HsaINT0070372 @ hg19
Intron Retention
Gene
ENSG00000136935 | GOLGA1
Description
golgin A1 [Source:HGNC Symbol;Acc:4424]
Coordinates
chr9:127700856-127702434:-
Coord C1 exon
chr9:127702385-127702434
Coord A exon
chr9:127701146-127702384
Coord C2 exon
chr9:127700856-127701145
Length
1239 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CTCTTTCATCTGATTTGTAGATC
3' ss Score
7.91
Exon sequences
Seq C1 exon
GACAGAATGCTTTGACCTCCAAGCTGTTTTAAATCTAGTAGATAAGCCAG
Seq A exon
GTGAGTAAGTGGTTTACACACATTGAAAGTAAAGTTTCTGAAGAATTGTACAGCCTTAATGGAGGATCTGAAGTGGTAAGATGGCATTTGTGTATCTCAGAGCAGAGCTTAGGTATCCTCCACAAAACATGGAAAGTTAAGGTTGGAACCAGAATATTAGTGTTTTATACACCATTAGGAGGAAAAGGTTTTTGAATCTTACTTTGAATATCATGTCAAACATTCTTAAGAAAAGAAACTGTGAGGCCGGGCGCAGTGGCTTATGCCTGTAATCCCAGCACTTTGGGAGGCCAATGCAGGTGGATCATCTGAGGTCAAGAGTTTGAGACCAGCCTGACCAACACGGAGAAACCTCGTCTCTACTAAAAATATAAAATAAGCCGGGCATAGTGGCGCATTCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGGTGGAGGTTGCGGTGAGCCGAGATAGTGCCATTGCATTCCAGCTTAGGCAACAAGAGCGAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAGAAAATAAACTCATTGGAGGTAATTTTATCAAACTCAAAACCACACAGCGTCTCTAGAAAATGTTCAAGGATATCAGATACTTATATAATAGAGTTGTCTGGTGTGTCTTCTTTTTTCTGTTACCAGCTTTTCCTATTGGACAGTTGATTGCAAACCATCCTGAAACAGTAGGATATTACACCTTTTACATATTGAATTACATATTGAATATTGAATTACATATGAATTGAATTACATGCATTTTTGTCTTCAACTTAAAGAACACTAAACTGTAGTTAAGCTTATTGGAGGAAGGATTTGAAATCATTAAGTCATGAATATATGATGTTGATGTCTGCTCTGGGACATTTTACCAAGTGTGTTATATGTCATAGCCAACATGTAATTAAAAAAAAAAAACGTAGAGATTTGTGAATCAGAGTCCTCTGTTCAAATACCAGCCCTTCCACTTAGCCACACAATCTTTGGTAGGTTACTTCATCTTCTTGAGACTGGGTTTCTTCATCTGTATATGCATATGAAGCACCTGAGTGCTTTTTAAATGTTTAGTAATTGTGTTCTATAAGTGTACATGTAAGTTATGAAACTTAGTTTTGAAATCTAAAACTTAACAACTCAGATGCGAAATCTTTCCAATGTTTAACTTTTGAACTGTCTCTTTCATCTGATTTGTAG
Seq C2 exon
ATCCTGTGTTGCCATAAGCCCTTGGCCCACATTTAAGTGGGAATGCAGCTAGCTTGGATGTCTGAAACTTTGTAGGCGCCTCTGTCTGAATCCTGAACACAGGCACCAGGACTACTGAGAGCTCGTCATCTGTGCAGGATAGCCACACAGCAAACATGTTTGCAAAACTGAAGAAGAAAATTGCAGAAGAGACTGCTGTTGCTCAGAGGCCAGGAGGTGCTACTAGGATCCCACGGTCTGTGAGCAAGGAATCAGTTGCCTCAATGGGAGCTGACTCAGGAGATGACTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136935-GOLGA1:NM_002077:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.733
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF068106=Phage_GP20=PU(21.2=40.0)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAATGCTTTGACCTCCAAGC
R:
TCATCTCCTGAGTCAGCTCCC
Band lengths:
334-1573
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)