HsaINT0147320 @ 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
chr1:156123322-156124508:+
Coord C1 exon
chr1:156123322-156123555
Coord A exon
chr1:156123556-156124340
Coord C2 exon
chr1:156124341-156124508
Length
785 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CCGGGTGCCTGTTTCCCCAGAGC
3' ss Score
7.68
Exon sequences
Seq C1 exon
GATCTGTCACAACTCGAGAGGTGGAAATTCCGGTTTCCCTGGCCTAGAGCTCCCAGTGCTGGCTTTGGCATGATGGGCACCTGGAGGGCCGCACTCCCGTTCCAGCCAGGCTGAGCCTTCTGTCCCCTGCCTCTGGGGCCTGGGAACCCCCCTTCTTCTTTCTCCTGAATGGCACCCCCGCCCTAGAATCCAGACACCGAGTTTCCCACTGTGGCTGGTTCAAGGGTATGTGAG
Seq A exon
GTGAGATGGGTGGCTTGGGGTGGGTGGTCTTGGGGAAGATTATGTAGAGGCCCAGGGAGGCAGACACAGGAGCAAGAGACAAGGGGGCCGGGGAGCTGCAGAGGCTGGGAGCCGGCCAGCCACCCCTGCCCAGGCAGCTCCCCGGGAAATGCTGATAACCAACCTGGTGGGATGGACCCTCATTGCCTCCCTGGAAGTATCAGGCCAGGCAGGCCTGAGCCTCAAAGACCCTGAACCCAGCTGGGGCTGGGGGAGAGGTTAGAGCAGGCAGACTCAAACCCAGTCTGCCTACCTGGGTCAGAGCTGAGTATGAGGCACAGGTGTCAACAGATCTGAAAGTGACAGGAGAGTAAGGTCTGAGGAATTTATATTTTGGGTACAGGAACCTGCTCCCCAAAATGTTCCCTGCCCAGAGCCAGGCAACGGTTTGGGCTTGGGCTATGAGAAGAGGGAAGGCAAAGGAGGAAAGACAGGAAAGACTTCCTGAGAGTAAGGCAAAAAAAGGCAAACCAGAGCTGTTGGTGAGAAGACAACAGAAGAAGCAGGATAGGGGAGACCTGGGCTCCTACCCATAGGGGACAGTGAGGTGACAGGCTGAGGCCTGGAAGGATGATGAAAGTGAGACCGTCTTAGGGCCCTTCCAGATAGGGAACCTTCTCTGCCCCAATGCCCCACCCCTGCCACCAATACACACGCTTCTGCTGCCTGGGGCTCTCCTATTGGTCCTCGGGGGGATGTGGTAAGAACTGCTCACCCAGAAAGTGCCCGGGTGCCTGTTTCCCCAG
Seq C2 exon
AGCTCCCTGGTGACAGTCTGTGGCTGAGCATGGCCCTCCCAGCCCTGGGCCTGGACCCCTGGAGCCTCCTGGGCCTTTTCCTCTTCCAACTGCTTCAGCTGCTGCTGCCGACGACGACCGCGGGGGGAGGCGGGCAGGGGCCCATGCCCAGGGTCAGATACTATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196189-SEMA4A:NM_022367:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.066
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGCTGGCTTTGGCATGATG
R:
AGTATCTGACCCTGGGCATGG
Band lengths:
342-1127
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)