAGGGCAGCTTTTTGCTTTTCTTGTCTAGTCTTTTTTCCTGTGCAGTCACGAGTGCATTTTACCTAATTTACACATGAAAATGCTCTTAGAAAACGCAAAGCCATCAGGCACCCTCAAATCAGTGCTCCTGGCCAGCCCTCCCAGTGGGACATTACAGATCAGTGTGTGACATAACGTCTTCCTTCATGCTATGTTAAGGAACAAGAAATTACTCTCTTGTAAATAATGTGCACTTTTCTTAAAGTTCTGATGTTCTTTTTGAAATCACATTTCAG
Seq C2 exon
GTGAAATTCAATCAAAAAATCTGTACAAGATTCCACTTAGAAACCTCGTGGGCAGAAGCATCGAACGACCTCTGAAGTCACCCTTAGTCTCCAAGGTCATCACCCCACCCACTCCCATCAGTGTGGGCCTTGCTGCCATTCCAGTCACGCACTCCTTGTCCCTGTCTCGCATGGAGATCAAAGAAATAGCAAGCAGGACCCGCAGGGAACTACTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136895-GARNL3:NM_032293:25
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.574 A=NA C2=0.320
Domain overlap (PFAM):
C1:
PF0078017=CNH=PD(0.1=0.0)
A:
NA
C2:
PF0078017=CNH=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACTTCACAGCAACTGCAGCT
R:
GTAGTTCCCTGCGGGTCCT
Band lengths:
343-1915
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)