HsaINT0005686 @ hg19
Intron Retention
Gene
ENSG00000188157 | AGRN
Description
agrin [Source:HGNC Symbol;Acc:329]
Coordinates
chr1:981777-982337:+
Coord C1 exon
chr1:981777-982115
Coord A exon
chr1:982116-982199
Coord C2 exon
chr1:982200-982337
Length
84 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGC
5' ss Score
5.97
3' ss Seq
CTCAGAGCGCGTCTCCCCAGGGC
3' ss Score
4.39
Exon sequences
Seq C1 exon
AGGCTGTTGCTCCCAGCACTCACCCGACATCTGCCTCCGTGACTGTGACCACCCCAGGGCTCCTCCTGAGCCAGGCACTGCCGGCCCCCCCCGGCGCCCTCCCCCTGGCTCCCAGCAGTACCGCACACAGCCAGACCACCCCTCCGCCCTCATCACGACCTCGGACCACTGCCAGCGTCCCCAGGACCACCGTGTGGCCCGTGCTGACGGTGCCCCCCACGGCACCCTCCCCTGCACCCAGCCTGGTGGCGTCCGCCTTTGGTGAATCTGGCAGCACTGATGGAAGCAGCGATGAGGAACTGAGCGGGGACCAGGAGGCCAGTGGGGGTGGCTCTGGGG
Seq A exon
GTGAGCAGGGATCAAGGACTTGGGGTGGGTGGGCAGGCGCCGAGAGGCTCCACCAGAGCCTGGGCTCAGAGCGCGTCTCCCCAG
Seq C2 exon
GGCTCGAGCCCTTGGAGGGCAGCAGCGTGGCCACCCCTGGGCCACCTGTCGAGAGGGCTTCCTGCTACAACTCCGCGTTGGGCTGCTGCTCTGATGGGAAGACGCCCTCGCTGGACGCAGAGGGCTCCAACTGCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188157-AGRN:NM_198576:18
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.991 A=NA C2=0.596
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139015=SEA=PU(0.9=2.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACTGATGGAAGCAGCGATGA
R:
GTCTTCCCATCAGAGCAGCAG
Band lengths:
168-252
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)