HsaINT0147466 @ hg19
Intron Retention
Gene
ENSG00000092421 | SEMA6A
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A [Source:HGNC Symbol;Acc:10738]
Coordinates
chr5:115823804-115824703:-
Coord C1 exon
chr5:115824584-115824703
Coord A exon
chr5:115823893-115824583
Coord C2 exon
chr5:115823804-115823892
Length
691 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAC
5' ss Score
5.54
3' ss Seq
AAGTGCCTGTTTGTCTACAGAAC
3' ss Score
7.51
Exon sequences
Seq C1 exon
ATGGAAAACTATACTCAGCCACAGTGACTGACTTCCTTGCCATTGACGCAGTCATTTACCGGAGTCTTGGAGAAAGCCCTACCCTGCGGACCGTCAAGCACGATTCAAAATGGTTGAAAG
Seq A exon
GTGAACAAACAATTAAAAGAAGGAGGGTCGGAGGGGAGGGGAATACACATCTTGTGGGAGATTTAGAGTCTGGAGGGACCAGACTGTATCTTCATTTGAGTAATGGCTTCTGACAGACAGAAACATGTAAATTGCATCTTTGGCTTCAACTGATTTATTTACCTCCCTTTTTTCCTTCCCCTGAGTTTCTGGAGTATTAACAAAACTACCAATGCCACAACAATAGAATACATTACATTCATGTTTTCTTGCTTCAAGCTCTCATTTCTGAGTTCTGCATGAAAAGAACTGAACAATGTATTCATGGAAGGGGACAGGGGCTTGGAGGTGGTGGAGAAGAGGAGAAAAGCTATTCACAACCCTGTATGAGTCAGGGTGACAAGGCAATGTATACAAAATCTTCTCTGTAATAGGGGCATTCCATTGTGGAAAATAAAATTACAGAGATATGCAAAATTCCATATTTCTTCATTGTTGATTGCAAAGCTTCTGAAAGAGATAATGTGTAAGTGTGAATGCCTTGTGAAATCACCAGCACTTGCATGTGTGAAGTCATTTGAAATGGTTAGTGTTAACCAAATGTCTAATGGTGCTACACTTTTAATTAATAACATGTCTTTGGCTACACTTGATTGAAATTCTGTTAACTCTGTTTGACATGTTCCCAATTAAAGTGCCTGTTTGTCTACAG
Seq C2 exon
AACCATACTTTGTTCAAGCCGTGGATTACGGAGATTATATCTACTTCTTCTTCAGGGAAATAGCAGTGGAGTATAACACCATGGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092421-SEMA6A:NM_020796:8
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:
PF0140314=Sema=FE(9.2=100)
A:
NA
C2:
PF0140314=Sema=FE(6.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAAAACTATACTCAGCCACAGTG
R:
TTCCCATGGTGTTATACTCCACTG
Band lengths:
206-897
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)