HsaINT0155897 @ hg19
Intron Retention
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:242007179-242008438:+
Coord C1 exon
chr2:242007179-242007362
Coord A exon
chr2:242007363-242008325
Coord C2 exon
chr2:242008326-242008438
Length
963 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
TTGTCACCTCCTGCCCACAGGGC
3' ss Score
10.82
Exon sequences
Seq C1 exon
GACCCCGCCCTGTGGAAGGCTTCGAGGTCACCAATGTGACGGCTAGCACCATCTCAGTGCAGTGGGCCCTGCACAGGATCCGCCATGCCACCGTCAGTGGGGTCCGTGTGTCCATCCGCCACCCTGAGGCCCTCAGGGACCAGGCCACCGATGTGGACAGGAGTGTGGACAGGTTCACCTTTAG
Seq A exon
GTAAGAAGGGACACCCAGAGCATGGGGCTGGGGTGAAGGCAGGGGTGGGGGCTCGGGGACACGGGGCCCAGGTCTCGGGCACATTCTCCGTGTGTGGACTGTACCACCTGCCGCTCCTCACCTGAGCGGAGACAAAGGTCTCAGGTGAGCCAGCCTCAGACCCTGGAGGCTTCACTCCCGCCTCACCTCATCAGGGCTGCCAAGAGAGGATACACCTTGGTAGTGTTTTAAAGTGTCCAAAAAGAGCAGGAAAAGCTCAGAAAATCCGGGGGCACACTTTCCACACAGATCATGAGAGTGACTTGGCCCCTCAGAGAGCAGCGGCCAGCGAGGGTAGATGGTAGCAGCCCCGAGCTCTCCCAGGAGTCCCACAGTGGACCCCTCAGAGAGCAGCGGCCAGCGAGGGTAGATGGTAGCAGCCCCGAGCTCTCCCAGGAGTCCCACAGTGGACCCCTGTGATTTGGTCGCCAACCAAAGAGAAAGCTTCCGAATCGTGCTCAGCGCAGGCAGGGGTGCAGGAAAAGATCGGAGAGCGAGTGGGAAGGAAGACTCCAGCCAGCAGCTTCCTGGGGCTGGGGTGGCATTGGCCTCACGTTGTCCTGTGGTTTCCTGAGAATTTACATCAACTCACCTGTGCTGAGGGCCCGTCCCCCATCCCTGCACAGTGACCACTTCCCCCTTCTCTGGCCTCTCCCAGCTGAACACCGGCCCTCTGACCATACTGTAGCAGCCCCAAGCGCACCCGATCCTCCTCCGCTGCCCGGACTATGGGTTGGCTTCCCGCCCTAGGAGCACACGGCTCTGAGGGCCATGAGTCTGCCCCTCGTGGAGGTTGCCTGGGCCACCAGCAGCAGGATGACCTCCCCGCAGTCACCTCCTGCCTGGGGGAGCTGCGGTCTGGCAGCAGAGTCACACACAGGTCCCAGACATCCCTGTTCTCTCTTTGTCACCTCCTGCCCACAG
Seq C2 exon
GGCCCTGCTGCCTGGGAAGAGGTACACCATCCAGCTGACCACCCTCAGTGGGCTCAGGGGAGAGGAGCACCCCACAGAGAGCCTGGCCACCGCGCCGACGCACGTGTGGACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804-SNED1:NM_001080437:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.129 A=NA C2=0.487
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(70.6=96.8)
A:
NA
C2:
PF0004116=fn3=PD(28.2=61.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCCCTGTGGAAGGCTTC
R:
GGTGGCCAGGCTCTCTGT
Band lengths:
270-1233
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
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)