HsaINT0147326 @ 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
chr1:156124341-156126365:+
Coord C1 exon
chr1:156124341-156124508
Coord A exon
chr1:156124509-156126204
Coord C2 exon
chr1:156126205-156126365
Length
1696 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
CTGTCTTACTCCTCCAACAGGGG
3' ss Score
9.71
Exon sequences
Seq C1 exon
AGCTCCCTGGTGACAGTCTGTGGCTGAGCATGGCCCTCCCAGCCCTGGGCCTGGACCCCTGGAGCCTCCTGGGCCTTTTCCTCTTCCAACTGCTTCAGCTGCTGCTGCCGACGACGACCGCGGGGGGAGGCGGGCAGGGGCCCATGCCCAGGGTCAGATACTATGCAG
Seq A exon
GTAAGTGTCCGACAGCAGGAAGTGTGGGGATAGCAATAGAGAGCTGGAGGTGGGTGGAGGAAGGAGAGAGGAACAGAGGAGGGGAGGAAATGGATATGGAGAAACAGGGACACAGAGAGAGATGCCAGGGAGAAACAGAGGATCTCGGAGAAAGAGAGACACAGCCAGAAACAGAAGTCCAAAAGGAAAGAAAAGCCACTGGAGAGCAGATTGAGGAAAACAGGTGGCCACGGGGCCAGGGGCACGCTTCTTCCAGTTCTCCATGTTGGTAATTTTTCTTTCCTTCCTTAAATATCACTGTCACCAAGCTGGGCACCTCAAACTCCTAACTGCTTCACACTCCCAGGTACCCCAAAGTCAAGGCCCATGCTAGAAGACCATATGTGGACCCGGTGACCCGGAGCTCGCCAGGCCCATGCCAACCACATAGATCATGCTGGACCATACCATGTCCAGGACCATGGGATGGCTGGTTGGAGAATGGGCCCTGGAACCCACACACAAGCACAGCTTGGCTGGTTTCTTACTGAGACTGTGGAGGCTGCTGGCCCCCTCACCTCCAGGGAGAAGACTCAGGAAAGGATGTAGACACTGTAGGAGTTGTAGGTGACTGGGCATGGCTGTGTCTTTAGCATCTTTCTGGGGCAATTGGTAAAAGAAATGTATATTGCTCATTGATGCAGAGACCTCCTCTGTGTTGGATGCTGGGCGCACAAACACGGATAAGCCTCAGCCCCTGCCCTCAAGGTGTTCACAGTCACAAGGGGGAAGACATGAGCAATCAGACCATCAATACAGGGTGATCTGTTCAGCAACTGAGGGGTTTATGGCAGCTCTGGGGGAGGCCTGGCCTCCAGGAGATGCTCCTCCCTGAGGCTGGCCCTTCCATCCCGCAGCCACACCAGATTCCCCAACTTCTCCCCTCTGTACTGTGTAAGATTCCCTGAGCCTGCAAAGGTATCAATTAGCTAGTCAGCTTTCTAACTAATGCAACAGTGCAAGTGCTAATGAGAGAGGATCTGAGGAGCTCCTTCCTCCTTGCCGATGTGCCAGTGGGACAGGAAAATACACCCCCACCCACCCCACCATGCCAAGGTCATGGAGAGGACCTAGGTGAGCCTCCCACACCTGGCTCACCATCCCTGCCCAGGGGACATCCAGCCATGCCCACATGGATCTTTGAAGAAAAATGCTTCCTCTCTGTTCGTGGTGACTCTACTGGTGGGAATTTCCTTTAACAGAAGAGGAAGAAAGCAGGGGTGGTTGGGGGGATGGCGAGAGGGACTCTGACATACGCCCTCCTGTCTGCATATAGCTTTGCTGCTTGTGGCTGCCAACACTTTCCTGTTTGTCTGTCTGCCTGCTGCTCCTCATCCTAGTGAGGACCAAGGCGTCCTCCCCGACGGTAGCCCTCCCTGTCCCAGGCCTGGAAGAGCATCCACTGTGCCTCACTTTATTTCCCGTCCCCATTACCCTGCCTCTGGCTGCCTCTCCTCTCTACTGCGGGCTCAGCACACAACGCTCTTGTGTTGGGGTGGGGTGAAGGGAAGAACTGCTGGTGGAGGAGAGTGCATCTAGCTGCCAAGGCCTGGGGAGCACACTCAGGCAACCCTTCCCCTTCCCCCACTTTTATCTCAGGAGTCAGCTGCCTGCCCACCAAGTCCTCATCACTCTCTCTGTCTTACTCCTCCAACAG
Seq C2 exon
GGGATGAACGTAGGGCACTTAGCTTCTTCCACCAGAAGGGCCTCCAGGATTTTGACACTCTGCTCCTGAGTGGTGATGGAAATACTCTCTACGTGGGGGCTCGAGAAGCCATTCTGGCCTTGGATATCCAGGATCCAGGGGTCCCCAGGCTAAAGAACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196189-SEMA4A:NM_022367:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.066 A=NA C2=0.003
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(54.5=66.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACAGTCTGTGGCTGAGCATG
R:
CATGTTCTTTAGCCTGGGGAC
Band lengths:
318-2014
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)