HsaINT0067230 @ hg19
Intron Retention
Gene
ENSG00000128683 | GAD1
Description
glutamate decarboxylase 1 (brain, 67kDa) [Source:HGNC Symbol;Acc:4092]
Coordinates
chr2:171700555-171702131:+
Coord C1 exon
chr2:171700555-171700667
Coord A exon
chr2:171700668-171702015
Coord C2 exon
chr2:171702016-171702131
Length
1348 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
ATATGTCCGCTTGCTGACAGGGG
3' ss Score
5.51
Exon sequences
Seq C1 exon
GTTTACATATGAAATTGCACCAGTGTTTGTCCTCATGGAACAAATAACACTTAAGAAGATGAGAGAGATAGTTGGATGGTCAAGTAAAGATGGTGATGGGATATTTTCTCCTG
Seq A exon
GTAGGTTTCTCTTCTCTTCCTCTTCTCAAGGTTTGGGATTCTTAAGAATACAAAATATGAAGTAGGTTTATGGAAGAATAATGCCTTAACATTTTTTTTGGATACCCTGACTTCCTATTTTTTCAAGATGAAGGCTAACAAAAATGCTACATTCTATATGAATTAACTAACAAAGGCTATGCTTAAATCTGTAAAAACTGACAAAGGCTGTGTCTAGATAATGCTAAATAACCCCATTTTTTCTTTTTTCTTTTTTTTTTTTTTTTTTTGAGACAGGGTCTCACTCTGTCATCCAGGCTAGAGTGCAGTGGTGTGATCCTAGCTCACTGCAGCCTCGAACTCCTGGGCTCAAGCAATCCTCCTGCTTCAGCTTCTCAAGTAGCTGGGACTATAGGCATGTGCCACCATGCCCAGCCGTTTTAAAATTTCTTTTGTAGAAACAAGGTCTCACTATTAAACAACTCCATTCTGTCAACAGCAGTTTGATTATGCTGGGGATCAGTGAATCAAGATTATTAATTAATTGATTGATTTCAGCCAAAATAGTATATCTACTTTGAATCTCTAGTTTGAAGTAGATAAAATAAGAATTTTTAAAACAAGAATAGGTATTCTGATGGTGTCAGAGACAGTGTGATTGTGTACAAGGGGAAAAGAAGAAATAAGAATTGCAGTTATCTAGGTAATTCAAGCAGACCACAAATTTGCCTAAGTTTAATTGTCAGATAATTAATGTAAAATTAACTAGTTTGTGTTGGCCAAACATACATAGTTATGTCAGTTCTCCTTGTGTCTTTATTTAGGTAAACATGAGTTTGTTCTTATTTTAATAAACTTAGAGCTCTCCTAAATGACTCAGTAACTCAGTTGGGCTGAAGAGAGCACCTAGGCAGGTAACCAAGAAATGTCATTGTTTCTTTCTGTAAGCTCCGTTACTCTTTCTTTCTCTGTCTTTCTGAACTCAGGGAACAGATTCATCTTTGTTCAGTAAATAGATTGAGCAGAAAGTAAAGCAGGAAGGATATAACTCACCTATCCCTTTGCAGCCACTGATGCAGCTACCTCTTATATTTCTGTCTAGACTTCAGGTGGAAAGCGCACTGAAGTACACGAATCACCTCCAGCCAAATTGCCTAGATAGCTTTGGTAATAAGTGTGACTACTTGTATTCCCAGGGTAAAGGGTCCAGTGGGAAGCCCCAGCAATAGGGAAGCCAGCAAAACCTATCAGGATATTATCCTTTCGCTTCCTGACCTCCCTTGTCTCTTGAGACACCAGCTCAGCGTTCGTTTTTAGAAACAATAATCAAAGAGCCCCAACACCTCCCAATATGTCCGCTTGCTGACAG
Seq C2 exon
GGGGCGCCATATCCAACATGTACAGCATCATGGCTGCTCGCTACAAGTACTTCCCGGAAGTTAAGACAAAGGGCATGGCGGCTGTGCCTAAACTGGTCCTCTTCACCTCAGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000128683-GAD1:NM_000817:7
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=0.010
Domain overlap (PFAM):
C1:
PF0028214=Pyridoxal_deC=FE(10.1=100)
A:
NA
C2:
PF0028214=Pyridoxal_deC=FE(10.1=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:
TATGAAATTGCACCAGTGTTTGTCC
R:
CTGTTCTGAGGTGAAGAGGACC
Band lengths:
222-1570
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)