HsaINT0155904 @ hg19
Intron Retention
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:241973152-241974147:+
Coord C1 exon
chr2:241973152-241973292
Coord A exon
chr2:241973293-241973984
Coord C2 exon
chr2:241973985-241974147
Length
692 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
TGCCCCCACCCCACCCCCAGGCT
3' ss Score
8.63
Exon sequences
Seq C1 exon
GTCAACACATTCCAGACTGTGCTCATCACAGACGGCAAGCTCTCCTTCACCATCTTCAACTATGAGTCCATCGTGTGGACCACAGGCACACACGCCAGCAGCGGGGGCAACGCCACTGGCCTCGGGGGCATCGCAGCCCAG
Seq A exon
GTAGGCGAGTGCAGTCGGTGCTCTGTGTTCAGAACCCCTGCTCCCCACAGCCAGGACTGTCATGAGCTGATGAGGTAGGCAGGGGCTCACCATAGGCAGATCCCCCAGTACCGTGCAGAGGCCAACGAGAGACATCCACAACCATCCCTGAGGCCTCTCACTGCCCAAAAACAGAAACATCCTCAGGCCCAAAGGCACCTTTGTCCCCCTGACCTGCCCCGCCCTGCCCCTGCAGTCCCCTTTAACAGCTGCAACAGCAACAGAAATGTCCTCTGCTCCTTGTGCCCTGCAGTCTGGCCTAGCCAGTGACACAAGGGACCACAGCCGGCAGGAAACCCCGGGTGTGGAGGGAATGAAACAGGACAATGGCCACAGGGTCAGTGCTCCCCAGGCCCGAGAGTGCCTTTGGGCTGTGCGCACCCCCACTCACCTCCTGGCCACCTGCTTTCTCTTGGGTTCATACTTGCCCCTGGCCCCAGGGGAGGCCCAAGAGCCCAGAGGTGAGCTGCCGGAGGACTGGGCTGGGGAGCCAGGGCCAGCCCTCTCCTTGGCTCCCAGGAACGGTTGGCTGAGGTCAGGACCTGGCTGGGAGGTTGCCGACCCTGGCAGGAACATGGTGGGGGCAGGGTAACCCCCACCTCTGTAGACCTGGGGAACTGGCCTCCCTCACTCTGCCCCCACCCCACCCCCAG
Seq C2 exon
GCTGGCTTCAACGCAGGCGATGGGCAGCGTTACTTCAGTATCCCCGGCTCGCGCACAGCAGACATGGCCGAGGTGGAGACCACCACCAACGTGGGTGTGCCCGGGCGCTGGGCGTTCAGAATCGATGATGCCCAGGTGCGCGTGGGGGGCTGCGGCCATACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804-SNED1:NM_001080437:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.055
Domain overlap (PFAM):
C1:
PF061199=NIDO=PU(50.5=97.9)
A:
NA
C2:
PF061199=NIDO=PD(47.3=78.2)
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:
TCAACACATTCCAGACTGTGCT
R:
GCACCTGGGCATCATCGATTC
Band lengths:
279-971
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)