HsaINT0147327 @ 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
chr1:156126205-156127923:+
Coord C1 exon
chr1:156126205-156126365
Coord A exon
chr1:156126366-156127860
Coord C2 exon
chr1:156127861-156127923
Length
1495 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
TCCCAACTCCCCACTTTCAGATA
3' ss Score
9.32
Exon sequences
Seq C1 exon
GGGATGAACGTAGGGCACTTAGCTTCTTCCACCAGAAGGGCCTCCAGGATTTTGACACTCTGCTCCTGAGTGGTGATGGAAATACTCTCTACGTGGGGGCTCGAGAAGCCATTCTGGCCTTGGATATCCAGGATCCAGGGGTCCCCAGGCTAAAGAACATG
Seq A exon
GTGAGGAGTCCAGGGATAAAGAGTGTGGGCTGGGAGTGAAGAGGGGGCCGGCAGCTACCCTGGGCTTGGCTGCCTGTGCATGAATAACTTAGTTGCTGTTATCTGTAATCAGCAGTTCTCTTTATATGTATATCGTGACAATATAACAGACAGGAAATGTCGTGGCCTCACTTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCCGTTGCCCAGGCTGGAGTACAGTGGCACGATCTTGGCTCACTGCAACCTCCGCCTCCCAGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGCACTAGCATGCACCACCATGCCAGGCTAATTTTAATAGAGACGAGATTTTACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCGCCTGCCTCAGCCTCCCAAAGAGTTGGGATTACAGGCGTGAGCCACCGCACCCGGCCTGTGACTTCACTCTTCACTGGTATTGTGAATAGTGATTGAATAATATTAATTGCAAAAATGGCTGATATGGAAATCATTGACATATGAGATAAACACTGACTCAAATTATATCAATAATTTGATATCTACCCACTAGTAGAAATCACTGATGCTTCTGTGTCTTTTTTTTTTTGAGATGGAGTCTCACTCTGTTGTCCAGGCTGGAGTGCAATGGCGTGATCTTGGCTCACTGTAACCTCTGCCTCCTGGGTTCAAGCAATTCTGCCTCAGTCTCCTGAGTAGCTGGGATTACAGGCGCCCGCCACTAGGCATGGCTGATTTTTCTGTTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGCCTGGTCTCGAACTCCCGACCTCAGGTGATCCATCCGCCTCAGGCTTTCTAAGTGCTGGGATTACAGGTGTGAGCCACTGTGCCTGGCTGCTTCTGTCTTAGTCGCCCTATTAATGGGAACAATGTGAGGAAGGAAGGAAGAAAGGGAGAGAAGGCACTAGCAATATTAGCAATCACCTCCATGGTTCATGTATCCTGATGTGTAGTCTGCTGACCACCTGCACATATGAGATGCTGGTTAAAAATGCAGATTCTCTAAGGCGTGACCCAGGAACCAACTTGTTAAACAATTTCCCCAGGAAATGTGCGGTTTGACAACTGCTGCCATATATACCATTCATCGTGTTAGGTGTTTTGTATATGCCACCTGGTTGTATCTGCCAGTAGCCTATGAAATTGACCAAGATCTCTCAGTCAGGAAATAGCCAAGTCTAGATTTAAACTTGGGTCTGTCTGATTCCTTAGGCTGTGTTCAACTATGGAGCTATGTCTGATACCAGTATTATTCAAGTAATAGCCATGGTCACAAACTGATGTTATTACTGCCCATCAGCATGTCACTAACCACCATGTCTGCTGGTTATTTCACATCAGAGCAGAGAAGGGAGGCAGGTCACAGCTAGAACTGAGGACCTTATTTCTTTTCATCTCGCCCTCCCAACTCCCCACTTTCAG
Seq C2 exon
ATACCGTGGCCAGCCAGTGACAGAAAAAAGAGTGAATGTGCCTTTAAGAAGAAGAGCAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196189-SEMA4A:NM_022367:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.003 A=NA C2=0.085
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(54.5=66.7)
A:
NA
C2:
PF0140314=Sema=FE(30.3=100),PF0140314=Sema=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATGAACGTAGGGCACTTAGC
R:
TCATTGCTCTTCTTCTTAAAGGCAC
Band lengths:
222-1717
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)