HsaEX0026100 @ hg19
Exon Skipping
Gene
ENSG00000115414 | FN1
Description
fibronectin 1 [Source:HGNC Symbol;Acc:3778]
Coordinates
chr2:216236632-216238134:-
Coord C1 exon
chr2:216238045-216238134
Coord A exon
chr2:216236832-216237098
Coord C2 exon
chr2:216236632-216236738
Length
267 bp
Sequences
Splice sites
3' ss Seq
CTCTAACCTCTCTCGGCTAGACG
3' ss Score
4.08
5' ss Seq
TAGGTGAGG
5' ss Score
7.65
Exon sequences
Seq C1 exon
GCCTGGAACCGGGAACCGAATATACAATTTATGTCATTGCCCTGAAGAATAATCAGAAGAGCGAGCCCCTGATTGGAAGGAAAAAGACAG
Seq A exon
ACGAGCTTCCCCAACTGGTAACCCTTCCACACCCCAATCTTCATGGACCAGAGATCTTGGATGTTCCTTCCACAGTTCAAAAGACCCCTTTCGTCACCCACCCTGGGTATGACACTGGAAATGGTATTCAGCTTCCTGGCACTTCTGGTCAGCAACCCAGTGTTGGGCAACAAATGATCTTTGAGGAACATGGTTTTAGGCGGACCACACCGCCCACAACGGCCACCCCCATAAGGCATAGGCCAAGACCATACCCGCCGAATGTAG
Seq C2 exon
GACAAGAAGCTCTCTCTCAGACAACCATCTCATGGGCCCCATTCCAGGACACTTCTGAGTACATCATTTCATGTCATCCTGTTGGCACTGATGAAGAACCCTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000115414_CASSETTE1
Average complexity
S*
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (No Ref)
Show PDB structure
Features
Disorder rate (Iupred):
C1=0.341 A=0.944 C2=0.626
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(27.2=71.0)
A:
PF0004116=fn3=PU(9.0=10.8)
C2:
PF0004116=fn3=PU(50.7=23.7)
Other Inclusion Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGAACCGAATATACAATTTATGTCA
R:
GGGTTCTTCATCAGTGCCAACA
Band lengths:
181-448
Functional annotations
There are 1 annotated functions for this event
PMID: 11246004
This event
The alternatively spliced IIICS segment possesses the major alpha4beta1 integrin-binding sites. The exon is associated to HsaALTA0003426 and other complex AS events.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- 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)