HsaINT0147272 @ hg19
Intron Retention
Gene
ENSG00000170381 | SEMA3E
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E [Source:HGNC Symbol;Acc:10727]
Coordinates
chr7:83021871-83023654:-
Coord C1 exon
chr7:83023613-83023654
Coord A exon
chr7:83022038-83023612
Coord C2 exon
chr7:83021871-83022037
Length
1575 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGT
5' ss Score
10.75
3' ss Seq
CCTCTTTCTGATTTCTGTAGCAA
3' ss Score
7.92
Exon sequences
Seq C1 exon
GATCCAGTTCCTATTATTTCTATGGAGATTTCTTCAAAGCGG
Seq A exon
GTAAGTTCTGTGTGTGTGTGTGTGTAGGTGTGTGTGTTCTATATGTGAGCTAAGGTAAGGTCAAAGGATATGAGAACATTAGTACATGTGCTTAAATATGAACTTATTACAGTTTTATTTTTCTTTTATTACTTTATTTTATTGTAGTAAGAACTTTTAACATGTGATCTACCCTGTTAACAAAATATTAAGCATACAATACATTTTTAATGGTTATAGGTACAGTGTTATACTGCAGACCTCTAAACCTTATTAATCTTGTTTGACTGAAACTTTATGTCCATTGATTGATTCTGACAAAAGTTTATCATGATTTACATTTGATACTTGTTTTCATTTTCTATCTCTATAGAAAGGAAGATGAGAGTAGTTTTACTTCTACAATCATGATAACACTTTATTCCCTGGTTATTTTTCACTAATGTTTTTCAAAAACAATGGTAACAATGATAATCCAATAGTGTGCAAGAACAATGATAATCCAATAGTGTGCAAGGAAACACACCTCCTTTCCACTTCACTGAAATCAGTTTGGTGTAAACTTCTTTAGAAACAGTTGTTGCATATATTGCCCCAAATTTATTTATAAATAATCCTTCATGTTCAGGCAAAAGGAAAGATATTATATTAAATGTTCAGCCACTTGTTCTGTAGATAGATAGATAGATATACACATCACTCTTCTAAATGTTATATGTCAATATTTAAAAGACTATTTGCTTTCCAAATCTCTTATTAGTTTTTGCTATAGATTTGTTTTCTGTTTTTGAGATAAAGTCTCACTGTGTCACCCAGGCTGGAGTTCAGTGGTGCAATTACAGCTCACTGCAGACTCAACCTCCCCAGGGTCAGGTCATCCTTCTGTGTCAGCCTCGTGAGTAGCTGAGACCACAGGCACATATTACCAGCTAATTTTTGTATTTTTTGTAGAGACAGGGTTTCGCCATGTTGCCCAGGCTGGTCTCAAACTCCTGGGCTCAAGCAATTTACCTGCCTTAGCCTCCCAAAGTGCTGGGATTACAGGCATAAGCCACTACAGGCATAAACCCAGCCGTTTCTATAGATCTTTAAAGGAAGATCCACAGTGTTGGGTAATGCAAGATAATGAACACAGCTTCTTGAGTTCTTGTCAAGTTCAGTGTAGCAATTTTGGTACTCCTGCATTTATGTCTATGAATGTTTCTCAAATATTAGAGAAATGAAAGTATAAATATTATCTATATTGAACAACTGCTATAATTTTTTTTTTTTTTTTTTGAGATGGAGTTTCTCTCTTGTCGCCCAGGTTCCACCTCCACATCCTAGGTTCAAGCAATTCTCCTGCCTTAACCTCCAGAGTAGCTGAGATTACAGGCATCCGCCACCATGCCTGGCTAATTTTTTGTATTTTTAGTAGAGATGGGGTTTTGCCATGTTGTGCAGGCTGGTCTCAAACTCCTGAAACTGCTAATTTAAGTGAATTAAATTTAAGTGAATTTTTTCTGAGGTGATTGTGTATAAATGTGAAAACTAGGTGTAATAGCTCAGTGAAAGTTTTGTCCATTTCTGCTAGTGACCTCTTTCTGATTTCTGTAG
Seq C2 exon
CAACAGCTGTATATTGGATCTGCTTCTGCTGTGGCTCAAGTCAGATTCCATCACTGTGACATGTATGGAAGTGCTTGTGCTGACTGCTGCCTGGCTCGAGACCCTTACTGTGCCTGGGATGGCATATCCTGCTCCCGGTATTACCCAACAGGCACACATGCAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170381-SEMA3E:NM_012431:13
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(2.9=100)
A:
NA
C2:
PF0143720=PSI=PU(65.5=67.9)
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:
TCTATGGAGATTTCTTCAAAGCGG
R:
GCATGTGTGCCTGTTGGGTAA
Band lengths:
185-1760
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)