HsaINT0065292 @ hg19
Intron Retention
Gene
ENSG00000115414 | FN1
Description
fibronectin 1 [Source:HGNC Symbol;Acc:3778]
Coordinates
chr2:216225179-216226802:-
Coord C1 exon
chr2:216226692-216226802
Coord A exon
chr2:216226350-216226691
Coord C2 exon
chr2:216225179-216226349
Length
342 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
TCCTTCTTCCTTTTTAACAGAAT
3' ss Score
10.19
Exon sequences
Seq C1 exon
GGCTGGCGCTGTGACAACTGCCGCAGACCTGGGGGTGAACCCAGTCCCGAAGGCACTACTGGCCAGTCCTACAACCAGTATTCTCAGAGATACCATCAGAGAACAAACACT
Seq A exon
GTAAGTGCATTAGCAGCACAAGTGTGTTCCCTCATACTAGACAGTCTCTTTCTACAGGTATCTTTCTTCAGAATGAACCAAGTGTTTTAATTAATTAAAAAAAAAAACAACTCATAAATGACTTAAGTGAAACACTGTATTCCATAATATAGTTTAAGTTATAATTTATGTAACTCTTGAACATCTCCTATTGCCCAGTATGCTGCTAGGTTCTTGAAACTAGGAAGAAATATTATCCTATCTATAAGCAGCTGTCATGAGTCCCCACCTCCCCGCATTTTTTTTTCTGTACACTTTACAGTATTTGCCACTAATTTTTTTTTCCTTCTTCCTTTTTAACAG
Seq C2 exon
AATGTTAATTGCCCAATTGAGTGCTTCATGCCTTTAGATGTACAGGCTGACAGAGAAGATTCCCGAGAGTAAATCATCTTTCCAATCCAGAGGAACAAGCATGTCTCTCTGCCAAGATCCATCTAAACTGGAGTGATGTTAGCAGACCCAGCTTAGAGTTCTTCTTTCTTTCTTAAGCCCTTTGCTCTGGAGGAAGTTCTCCAGCTTCAGCTCAACTCACAGCTTCTCCAAGCATCACCCTGGGAGTTTCCTGAGGGTTTTCTCATAAATGAGGGCTGCACATTGCCTGTTCTGCTTCGAAGTATTCAATACCGCTCAGTATTTTAAATGAAGTGATTCTAAGATTTGGTTTGGGATCAATAGGAAAGCATATGCAGCCAACCAAGATGCAAATGTTTTGAAATGATATGACCAAAATTTTAAGTAGGAAAGTCACCCAAACACTTCTGCTTTCACTTAAGTGTCTGGCCCGCAATACTGTAGGAACAAGCATGATCTTGTTACTGTGATATTTTAAATATCCACAGTACTCACTTTTTCCAAATGATCCTAGTAATTGCCTAGAAATATCTTTCTCTTACCTGTTATTTATCAATTTTTCCCAGTATTTTTATACGGAAAAAATTGTATTGAAAACACTTAGTATGCAGTTGATAAGAGGAATTTGGTATAATTATGGTGGGTGATTATTTTTTATACTGTATGTGCCAAAGCTTTACTACTGTGGAAAGACAACTGTTTTAATAAAAGATTTACATTCCACAACTTGAAGTTCATCTATTTGATATAAGACACCTTCGGGGGAAATAATTCCTGTGAATATTCTTTTTCAATTCAGCAAACATTTGAAAATCTATGATGTGCAAGTCTAATTGTTGATTTCAGTACAAGATTTTCTAAATCAGTTGCTACAAAAACTGATTGGTTTTTGTCACTTCATCTCTTCACTAATGGAGATAGCTTTACACTTTCTGCTTTAATAGATTTAAGTGGACCCCAATATTTATTAAAATTGCTAGTTTACCGTTCAGAAGTATAATAGAAATAATCTTTAGTTGCTCTTTTCTAACCATTGTAATTCTTCCCTTCTTCCCTCCACCTTTCCTTCATTGAATAAACCTCTGTTCAAAGAGATTGCCTGCAAGGGAAATAAAAATGACTAAGATATTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000115414-FN1:NM_212482:45
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.355 A=NA C2=0.217
Domain overlap (PFAM):
C1:
PF0003913=fn1=PD(8.3=8.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACTACTGGCCAGTCCTACA
R:
GAAGCAGAACAGGCAATGTGC
Band lengths:
357-699
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)