HsaINT0147454 @ hg38
Intron Retention
Gene
ENSG00000092421 | SEMA6A
Description
semaphorin 6A [Source:HGNC Symbol;Acc:HGNC:10738]
Coordinates
chr5:116478014-116478718:-
Coord C1 exon
chr5:116478542-116478718
Coord A exon
chr5:116478155-116478541
Coord C2 exon
chr5:116478014-116478154
Length
387 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
ATCTTGCCTGATGAAATTAGATG
3' ss Score
1.63
Exon sequences
Seq C1 exon
ATACCGCCTTACCAAAATTGCAGTGGACACAGCTGCTGGGCCATATCAGAATCACACTGTGGTTTTTCTGGGATCAGAGAAGGGAATCATCTTGAAGTTTTTGGCCAGAATAGGAAATAGTGGTTTTCTAAATGACAGCCTTTTCCTGGAGGAGATGAGTGTTTACAACTCTGAAAA
Seq A exon
GTAAGTGGAATATTTGGTTCTTTCTTAGTAATTATTTGTTATGCTATTATGGCCCCTTTCATTCAGAGAAAATCATGACCGACTGAGGTTTTATGCATTTTTAGATGACTTTTTAGTGCTGTTTGTAAAAATTTAACACCTAAAAAGCATTATTTTCTCCTTGCCAATGTGTGTGTGTGTGTTTATATAGATACATATATGTGTGTGTGTTTATATAGATACATATACATGTGTGTGTTTACGTGTGTGCAAGAGCAGAAGGGTTTGTTTGTTTCACCGCCAGTTAGATTAAGAGATTGCCTTGTGGGCTGGGAAGTGGGATGTGAGGGTGGGGCCGAGAAAAAGAGAAGAGTCTATTAATGATATTATCTTGCCTGATGAAATTAG
Seq C2 exon
ATGCAGCTATGATGGAGTCGAAGACAAAAGGATCATGGGCATGCAGCTGGACAGAGCAAGCAGCTCTCTGTATGTTGCGTTCTCTACCTGTGTGATAAAGGTTCCCCTTGGCCGGTGTGAACGACATGGGAAGTGTAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092421:ENST00000343348:13
Average complexity
IR
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(13.5=100)
A:
NA
C2:
PF0140314=Sema=PD(3.4=31.2),PF0143720=PSI=PU(13.6=18.8)
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:
ATACCGCCTTACCAAAATTGCA
R:
TTTTTACACTTCCCATGTCGTTCAC
Band lengths:
318-705
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