HsaINT0147328 @ hg19
Intron Retention
Gene
ENSG00000196189 | SEMA4A
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A [Source:HGNC Symbol;Acc:10729]
Coordinates
chr1:156127861-156128277:+
Coord C1 exon
chr1:156127861-156127923
Coord A exon
chr1:156127924-156128178
Coord C2 exon
chr1:156128179-156128277
Length
255 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
AAATTCTCTGTCTCCCTCAGACA
3' ss Score
8.59
Exon sequences
Seq C1 exon
ATACCGTGGCCAGCCAGTGACAGAAAAAAGAGTGAATGTGCCTTTAAGAAGAAGAGCAATGAG
Seq A exon
GTAAGTGGAGGTGGGGGAGTAGGGGTAGAGTGGGTAGAGAGCTCTGGCATCCCTAGACCATCCCTGGATGACCTCAGGTTGGGCGGCAGTGGAGGGCACTTGTTTGCACGGTTATCTCCTGGATTATGTTCTACAGAGGCGTACAGGGACTGCCCCAGCATTACCTAGCCTTTCTCCTCAGTGAGGGGGCAGCCTCTGGGGGTCCAGCAATTTGAGTCAGGTGGCCTGGAGACCTAAATTCTCTGTCTCCCTCAG
Seq C2 exon
ACACAGTGTTTCAACTTCATCCGTGTCCTGGTTTCTTACAATGTCACCCATCTCTACACCTGCGGCACCTTCGCCTTCAGCCCTGCTTGTACCTTCATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196189-SEMA4A:NM_022367:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.085 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(30.3=100),PF0140314=Sema=PU(0.1=0.0)
A:
NA
C2:
PF0140314=Sema=FE(14.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGCCAGCCAGTGACAGAAAA
R:
AATGAAGGTACAAGCAGGGCTG
Band lengths:
156-411
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)