HsaINT0147329 @ 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
chr1:156128179-156128615:+
Coord C1 exon
chr1:156128179-156128277
Coord A exon
chr1:156128278-156128509
Coord C2 exon
chr1:156128510-156128615
Length
232 bp
Sequences
Splice sites
5' ss Seq
ATTGTGAGT
5' ss Score
7.35
3' ss Seq
CAGCCTCTCTCCCCATTTAGGAA
3' ss Score
10.79
Exon sequences
Seq C1 exon
ACACAGTGTTTCAACTTCATCCGTGTCCTGGTTTCTTACAATGTCACCCATCTCTACACCTGCGGCACCTTCGCCTTCAGCCCTGCTTGTACCTTCATT
Seq A exon
GTGAGTTCTCTGGTGCCCAGCGCTCAGGCCCCCAAGCATCCCTTCTCACATCTACCCACGACTTTCCTCTGTAGCTCTGGAAAACTCTGGCCTTCCAGATGCAGGACCCTCATGAACTTCCTGGCCCCAGACCAATTTCCCTCTATGTCCCTTTCCCTTCCTTCCTCAAGCCCCTCATTTCCCAGATGTGAGACCTTGGCGTTCTGGCCCCCCAGCCTCTCTCCCCATTTAG
Seq C2 exon
GAACTTCAAGATTCCTACCTGTTGCCCATCTCGGAGGACAAGGTCATGGAGGGAAAAGGCCAAAGCCCCTTTGACCCCGCTCACAAGCATACGGCTGTCTTGGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196189-SEMA4A:NM_022367:5
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.102
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(14.6=100)
A:
NA
C2:
PF0140314=Sema=PD(10.6=19.4),PF0140314=Sema=FE(30.2=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:
ACACAGTGTTTCAACTTCATCCGT
R:
CCACCAAGACAGCCGTATGC
Band lengths:
205-437
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)