HsaINT0147365 @ hg19
Intron Retention
Gene
ENSG00000187764 | SEMA4D
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D [Source:HGNC Symbol;Acc:10732]
Coordinates
chr9:92002301-92003707:-
Coord C1 exon
chr9:92003551-92003707
Coord A exon
chr9:92002524-92003550
Coord C2 exon
chr9:92002301-92002523
Length
1027 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGC
5' ss Score
8.02
3' ss Seq
CGGGGATTTTCTCCCTGCAGTGC
3' ss Score
7.93
Exon sequences
Seq C1 exon
GAACAACGTGGGGCTGTCGGCAGTGTGCGCCTACAACCTGTCCACAGCCGAGGAGGTCTTCTCCCACGGGAAGTACATGCAGAGCACCACAGTGGAGCAGTCCCACACCAAGTGGGTGCGCTATAATGGCCCGGTACCCAAGCCGCGGCCTGGAGCG
Seq A exon
GTGAGCTGGGGCACTGGGGGCGGGCCGTGCTTTCCCTTCAAGGCCCAGGGCATGGAATCCAGTACAGGCACTGGGGCCTGCTCATGGGCTGGGTACCTGGCCACGCCAAGGCTCTCTGCATTGGGACAGGGACGGCCGATGAGCACAGCTCATCCTTCTTCCCTTTTGCATGTTACGTAACAGCCATTGCTACACTATTGCACAAACAAGAAGGCTGGGGCAGCTGTTTTGCACAATTAACATTGCATAACAATTAGGTCTGTTTCATTTTCAGTTTCTTACAGAGAAACACATGATTCCTTGGCAAAGGCCTCTGCACTGTCCACTAGTCAACAGGAGTCACATTTTTTCCTCCTAAATATAGTGAACTTTATGTAGAAATTGGGAATTTCCAGGCCGATTCCTTCCCTCACATGGGGAAATGGGTGTGACAGGCATGTGCACAGCCCTCTGTGGGGCTGTGACCTACATGGGGTGTCCTGGCCCTCAGAGTTCACTGCAGCACCAGCTCCCTCCCAAGGGCAGCTGTCCCTGACACCATCATGGCTCCTTCTATGCATAGCTTCGTAAAATGTGTTCACTCATGGTCACAGATTTTGGTTTACACACATCAGGGAGCTAGAACAGGAAAAAAGAATCCCTCAGGCTCTTATGCTATTTTAAATTGTCCTGGTTTTAGCCATGTTTAGCATTCTTTTCATGAGAAAGCTGCAAATCAGTGTTCTGTTTTTTAATTTCAAAAGCTCAATAAGTGTTTTTCACTTACAAATAGATAAAAATTCCTTCCCTGAGTATGTATCGTGAATGCAATTCTGTCTTGCAGATGTGTTTTATAACTGTGTCCTCTGCTGGCTGGGGAGAGGCCACCTTTCCTCATAGTAAAGTTATTCACTGCTACCCTCATTTCAAGGCATGCATTGTGTGGTTTCCAGGTTTTGCAGCCCCCCCTGCGTTGGCTGCTTGTGTGGAAGCACCCGTTGCGTGGTGGGACACGAGCACGTTAACAGCGGGGATTTTCTCCCTGCAG
Seq C2 exon
TGCATCGACAGCGAGGCACGGGCCGCCAACTACACCAGCTCCTTGAATTTGCCAGACAAGACGCTGCAGTTCGTTAAAGACCACCCTTTGATGGATGACTCGGTAACCCCAATAGACAACAGGCCCAGGTTAATCAAGAAAGATGTGAACTACACCCAGATCGTGGTGGACCGGACCCAGGCCCTGGATGGGACTGTCTATGATGTCATGTTTGTCAGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000187764-SEMA4D:NM_001142287:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.132 A=NA C2=0.016
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(12.0=100)
A:
NA
C2:
PF0140314=Sema=FE(17.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACAACCTGTCCACAGCCGAG
R:
TGTGCTGACAAACATGACATCA
Band lengths:
348-1375
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)