HsaINT0005692 @ hg19
Intron Retention
Gene
ENSG00000188157 | AGRN
Description
agrin [Source:HGNC Symbol;Acc:329]
Coordinates
chr1:983392-984439:+
Coord C1 exon
chr1:983392-983745
Coord A exon
chr1:983746-984246
Coord C2 exon
chr1:984247-984439
Length
501 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
CTCCCGGTCGCCCTTTGCAGTGC
3' ss Score
8.63
Exon sequences
Seq C1 exon
ACTGGTTTCCTGCGTTTATCACGGGGGCCACGTCAGGAGCCATTGCTGCGGGAGCCACGGCCAGAGCCACCACTGCATCGCGCCTGCCGTCCTCTGCTGTGACCCCTCGGGCCCCGCACCCCAGTCACACAAGCCAGCCCGTTGCCAAGACCACGGCAGCCCCCACCACACGTCGGCCCCCCACCACTGCCCCCAGCCGTGTGCCCGGACGTCGGCCCCCGGCCCCCCAGCAGCCTCCAAAGCCCTGTGACTCACAGCCCTGCTTCCACGGGGGGACCTGCCAGGACTGGGCATTGGGCGGGGGCTTCACCTGCAGCTGCCCGGCAGGCAGGGGAGGCGCCGTCTGTGAGAAGG
Seq A exon
GTAAGGATGTCCACTGCAGAGGAGGGCGGGGAGGCAGCAGGGTGGGGGCAAGGATTGGGGGTGGGGCTAAGCCACCATCAGGCTTTGAGTTGGGGGCAGGAGCCCGGATTAAGGCGGGGTTTCGGCCAGATGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGGATCACCTGAGGTCGGGAGTTCGAGACCAGCCTGACCAACATGGAGACACTCTGTCTCTACTAAAAATACAAAATTAGCCGGGCGTGGTGGTGGGCGCCTGTAATCCCACCTCGTGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGCAGGCGGAGGTTGCGGTGAGCCAGGATCGCGCCACTGCACTCCAGCCGGGGCAAAAAGAGCAAAACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAGCAGGGGGCGGTTTCAGGGATAAAAGTGGGGAATCCTCGGAGCTTTTCCAGCCGGCCCTCCCGGTCGCCCTTTGCAG
Seq C2 exon
TGCTTGGCGCCCCTGTGCCGGCCTTCGAGGGCCGCTCCTTCCTGGCCTTCCCCACTCTCCGCGCCTACCACACGCTGCGCCTGGCACTGGAATTCCGGGCGCTGGAGCCTCAGGGGCTGCTGCTGTACAATGGCAACGCCCGGGGCAAGGACTTCCTGGCATTGGCGCTGCTAGATGGCCGCGTGCAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188157-AGRN:NM_198576:23
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.597 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=27.7)
A:
NA
C2:
PF0005418=Laminin_G_1=PU(25.0=50.8)
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:
GTTGCCAAGACCACGGCAG
R:
GTTGCCATTGTACAGCAGCAG
Band lengths:
351-852
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)