HsaINT0147322 @ 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
chr1:156142617-156144731:+
Coord C1 exon
chr1:156142617-156142797
Coord A exon
chr1:156142798-156144612
Coord C2 exon
chr1:156144613-156144731
Length
1815 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
CTCTCTCTGTCTCCCCATAGCCA
3' ss Score
12.08
Exon sequences
Seq C1 exon
TGCTCAGTGGGCCCCTCCTCTGATAAGGCCCTGACCTTCATGAAGGACCATTTCCTGATGGATGAGCAAGTGGTGGGGACGCCCCTGCTGGTGAAATCTGGCGTGGAGTATACACGGCTTGCAGTGGAGACAGCCCAGGGCCTTGATGGGCACAGCCATCTTGTCATGTACCTGGGAACCA
Seq A exon
GTGAGTAAAGAGTTCCGGGACATCCCCCAGAGGACTAGAGCAGAGGATGCCCCCAGGTTGAGGAGGGAAACCCTTGAGTTCATTCACTTATTCATTCAACAACTGTTTACTGAGCACCTGCTATGTGCCTGGCATTCTGCTAGGTTCTGGAAATACAGCAGAGGAGCAAAACAGTCCACTCCCTACCCTTTCTGAGCTTCCTATGGTGGGGGAGGCAGACAGGGAGGTCTTTGGTGGCTTTATCAAGAGCTGTGTGTCTTATGAGGGAAGCTATGTTAGAGGAATGAAAGGTGAGTGGGTGGAGGGGAGCTGGAAACCGCACATGTAGAGATCACTCCTTCAGGAAGCTCGTCTGTGAAGGGAGAGAGGAAGGAGGTGGTGGCTGGAGCACGGAGTGGGGCGCAGCTGGGGTTCTTGGTTTTGTTTTTTCCCCCTCCTTGCCCCCAGGGTTCTTGTTTTGTAGACAGGAAGGACTAAGCATCTAGTAGACAGGGGGATGGCAAAGAGATGGGTAGAAGAAGGGATAAGTGGCAGGTAAAGTTGTGGCGGGAGCAGGCGGCCAGAGTCCAGGACACATGTCGAGCTGGGCAGCTGTGGGTGGCGGGGGGGACAGCACCTGAGCTGGGCTGGGAGTGAAGCTGTAGCAGCGGGGTGTGACTTGGTGGGTGTGCAGGCTCAGGGTAGGAAGCCAAGGGAGCTCTTATTTGAAGGCTTTTGTGTTCTCTATGTAGGTGGAGGACACAAGGTCATGAGCTGGGAGTGAGGGGGCAGGAAAGGTGGGAGGTTTGAGGAGAGAGAGGTAGATTCAAATAGCCATTGTGGGCTGGGCACAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATTGTGAAACCCGTTTCTACTAAAAATACAAACAAATTAGCAGTGTGTAGTGGCACGCACCTGTAATCCCAGCTACTCGGGAGGCTGAGTCAGGAGAATCACTTGAACCTGGGAGGCAGAGGTTGCAATGAGCCAAAATTGTGCCACTGCCCTCCAGCCTGGGTGACAAGAGTGAAAATCCGTCTCAAAAAAAAAAATAGCCATTGTGGAAAGAGGGAGACGGAGTCAGCAGAGAATGCAGCAAGACTGCCCAGGCAGACTGCTCAGGCAGGATAACCTTGAGGGTCAGTGGAAGAAATTTGTCAAGTTCATTCATTCCTTCAGGACAGATTACTAGGCACTGTATCAGCTGTGCATGTATTGGGTATACAGCAGAGAACAAAACAGTCAAAAATCTCAGTCTTTGTGGAGTGGATGGAGACAGACAATAGCATCCTGAATAAGTAAATTACATGGCACATCATGAGATTTGAGTCACGTAGAGGTGTGTGCGGGGGAATCAGGAATGCCAGGTAAGGAGGTTGCACCTGTTAAAAGGGTGGCCAGGTAGACCTCACTGAGGTGCTTGATGGATGTGAGGGAGGCAGGTGATGTGATTTTCTACAGAAGCACCCAGCCGCCCACTGTTTCATGCCTATGGAGAAATAGCTGGGTTTCTCCAGGGACAAAGTTTTGTCAGGGAGTTGCAAAGGAAGGACAGGGGTCCAAGGGATTTTAGTCATTTACAAGAGACTGCCATCTCCATGGCACAGAGGAAGGTGAATGATCTGGCTGACCCGCGCCCAGTACATATCACCCTCAGAAGGAGCTTTCTTACAGCTGGGGAGGCCCCCGGAAGTTGGGAAGGGATCTGTGGATGAGATGAGATGACTTCCACTCTCTCTGTCTCCCCATAG
Seq C2 exon
CCACAGGGTCGCTCCACAAGGCTGTGGTAAGTGGGGACAGCAGTGCTCATCTGGTGGAAGAGATTCAGCTGTTCCCTGACCCTGAACCTGTTCGCAACCTGCAGCTGGCCCCCACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196189-SEMA4A:NM_022367:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.049 A=NA C2=0.050
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(14.5=100)
A:
NA
C2:
PF0140314=Sema=FE(11.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
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:
AGTGGGCCCCTCCTCTGATAA
R:
GCAGGTTGCGAACAGGTTCAG
Band lengths:
278-2093
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)