HsaINT0147460 @ hg19
Intron Retention
Gene
ENSG00000092421 | SEMA6A
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A [Source:HGNC Symbol;Acc:10738]
Coordinates
chr5:115837906-115840678:-
Coord C1 exon
chr5:115840541-115840678
Coord A exon
chr5:115838024-115840540
Coord C2 exon
chr5:115837906-115838023
Length
2517 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
CCCATCTCCTCTTTTCACAGATA
3' ss Score
10.77
Exon sequences
Seq C1 exon
GGTGAAGTAGAGAAATAAAGTCTCCCCGCTGAACTACTATGAGGTCAGAAGCCTTGCTGCTATATTTCACACTGCTACACTTTGCTGGGGCTGGTTTCCCAGAAGATTCTGAGCCAATCAGTATTTCGCATGGCAACT
Seq A exon
GTAAGTACCCATGGTCTCACTCAGTGTCTCCCTTTGAGAACATTTTAGCCTGAATCAGCCTAGCAAAAAATAAAACTGAAAAATGAAATAGAATAGGTGACTTATTAGTCCTCTGTATGTGGCAAAGGTGGCTAATTCAAGTCTAGTCAAATTGATAGGATGATTTTTCTATAACTCCATCAGATGTTGTTGTGGGGACACGTGTGAGGATTTGAAACGCCCCTCGTAACCCTGATGAAGTCTCAGCTACTACATCGAGGCTGCCGTGTTCATGCCTTAAAATCAGCTCTGTGGGAGAATATCGCTATGATCTGGGTATTGGCAGTATTACTCGCTTTTATATATAATTCATATATCCGGACTGTTGCAAAATATGAACAAAAAGTAATGACCATTTTGGAGTACTTCAGAGAAAAATTTTTTTTGGACTTAGAAGTTACATAGTTAATAGACTTTGGTAAAGAGAAATTAATTTATAGAGGACCCATTTTAACTGTTTATAACTTTCCTTTGGTCTCTGCTTCATTGTCAGGAGTAGATACTAACATGATTAAGAATTCAGCTGTCTCCTCAAAAGAGGAGAGTCCTGCCTATGTGTTGGATGGAACATTCAATTTACCACTTTTTTTTCATGCCCTTCAAAAGGCTTAAGTATTTTATTACAGTAAAAATGTAAGAGAGCATTTTTTTCCTAAATATCTCTTTTCATAGTAATGACCCCAAAACAAACACTGAGTGAGCCATACAAAGGTGTCTAACATTAATATGCAATACTAAGGAGATCCAAATATGCCCAGTGTTCAGCTGTTCTTTCTGGGTTGGAAGAAAATGAGGTAGCAAAACTGACACACAAAACAATTAGAGTCCAGAGTCAAAGGGCATTATTAAGACCAAATGTGTAGTTCAAGTTCATCATTCCTGAAATAGCAGAGTCCACCTAACTCAAGGTTCCAAACTTAATAAACATTTATTTATTTCCATTTGAGGTAAGTTTTCTGTCTTGGATGCCCGAGTATAGAAGGGACTCCAGGGCAGGGCGCGGTGGCTTACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCATGAGGTCAGAGGATGGAGACCATCCTGGCCAACATGGTGAAAACTGTCTCTACTAAAATACAAAAGAAAAAAAAATCAGCTGGGCATGGTGGTGCATGCCTGTAGTTCCAGCTACAGGAGGCTGAGGCAGCGGAATACCTTGAACTGGGGAGGCGGAGAGTGTAGTAAGCCGAGATCACACCACTGCACTCCAGCCTTATGACAGAGCGAGACTCTGTCTCAAAAAAAAAAAAAGAAGGGACTCCAGCCCAAATGGACTACTGTAAGCCACCCTTCAGTGATCACTCAAATCCATGATCGTAGAGACATTTGAGTTGTTTTAGCAATCTCCTTGATGAATGGGTACATGAAATTTCAAAGCAGTGGAAGGGAAAGCACAAGATTGTCTTATACCAAGCTCCCTTGTAAATAAAATATAGTAAGGCTCCTGATAAGATACCCACTGTGAGTAATGGTCAGATACTACAAGGGTGTAAAGTGAGGGTCGAAGCATAAATCTGTGAATGGTTTTCTAGTCATCATTTACACCCCCACCCCTCTCCAGAAAACAAGTGCCTTTTAAATGTGGCTCATCTTTCTTTCCTCCTGAGTTTGTCTGGAGGCTCGCCAGTGCTCTGGAGATCGTAGGTGTAAAGGCAGAGATGTTGAGATGTAGGTATTTTTAAAGGCCAGATCTCAATACAGATTGGCCACTCTCAGCCAAAGAGAAGTGTAGGAAAAGAGAAATATGCTCATTGACTCACCAAGTCAGGGAAAATTTCAGATCACCTGACTGGCTACACTCAGTTTGACCCTGTCCTGTCAAAGCCCACATCTCTGTGAAATTGTTAGCCAATTGCTTAACTCAAGGGTGAACTTCCCACAGTTCCTAGAATGCCAACCAACCTCTCAGGGGCTGCCTTCAATAGTGGATTATTCCAACTGGACGCCTGTGGAGACTGTATTTTTCTTCTGGCTCCTGGACAAGGGCTCTCGCCTCCAGACCACATTGCATTTGTGGTGATTGATGGGAAGGCTGCTTTGAAATAGTTTTGTCCCGAGACAAGATCTTTGGCAGACTGCCCCCTCAGGCTTAGCTCTACAGAAGATGAAAAGAAAACTGTGGAAGAAAAGAGCACCTTCATGCAAAGGGTTCACTAGCGAGTTGAGCCCTGAGAAAGAGAGACAAATCAAAAATTGTGACACTTAGAAATATAAATCCAGGCTTATAATTATCTAGAAATGAAAGTGTAACTTGATGAACCTTAAGGAGCACTCTTCTATCATATTTCCTAAAATAACAGACTCATATGGAAATGGAAAATGGTGGCATGGTCTGACTTAAACACGGGTTTCTTTTGTGACCTGTCTCCCTCCCCTCCCTACCCTGTCAATTCCTGGCTTGATTTGCTTTTCCTTTCTTGCCCCATCTCCTCTTTTCACAG
Seq C2 exon
ATACAAAACAGTATCCGGTGTTTGTGGGCCACAAGCCAGGACGGAACACCACACAGAGGCACAGGCTGGACATCCAGATGATTATGATCATGAACGGAACCCTCTACATTGCTGCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092421-SEMA6A:NM_020796:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.025
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(28.8=42.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)