HsaINT0070374 @ hg19
Intron Retention
Gene
ENSG00000136935 | GOLGA1
Description
golgin A1 [Source:HGNC Symbol;Acc:4424]
Coordinates
chr9:127643450-127644233:-
Coord C1 exon
chr9:127644063-127644233
Coord A exon
chr9:127643537-127644062
Coord C2 exon
chr9:127643450-127643536
Length
526 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAG
5' ss Score
8.27
3' ss Seq
CAAAACTTACTGTGTTTCAGGCT
3' ss Score
6.96
Exon sequences
Seq C1 exon
AAAATCAGACCCGATAATGAGCTCTTCGAAGTCCGGGAGAAACCTGGACCTGAGATGGCAAACATGGCGCCTTCCGTCACGAATAACACTGACCTGACAGATGCCCGCGAGATCAACTTTGAGTACCTTAAACATGTGGTTTTAAAATTCATGTCTTGTCGCGAATCCGAG
Seq A exon
GTAAAGGGCTTTTGAGGTGTCTTTTGGGTATTGAGGCCCCGCCCTACAGTCTGTCCTGCAGGGACCCCTGCCCAGCCCCTTTCTCTCTTTTCCTCGTACATCCTGGTTTGACGCCCTTGTGGTCACCCAGTCATTTCTCCTGCTGGCGTTGGCCTGCGGAGTGAGCGGCTGGCGGGAGAGGCCGTGCAGGAACTGGCTCCTGGTGGGAGACATAGGCTCCACTTCTAAATCCTGGCCTGGGTGCTGAGGCCAGAGGCCGGAAGCCGGGAACGGAATCCACCCATCGCTCCTGGGTCCTGCCAAAGGGTAGGGTAGCTGCTGGGGCAGTTCCCTTAAGCCTGCCAGGCCCCCGAGGATGCAGGGGAAGAAAGAACCTATCATTGCTGCCAAACTTCAGAGTGCCAGAGCGTCACCCACCACCTGGTCCTGCTAACCAAAGCAAGCAGGAAATGCCACGTAGCTCCCCCGACCCCACCCCGCCTCACCTTCACCAAGGCCTATGGCAGCAAAACTTACTGTGTTTCAG
Seq C2 exon
GCTTTTCATCTTATAAAAGCTGTGTCAGTGTTGCTGAACTTTTCCCAAGAGGAGGAGAACATGCTCAAGGAAACTCTGGAATATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136935-GOLGA1:NM_002077:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.484 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0146515=GRIP=PU(46.7=36.8)
A:
NA
C2:
PF0146515=GRIP=PD(48.9=75.9)
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:
AAAATCAGACCCGATAATGAGCTCT
R:
TATTCCAGAGTTTCCTTGAGCATGT
Band lengths:
254-780
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)