HsaINT0155901 @ hg19
Intron Retention
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:242011211-242012779:+
Coord C1 exon
chr2:242011211-242011293
Coord A exon
chr2:242011294-242012680
Coord C2 exon
chr2:242012681-242012779
Length
1387 bp
Sequences
Splice sites
5' ss Seq
CACGTGAGT
5' ss Score
9.3
3' ss Seq
CACCGCCTGGCTTCTCCTAGAAC
3' ss Score
6.7
Exon sequences
Seq C1 exon
GTTCTCGGAGCTTGTGGACGGCAGAGGAAGAGTGAGCGCCAGGTTCGGTGGCTCACCCAGCAAAGCAGCCACCGTGAGATCAC
Seq A exon
GTGAGTGCCAGGGCCTCCCCACCCACCTTGGTGGCCCACCCTCGTCCTCACTGCCACTCTCACCAGGTCCTGTCCCCTACATGATGAGCCCACCCCCACCGCCAGCGCAGTCTCCAGCCAGTGACCCCCACCCCGACTGTGCACAAGGCGCGGGGCTCGTGGGCCGCCGGCAGCATGCACCTCCATGGCAGGAGGGGCAGCTCGTGAGGGCCTCACGTCAGTGTGTGGGCTGGAGGCGCAGGCTGCTGGTAGGGCACGCAAGAGAAGATAAACATTTTAGAAGCAGGTCTGAGACATTACAGCAGCTTTATTTGCCAAAGTAGGGCTCTGAGCTTTGTTTTAGTAAACCATGGGCAGGAGGCCATGAGGGTCTAACCCGCCACTCCGAGTGTGGTCCGGCAAATCCTCCGCCACTGTCCTGGCAAGATCTTCCCGGTGGCAGCAAGGCTGATGGGCCCAGGTGCCTTGGGCCCTTCCCACCGGGTTTACTGGGTGAGTGCCGCTCTGGGAATCTGCCTGTGATTCTGACACAGAAGCCCTGAGACATGTTGGCAGGAGTGAGGCAGGCGCGACCCTGCCCCAGAGGGGACCTCTCTGGCCCTTGCCTCTCACCTGGAAGGCCAGGTGGTCATCCTCATGGAACTCCCCAACAGAGCCTAGTCACCAGTTTAATGAACACGCTCTGAGCAAAAACTCCTCAGGCAGAGGAGGGAGGGAAATGCAGCAAGGAGAGTGGCAAGCAGGGACCAGAGCCCTGGGGTCCCTGCCGCACGGTGAGCAGGGGAGAGAGCCCCCAGCAAGGTGTCTGAGGAGAGGGCAGGCAGCTGCCCGGGATGCCCAGTGGTGGGCAGGTGAGATCTGGAGTACAGAGGGGGGCCCGTTGTACTTGCAGCTATGGAAGCGGATATGAAGTGCCCGAGGGTGCGGTTGAGATCCCTGCATAAGAAGTGATGCAGTTGGGGGCGAGGGCATGAGGAAGGTCAGTACAGACTGAGGGCAGCTCAGAAAGAGCAGGGGGTGCCACAGCCTCCAAGAAGCAGGGGTGGAAGGAGAGGAATGCAGAATTTGACCCTAAGAAGAAAGCAACCGCATCAGCCGTGAGGATGGGGCCTCTCAGCATGATCAGTGGTGGCTGTCCCTGAAGCAGCTCTGAGGGGGCCCTGCAAGGGGAAGGCCGAGCCCCTCCAGAGGGTCAGCAGGAGGGTGAGGCCAGCCCTTCAGGGGAGGCAGCTCTGGGGCCGACAGGTGCTGGGGCCACGCAGGGAGCCTGGTCCCCACCAGGGACATCCGTGCTCCCTGAGATATAGAAGCACTCAAAAGGGTGGCCCCAGGACCATCCCGGGTGCAAAGCAGCTGCGCCGTGTGGTCACCGCCTGGCTTCTCCTAG
Seq C2 exon
AACCCACAGCCTCGGCGCAGCTCGAGAACATGGAGGAAGCCCCCAAGCGGGTCAGCCTGGCCCTCCAGCTCCCTGAACACGGCAGCAAGGACATCGGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804-SNED1:NM_001080437:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.971 A=NA C2=0.918
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCTCGGAGCTTGTGGACG
R:
TTCCGATGTCCTTGCTGCC
Band lengths:
182-1569
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)