HsaINT0155818 @ hg19
Intron Retention
Gene
ENSG00000165684 | SNAPC4
Description
small nuclear RNA activating complex, polypeptide 4, 190kDa [Source:HGNC Symbol;Acc:11137]
Coordinates
chr9:139270801-139273751:-
Coord C1 exon
chr9:139271995-139273751
Coord A exon
chr9:139270934-139271994
Coord C2 exon
chr9:139270801-139270933
Length
1061 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
CTGCCTGGATTTTCTTTCAGGGA
3' ss Score
9.51
Exon sequences
Seq C1 exon
GCCACCTCTTCCCAAACGTGCCGGCTCAAGAAGCCTCAAAGAGTGCCAGCCACAAAGGGAGCCGAAGACTGGCGTCCAGCCGGGTGGAGCGCACCCTACCCCAGGCGTCCCTGCTGGCTTCAACCGGCCCCCGGCCCAAGCCCAAGACTGTGTCGGAGCTGCTTCAGGAGAAGCGGCTTCAGGAGGCCCGTGCCAGGGAGGCCACCCGGGGCCCGGTGGTGCTCCCGTCCCAGCTGCTGGTCTCCTCGTCTGTGATCCTCCAGCCCCCTCTACCACACACCCCACACGGCCGCCCAGCCCCGGGTCCCACCGTCTTAAATGTACCGCTCTCTGGGCCTGGGGCCCCCGCGGCAGCCAAACCTGGCACTTCTGGCTCCTGGCAGGAGGCTGGGACTTCAGCCAAGGACAAGAGACTCTCCACCATGCAAGCCCTGCCCCTCGCTCCTGTCTTCTCAGAGGCCGAGGGCACAGCCCCTGCTGCTTCCCAAGCCCCTGCCCTGGGCCCCGGCCAGATCTCTGTGAGCTGCCCCGAGAGTGGTCTCGGACAGTCTCAGGCCCCCGCTGCATCCCGGAAGCAGGGCCTGCCTGAGGCGCCACCCTTTCTCCCCGCAGCCCCCAGCCCCACCCCACTGCCCGTCCAGCCCCTCAGCCTGACGCACATAGGAGGGCCACATGTGGCGACCAGTGTCCCCCTGCCTGTCACCTGGGTGCTCACAGCCCAGGGGCTTCTCCCTGTTCCTGTACCAGCTGTGGTGAGCCTTCCCAGGCCAGCAGGGACCCCTGGCCCCGCAGGGCTGCTGGCCACTCTGCTGCCTCCCCTGACTGAGACTCGGGCGGCCCAGGGCCCCAGGGCCCCAGCGTTGAGCAGCTCTTGGCAGCCCCCAGCCAATATGAACAGGGAACCGGAGCCTTCCTGCAGGACAGACACCCCAGCTCCTCCCACACACGCCCTCTCCCAAAGTCCTGCAGAAGCGGATGGCAGTGTGGCCTTTGTCCCTGGAGAGGCCCAGGTGGCCAGGGAGATACCTGAGCCCAGGACGTCCTCCCACGCTGACCCTCCTGAAGCAGAACCCCCTTGGTCCGGGAGGCTGCCAGCCTTCGGTGGTGTCATCCCAGCAACTGAGCCAAGGGGGACGCCGGGGTCCCCCTCAGGGACACAGGAGCCCAGGGGGCCTCTGGGCCTGGAGAAGCTGCCCCTGCGCCAGCCTGGGCCTGAGAAGGGGGCCCTGGACCTGGAGAAGCCGCCCCTACCCCAGCCTGGGCCTGAGAAGGGGGCCCTGGACCTGGGCCTGCTGTCCCAGGAGGGCGAGGCGGCCACACAGCAGTGGCTGGGGGGCCAGCGGGGGGTGCGTGTGCCTCTTCTGGGCAGCAGACTGCCCTATCAGCCCCCAGCCCTGTGCAGCCTGCGAGCTCTGTCCGGTCTCCTACTCCACAAGAAGGCCCTGGAGCACAAGGCCACCTCCCTGGTGGTGGGGGGCGAGGCTGAGCGGCCGGCCGGAGCACTGCAAGCCTCACTGGGGCTGGTGCGGGGGCAGCTCCAGGACAACCCGGCCTACCTCCTGTTGCGGGCGCGGTTCCTGGCAGCCTTCACCCTCCCTGCGCTCCTGGCCACCCTGGCCCCCCAAGGCGTCCGCACCACCCTCTCAGTACCTTCGAGGGTGGGCTCTGAGAGTGAGGATGAAGACCTCCTGAGTGAGCTGGAACTTGCAGACAGGGACGGGCAGCCGGGCTGCACGACAGCCACATGCCCCATTCAG
Seq A exon
GTAGGGTGGGCGCCCAGCCCCACTTCCCCATGGCAGGCGGCGGTCCCTGGGGTGCCCTCGCCTGCCTGGAGCAGTGGGGTGGGGGCTGGTGGAAGTTGCGGGCAGGAAGGCTGGCTGCTGGGTGTCTTAGGAGGAGGAAGCTGGTTCCTGGCCTGCCCAGTTGCGTGTAGATTCTGCAGAAGTGGCCTCCCTTTGGGGCAGTGTGGAAAAGGGGAGAAGAGAGGCCTCATTCTCGTGCAGGAGCCTCCGGCCATCCTGATGCTGCCCAGCCAGGTGGCCTTGTCTGAGCGAGAAGCTCTGGGATGGACGCTGACCCGGCTCTGAGCCGCACACGCCACACACACGTGTGCTCCCAGGGTGGGCCATGGGCACAGTGGAGGGTGGTGGCTGTGTTTGTCTCTGGATTTCTGGGGTCCCAAAGGTCCCTCTCTGCTGTCACCTCTCTGAGTGTCCTTGGGGAGAGTTTTCCAATCTCTGTAGGTGAAACCATGTTTGGAACCCTGGAAAGCATGTGGAGCTGGGGCCCCCAGAGAGGCCTCCTCCCCTGGTGCCAGGGTGCCCACTTGCAGCAGCTGGGAGGCTGGCCTCCCTGAGAAACCACCAGAAGCAGGCAGCCTCAGCTGGACCTGTGGGCCTGTCATAGGGAGTGTGGCAGAGGGCCTTCCATCTCTCCCCAGGGTTGTGTCTCGCAAGTCCCTGGGCTGAAGTGTGGGAGGAAGCAATGTCCAAGAGTTGGGGAGGACCCCGGCCAGCCAGGGGAAGAGGCCCTCTGTGCCCCATCCATGTACAGCCTCCTGCCCTGCCTGGGTGTGATGGCTGTCCCATGGGGGAGTGGGAGGCCCACCAGAGGGATGGCTTGGATGGGGTCAGAGCCCCCGAGGGAGGGAGTGCACAGTCACGTGTGGCCCCAGGAGTGCCTGGAGCAGCTCCCGCCTGAGCTGAGGGTGCCCTGTCCCAAGTGGGACACTCACCCACAGGGCCCCTCCTCACTCCCGTCCCTTCCCCGTCCATCATGGCTCGGGGGTGTCACTCTTGTCCCCACTGCCTGGATTTTCTTTCAG
Seq C2 exon
GGAGCCCCAGACTCTGGTAAATGCTCTGCTTCCTCCTGCCTGGATACTTCTAATGACCCTGACGACCTGGACGTGCTCAGAACCCGGCATGCCAGGCACACCCGGAAGCGGAGGCGGCTGGTGTGAGCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165684-SNAPC4:NM_003086:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.766 A=NA C2=0.488
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCACTGCAAGCCTCACTG
R:
GTTCTGAGCACGTCCAGGTC
Band lengths:
343-1404
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)