HsaINT0147515 @ hg19
Intron Retention
Gene
ENSG00000137872 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:16770]
Coordinates
chr15:48051942-48052612:+
Coord C1 exon
chr15:48051942-48052104
Coord A exon
chr15:48052105-48052500
Coord C2 exon
chr15:48052501-48052612
Length
396 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
TAGCCCATTTTTACTTGCAGATT
3' ss Score
7.48
Exon sequences
Seq C1 exon
GTAGCTCAGTGGCATTTCTGAGCAGGGGCCACCCTGACTTCACCTTGGCCCACCATGAGGGTCTTCCTGCTTTGTGCCTACATACTGCTGCTGATGGTTTCCCAGTTGAGGGCAGTCAGCTTTCCTGAAGATGATGAACCCCTTAATACTGTCGACTATCACT
Seq A exon
GTAAGTCGTCTCAAGAACAGTCTTCTATTCTGAGAAGGAAGCTTTTCTGTTTTTCATTCTGTAAGCATGTTCATTTTCAGAAAGAGGCAGAGATTTTTTATGTCTTAACCTTGAATTTGCATCTGAGTTTATCAGTAATCATTTCCTAGTGTTTGGAGAAAACGGGGCAGTTTTGTTGGGTGCTTTTCTACAGCAACCTGTATATAGGTTATATATTTTGAGTTAAAAAGACCATTTGCTGACATTCACTGCCTTTTATTCATTTATATTCAAGACCTTAAGAGAGGAATTTAGTTAAAACCCTTCTACAACAAGTATATACAGCTAATCAATGCTGTTTATTGATCCCTCAGCTCCATAATCCTGAATGATGGTTTAGCCCATTTTTACTTGCAG
Seq C2 exon
ATTCAAGGCAATATCCGGTTTTTAGAGGACGCCCTTCAGGCAATGAATCGCAGCACAGGCTGGACTTTCAGCTGATGTTGAAAATTCGAGACACACTTTATATTGCTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000137872-SEMA6D:NM_153619:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(17.6=42.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGTGGCATTTCTGAGCAGG
R:
CTGCCAGCAATATAAAGTGTGTCT
Band lengths:
270-666
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)