HsaINT0147371 @ hg19
Intron Retention
Gene
ENSG00000187764 | SEMA4D
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D [Source:HGNC Symbol;Acc:10732]
Coordinates
chr9:91978345-91978865:-
Coord C1 exon
chr9:91978656-91978865
Coord A exon
chr9:91978443-91978655
Coord C2 exon
chr9:91978345-91978442
Length
213 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
GGACCCTGCTTGTTTTCCAGAAG
3' ss Score
7.27
Exon sequences
Seq C1 exon
GTCCTGCAGACATTCGCTTTGTCTGGGAGAAGAATGGGCGAGCTCTGGAGACCTGTGTCCCTGTGCAGACCCATGCACTGCCCGATGGCAGGGCCCATGCACTCAGCTGGCTGCAGGACGCCATCAGGGAAAGCGCTGAGTATCGCTGCTCTGTCCTCTCCTCAGCAGGGAACAAGACTTCGAAGGTGCAGGTTGCTGTGATGAGACCTG
Seq A exon
GTAAGTGATTCCCATGCCCACTGTTACCCTTTTATGAGGTAATTTTTCACTATTTACAATGGCAGTGAAAAAAACAGCTGGAAAGCATGCTTGCACGGTGGCATTCTGGGTTTGGGTTTTATTGGCTTTCCATTGAGAAAGGTGGCCAGTGGGCATCAAGGGTGCCATAAAGGCCCACAGAGCTTTGACCTGGGGACCCTGCTTGTTTTCCAG
Seq C2 exon
AAGTGACCCACCAGGAGAGGTGGACCAGAGAGCTCTCTGCCTGGAGGGCTGTGGCTGGGGAGCACGACCGGATGATGCAGAGCTGGAGGAAGGCGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000187764-SEMA4D:NM_001142287:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.073 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0765410=C1-set=WD(100=78.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTGCAGACATTCGCTTTGT
R:
TCCTCCAGCTCTGCATCATCC
Band lengths:
299-512
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
- Pre-implantation embryo development
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)