HsaINT0005687 @ hg19
Intron Retention
Gene
ENSG00000188157 | AGRN
Description
agrin [Source:HGNC Symbol;Acc:329]
Coordinates
chr1:982200-982834:+
Coord C1 exon
chr1:982200-982337
Coord A exon
chr1:982338-982706
Coord C2 exon
chr1:982707-982834
Length
369 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TCACTGTACCTCCCCCACAGCCA
3' ss Score
9.3
Exon sequences
Seq C1 exon
GGCTCGAGCCCTTGGAGGGCAGCAGCGTGGCCACCCCTGGGCCACCTGTCGAGAGGGCTTCCTGCTACAACTCCGCGTTGGGCTGCTGCTCTGATGGGAAGACGCCCTCGCTGGACGCAGAGGGCTCCAACTGCCCCG
Seq A exon
GTGAGTGGACGGCTGGGCGAGGGGAGTGTGAGGATAGCCTGGGCTCGGCCGAGGTGCTGCCCCCTCGCCTGGGCAGCAGGTCAGTGCCGGGGGTTATGGTCTTGGGACTCGGCCCCCTCAAACATGTGCGTGCCGGGGACCCCACGCCTAACCCGTCTCTCTCGTTGCAAGCCGGTGTGGCACACTGCTCTGAGGAGTCCTCCTGGTAACCGACACCAGCCCCACCCTGGGGTCCCCACTAACCTCATGACCATCTGACTAACATCCACCTTCCCTTGCACCCTTGTGGCTTGCTGCTGGGGCCTGTGCCTGGGCCAGCCTGGATGCCAGGCAGATGCCAGGCAGGGCCTCACTGTACCTCCCCCACAG
Seq C2 exon
CCACCAAGGTGTTCCAGGGCGTCCTGGAGCTGGAGGGCGTCGAGGGCCAGGAGCTGTTCTACACGCCCGAGATGGCTGACCCCAAGTCAGAACTGTTCGGGGAGACAGCCAGGAGCATTGAGAGCACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188157-AGRN:NM_198576:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.596 A=NA C2=0.279
Domain overlap (PFAM):
C1:
PF0139015=SEA=PU(0.9=2.1)
A:
NA
C2:
PF0139015=SEA=FE(37.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTGGAGGGCAGCAGCGT
R:
GGTGCTCTCAATGCTCCTGG
Band lengths:
256-625
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)