HsaINT0155899 @ hg19
Intron Retention
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:242009335-242011135:+
Coord C1 exon
chr2:242009335-242009616
Coord A exon
chr2:242009617-242010990
Coord C2 exon
chr2:242010991-242011135
Length
1374 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
TCCTCCTGCCTGCTCTGCAGCCC
3' ss Score
8.41
Exon sequences
Seq C1 exon
GGCCCCTGCCTCCAGCAAACCTGACCGCCGCCCGAGTCACTGCCACCTCTGCCCACGTGGTCTGGGATGCCCCGACTCCAGGCAGCTTGCTGGAGGCTTATGTCATCAATGTGACCACCAGCCAGAGCACCAAGAGCCGCTATGTCCCCAACGGGAAGCTGGCGTCCTACACGGTGCGCGACCTGCTGCCGGGACGGCGGTACCAGCTCTCTGTGATAGCAGTGCAGAGCACGGAGCTCGGGCCGCAGCACAGCGAGCCCGCCCACCTCTACATCATCACCT
Seq A exon
GTGAGTGCCGTGGGCCCTGCGCGTGGGCGGGGCCAGTGTTTGCCAGCCCTCCACCCTGTTCAGGACTGACCTGGCCCTGCAGGGGCCTGGGATGCCAGGCAGACAGCCTAGAAACAGGACCGTGTTAGCAGGGGAGGAGTCTGTGTATGAAAGTGGAGGCTTTTCAAACCCACAAGGAAAGGAAGGACTCATGGGCAGGTGGCACCAACAACTGGAATAATAAGCACATTGAGCCTCAGTTTGTGCCGGACCCTCCCGTAGATCCCAGACAGGCCGAGCATCACCTGAAAACGGGTGCCGAGGGTGGCAGCGAGGAGGAAGCCCCCGGAAGTGGCCTGCATTGCAGCCCAGGCCTGACCCACGAAGAGCCACTGGACACAGACAGACAAAGGGCCAGGAGGCCACAGGCAGGGGCCTGCAAGGCAGGCAGGAATGCTGGGGAGCAGAGGCACAGGGCAGAAGCCGCTCGGAGTGGGGACAGATGCTCCGAAGGGCTCAGGTCTGCTCCCAAGTGCAGGGGTGGCCCTTCCAGGCTCCACCAGGGTCCCGAACGCCCCACTTAGGTCTTCCAAGTTCACAGAAGGAGCAGTGGGAAAATGCAGGAGCAGAACAGGGAGAGAAGAAAGAGACGGAGACAAGCAGGGAGGAGAGGCCACGGCGGGACAGAGCAGAGCAGTGCGCGGCTCCCCAGGGAAGAGAGGGCTCTGACCCCAGGCTCCTCCCCAACCCGTGAGGCTGTGCTGGGGACACGAAGTGCATAAGCTTGCCGAGTTCTCAGACCCAACCCTGCCACCCCCACCAGCTTGGGGCCAAGCCCACCAGCCAGGCAGAAGGGGCAGGCTGGGACCTCTGTGAGCCGGCGTCAGAGTGAGAGGGAGAGGGAAGGGGAAGGAGGGCCCAGCCTGGGAGGCTGAAGGACGCTGTTAGGGTGACAGATGCACCCTCACTCTCAGGGCACATGCTGGGGTGGGGACTCCCAGCTGAAGCGTCCCATCAGGAGGCCACTGGGGAGAAGCACTGTGTCTCCAGGGCAGCCTGGGACCTGAGTCCGAGCCCGAGTGCCCAGCCCCTTGAGAACTTGAGTGACGGGCAGGGGCCTAGACTCAGCCCTGCCTCATGACTCCCAGGCCAGTGCACGCCTGTGTCATGGCTGCGCATGGCTCCTCCTCAGAAGGGATGCGGCGGGTGGGCTGGAAGGGAACCCAGGGCATCTGGGGAAGCCACAAGCACCTTGGATGACCACGGCCCACGCACATGCCCCCCTTCCCTTCTCCAAGCACGGCTGAGTGTGAGGGGCACCACCCATGCCACAGGGGCAGGGACAGGAGCAGAGGGCAGCCCCAGACCAGCCCCTTCCTCCTGCCTGCTCTGCAG
Seq C2 exon
CCCCCAGGGATGGCGCTGACAGACGCTGGCACCAGGGAGGACACCACCCTCGGGTGCTCAAGAACAGACCGCCCCCGGCGCGCCTGCCGGAGCTGCGCCTGCTCAATGACCACAGCGCCCCCGAGACCCCCACCCAGCCCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804-SNED1:NM_001080437:24
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.326 A=NA C2=0.997
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=86.3)
A:
NA
C2:
NO
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:
GCCTCCAGCAAACCTGACC
R:
GTCTGTTCTTGAGCACCCGAG
Band lengths:
344-1718
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
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)