HsaINT0073144 @ hg19
Intron Retention
Gene
ENSG00000180613 | GSX2
Description
GS homeobox 2 [Source:HGNC Symbol;Acc:24959]
Coordinates
chr4:54966248-54968122:+
Coord C1 exon
chr4:54966248-54967085
Coord A exon
chr4:54967086-54967748
Coord C2 exon
chr4:54967749-54968122
Length
663 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGG
5' ss Score
4.66
3' ss Seq
CTCTCTTCGCCGGTCCGCAGGAG
3' ss Score
9
Exon sequences
Seq C1 exon
GAGGAGCCTGAGCCGAGCGGTACTCCGCAGCATCACGTGCCAGGGTGGGGGGCTATAAAATACCCGAGCCGGGGCGCCGGGCGGGGGACGTGAGGACCAGCCCTCTCCGGGGACCCCTTTGTTCCCAGCCCAGACGCCAACACCTCTGCGTCCCCAAGGGCTTGACTGCCCGTGTCTGCGCGGCTCCCAGGGCAGAGCTTAGAACACTAGAGGAGAGGGGTCGCCGCGAACTGCCGGGGCTTCCAGCCACCCACCCCTCTCGACATGTCGCGCTCCTTCTATGTCGACTCGCTCATCATCAAGGACACCTCACGGCCTGCGCCCTCGCTGCCTGAACCGCACCCCGGGCCGGATTTCTTCATCCCGCTTGGCATGCCGCCCCCATTGGTGATGTCCGTGTCCGGCCCCGGCTGCCCGTCCCGCAAGAGCGGCGCGTTCTGCGTGTGCCCTCTCTGCGTCACTTCGCACCTGCACTCCTCTCGGGGGTCTGTGGGCGCCGGCAGCGGGGGCGCAGGGGCCGGGGTTACCGGGGCCGGAGGCAGTGGGGTGGCAGGGGCCGCAGGGGCACTGCCTCTGCTTAAGGGCCAGTTCTCTTCGGCTCCTGGGGACGCGCAGTTTTGCCCGCGGGTGAACCATGCGCATCATCACCACCACCCGCCGCAGCACCACCATCACCATCATCAGCCCCAGCAGCCTGGCTCGGCCGCGGCGGCGGCAGCAGCAGCAGCGGCGGCGGCGGCCGCGGCGGCCTTGGGGCACCCGCAGCACCACGCACCTGTCTGCACCGCCACCACCTACAACGTGGCGGACCCGCGGAGATTCCACTGCCTCACCATGG
Seq A exon
GTAGGGCGGGGTCTTGGGGCACCTGCGCTCCGCGCCTTTCGCGCTCCTGGAGCAAACTTTCCACCTCCAGTGGAGGAAGTGGGAGCCCGGGGACAGGGTGAAGAGAGAGGACGGGCTTTTAGTGTAACCGTAGAGTCAGCCACAGAAGTTCCACGAAAGTGGAAGTTAGTTTGCCAGCTTCTCCACTCAGCCTGGTGCGTTTTACTCCTAGTAGTAGGTGCTCGAGTATTGCCTTATTAATACTGGGGCCTTAGGGACCTCGAACGTCACGGCGGATAAACCAGAGGTTAACTGCTTGGGATTTGGGGTGGGTGTGTTTGAACCTGTGTGGCATCCCCGCGTCGGGGCGGCTAAAGCGTCTTGACGTTTTTGGCTAAGCCTGCGCGCTTCTCCGCTTGGCTCAAAGGGAGGCGATCAGATAGTGCAAGCCCCCATCCCTCTTTAATCCTGTGACTTCGCATCCTGCGCATCGAAGACCTTTATTTGCTTTGCACGTCTCTTTTCTTCCCCGCTAAGCAACCACGTGCCTTGAAATGGGAAAGGGATACAGATGTTCGGCTGGGCTTCCCCGGGTGGGTCCCTGAAATGCGTCCTGGTTAGCACATGGGGTGGGAGCACCTTGCCCGAGCCTTACCTCTCTACCCTCTCTTCGCCGGTCCGCAG
Seq C2 exon
GAGGCTCTGACGCCAGCCAGGTACCCAATGGCAAGAGGATGAGGACGGCGTTCACTAGCACGCAACTCCTGGAGCTGGAGAGAGAATTCTCTTCCAACATGTACCTGTCTCGACTCCGGAGGATTGAAATCGCCACTTACCTGAACCTGTCGGAGAAGCAGGTGAAAATCTGGTTTCAGAACCGCCGAGTGAAGCACAAGAAGGAGGGGAAGGGCACGCAGAGGAACAGTCACGCGGGCTGCAAGTGCGTCGGGAGCCAGGTGCACTACGCGCGCTCCGAGGATGAGGACTCCCTGTCGCCGGCCTCAGCCAACGATGACAAGGAGATTTCCCCCTTATGAGGGAGGGCCTCCTCCCTCACATCCCCCGCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000180613-GSX2:NM_133267:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.484 A=NA C2=0.476
Domain overlap (PFAM):
C1:
PF101524=DUF2360=WD(100=49.0)
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.0)
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:
GATTCCACTGCCTCACCATGG
R:
CCTTGTCATCGTTGGCTGAGG
Band lengths:
345-1008
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)