HsaINT0005700 @ hg19
Intron Retention
Gene
ENSG00000188157 | AGRN
Description
agrin [Source:HGNC Symbol;Acc:329]
Coordinates
chr1:986106-986749:+
Coord C1 exon
chr1:986106-986217
Coord A exon
chr1:986218-986632
Coord C2 exon
chr1:986633-986749
Length
415 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
CTTACCTGGCGTCCCCGCAGGTT
3' ss Score
11.24
Exon sequences
Seq C1 exon
GAGCAGGGAGCCAGTCACCCTGGGAGCCTGGACCAGGGTCTCACTGGAGCGAAACGGCCGCAAGGGTGCCCTGCGTGTGGGCGACGGCCCCCGTGTGTTGGGGGAGTCCCCG
Seq A exon
GTGAGTGCTCTGGGCCGCGAGGGGACTCCCGCTGCTGCCTGCTCTTCCTCCTCGGGCGGCAGCCCCGCCCCTGCCGGCGCTCACGGAGCTGTTTTTCTGTCCTGTTCTCTTGGCCGCCTGCCCTGTCCTCTGCCTCCTCTGCCTCCCTGCTCTCTGCTCTCGCTCTGCAACCCCACCCGCTCTTCGGAGGCCAGAAATCCCGCAAGGTACTGTCGGCCTCTCATCCGCTCACCGTCTCTGGCGCCTCAACCCCTAGGGTAGCTCCTCCCCCACTAAGGACCCTGCCATTTCTGTGTGATTAACGCTGCCCCCTAGATAGGCAATGGGCGGGTGGGGCGGGTGCGTGCAGGTGCCTGGGCCCTGGGTCTGCACCGTGGGTGGGCTCTGCACAGCCACTTACCTGGCGTCCCCGCAG
Seq C2 exon
GTTCCGCACACCGTCCTCAACCTGAAGGAGCCGCTCTACGTAGGGGGCGCTCCCGACTTCAGCAAGCTGGCCCGTGCTGCTGCCGTGTCCTCTGGCTTCGACGGTGCCATCCAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188157-AGRN:NM_198576:30
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.289 A=NA C2=0.025
Domain overlap (PFAM):
C1:
PF0005418=Laminin_G_1=FE(28.0=100)
A:
NA
C2:
PF0005418=Laminin_G_1=FE(28.8=100)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGGGAGCCAGTCACCC
R:
CTGGATGGCACCGTCGAAG
Band lengths:
224-639
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)