HsaINT0155906 @ hg19
Intron Retention
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:241973985-241976332:+
Coord C1 exon
chr2:241973985-241974147
Coord A exon
chr2:241974148-241976206
Coord C2 exon
chr2:241976207-241976332
Length
2059 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
GCCCCTCCCTATGTCTGCAGCGT
3' ss Score
9.67
Exon sequences
Seq C1 exon
GCTGGCTTCAACGCAGGCGATGGGCAGCGTTACTTCAGTATCCCCGGCTCGCGCACAGCAGACATGGCCGAGGTGGAGACCACCACCAACGTGGGTGTGCCCGGGCGCTGGGCGTTCAGAATCGATGATGCCCAGGTGCGCGTGGGGGGCTGCGGCCATACAA
Seq A exon
GTAAGAGGACAGAGGAGCAGCTTGGGGTGGGAGCGGGCTGAGGAAGGGGGTTGATGGCAGAGGAGAGGTGGAGACGAAGGGGGCTGGATGCTGACGGGGAGAGCAGGAGCACTTGGGTGTCCAGCCCAGCCCACCTCAGGCGTGTGAAACTAAGGAAAGCCTGGCTGGTCCTGCAGCCTCAGCTTCCCCTAGAGAAGACCCCACACACACACTGCTCTGGGTTGGAGGGAACCCTCTGGAGACTGTGCCCTAGAGAAGATCCCGCACACACACTGCTGTGGGTTGGAGGGAACCCTCTGGAGACTGCGGGTTTCGGGGGTAAAGAGTTCTGGGTCCTCAGGGGAGGAGGAGCCCAGGGACACCTCTCCCTGGGACCATGTGGTCCCTACTCTCCCCTTATTCCCACCCAGCCTCCTGCCTGGGCTGGGGGAGGAGCAGCATGTGGTCTCTGACCCTCAGGGCCACCCATGAGGCAGGTCCTCTTACCACCCAGGTCCTCATTTTTGCCAGCGGGCTTGCTGCTTGGTGGGATTTGGTGACTGCTTGACAAACCCAAGCATCACGTCTACAGGGGAGTTCCAGGGGTCCTTCCAGCCCACAGTGCACAAACGGACGGGGTGGGTGTCCCTCCCAGGGGTGGGCACGTGGTTTGTGGGAACAGCCAGGGCGGCAGCAGAGCCATAGATGGTAGCCTTAGCCCTGCTGCTGTGCGGCCTTGGGAGCCAAGGAGCCTTCAGAAATCACTGCTTACACTTGGGGCGAGGGCAAGCGACTGATCCGCTCCACTGAGGGCGGCGCATCACAAGCCCTGCCAAGCCTGGGGCCGCAGTGAGGCTCGCACCGGGACCTGCCCCAGACTCGCCTCCCAGCCGCGAGCATCTAGGCTACGAGAGGGGAGAGGGGCCGCATCTCCGCAACACTGAGTCCCCAGAGAACACGACAGGGGTAGCAGATGCGCGCGCACCACTGTCGGGGCGGAGGCGGGGTGCAGGCGCGCCATGGGGTGGGGGATGAGGGGTAGAGAGTGTGGGGGTGGGGGATGGGGTATGCAGGTGCGCCACAGGGTTGGGGATGAGGGGTAGATGGTGTGGGGATGGGGGGTGCAGGCGCGCCACAGGGTTGGGAGTGAGGGGTAGAGGGTGTGGGAGGTGGGGGCGTGCCATGGGGTGGGGGGTGCAGGCGTGCCACGGGGTGGAGGGGTGGGGGGTGCAGGTGTGCCACGGGGTTGGAGGTGGGGCGTAGTAGGGGTGGGGGGCGGAGGCGCGTCACGGGGAGGGGAGTGGGGGGTGGAGGTGCGTCACGGGGTGGGTGGGGGGTGGAGGTGCGTCACAGGGTGGGGGGTGGGGGGTGGAGGCGCATCACGGGGTGGGGGTTGGGGAGTAGAGGCGCGCCACGGGGTGGGGAGAGCACCGCGCGCTCATGGGAAGAGGAAAGATGCAGTCGCAGGGCGGGAAGACCCATCTGAGGGCTGCAGGTGGTGCCGCGACGAAGGAGGCCCGAGGAGCCCGAGCTACCCACACACTGGGGCACGAACAGGCCCCCGCTTGCATCTGAGCTTAGGGAGTCCGGGCTCACGGGGCGGGGAGCCCAGAGCGGCCGCCCAGCATCCGAGGGACACAGCCCTCCTGCAGCCCCCAGCCACACCCCCTGCGTGGCCCGCCTTGTCCCAGAAACGCTGACATGACGGCTGAGTGCCAGCCTCGGGTTTTCCACGCCAGGAACCCTGGAGGGGAGGCGGAGTGTGCCAGTTTTTAGACCTGTCCACGGCAGCGCTGAGAGGGATGGAGGGGACGGGGTGCTGGTGTGAGTCGCTTCAGGGAGTCCGCCCCACACGAAGCCACCTCCCCAGAGGCCACGCCAACAGCACCGCCCCTGCTCCCCTGCTCCCCTGCTCCGACCTAAAGTGAAACCTGAAACCTGGCTGCTTTGCTGCGGTCACCCGGGCACCCAGAGGCCGACCTTTTGGGTCAGGGGAGGGAAGGGAGATGCGGATGGGAGTGGCTCTCCTGCCGAGTCCGGAGGCAGCGGCTGAGGCTCCAGCCCCTCCCTATGTCTGCAG
Seq C2 exon
CGTCCGTGTGCCTGGCCCTGCGCCCCTGCCTCAACGGCGGCAAGTGCATCGACGACTGCGTCACGGGCAACCCCTCCTACACCTGCTCCTGCCTCTCGGGCTTCACGGGGCGGAGGTGCCACCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804-SNED1:NM_001080437:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.055 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF061199=NIDO=PD(47.3=78.2)
A:
NA
C2:
PF0000822=EGF=WD(100=83.7)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)