DreEX0033144 @ danRer10

Exon Skipping

Gene

ENSDARG00000019815 | fn1a

Description

fibronectin 1a [Source:ZFIN;Acc:ZDB-GENE-000426-1]

Coordinates

chr9:15446425-15448566:-

Coord C1 exon

chr9:15448429-15448566

Coord A exon

chr9:15448002-15448160

Coord C2 exon

chr9:15446425-15446622

Length

159 bp

Sequences

Splice sites

3' ss Seq

TATATTTGTGTGTATCACAGACC

3' ss Score

8.29

5' ss Seq

TTGGTAAGA

5' ss Score

8.85

Exon sequences

Seq C1 exon

CGGAGCGCTGTTATGATAATACAGCTGGCACCTCCTACATGGTTGGTGAGACCTGGGAGAAGCCCTACCAGGGCTGGATGATTGTGGACTGCACCTGCCTCGGAGAAGGAAGTGGACGTATTACATGCACATCCAGAA

Seq A exon

ACCGCTGTAATGACCAGGACACACGCACTTCTTACCGGATTGGGGACACGTGGAGTAAGACGGACTCTCGTGGACACGTTTTACAGTGTTTGTGTACTGGTAATGGACGTGGAGAGTGGAAGTGTGAGAGGCATGCTTCTCTGCACACTACTAGTCTTG

Seq C2 exon

GTACTGGGTCTCGTGTTGTGACCAATGTCCAGCCAGCAGTGTACCACCCACAAGGGGTGCCTGAACACCCTGTGGAGGGATCCTGTCTGACTGAAGCAGGTGTTTCCTATGCTCCAGGCATGCGCTGGAGCAAGGCTCAAGGTAGCAAGCAGATGTTGTGTACCTGCTTAGGAAACGGTGTCAGCTGTGAAGAGTCAG

VastDB Features

Vast-tools module Information

Secondary ID

ENSDARG00000019815-'4-6,'4-5,5-6

Average complexity

S

Mappability confidence:

100%=100=100%

Protein Impact

Alternative protein isoforms (Ref)

No structure available

Features

Disorder rate (Iupred):

C1=0.000 A=0.056 C2=0.119

Domain overlap (PFAM):

C1:

PF0003913=fn1=WD(100=85.1)

A:

PF0003913=fn1=WD(100=74.1)

C2:

PF0003913=fn1=WD(100=52.2)

Main Inclusion Isoform:

ENSDARP00000017129

Main Skipping Isoform:

NA

Other Inclusion Isoforms:

ENSDARP00000112231

Other Skipping Isoforms:

NA

Associated events

Conservation

Human

(hg38)

chr2:215428180-215428338

HIGH PSI

HsaEX6018351

(FN1)

Human

(hg19)

chr2:216292903-216293061

HIGH PSI

HsaEX6018351

(FN1)

Mouse

(mm10)

chr1:71645547-71645702

HIGH PSI

MmuEX6025145

(Fn1)

Mouse

(mm9)

chr1:71692121-71692276

HIGH PSI

MmuEX6025145

(Fn1)

Rat

(rn6)

chr9:78960981-78961136

HIGH PSI

RnoEX6040248

(Fn1)

Cow

(bosTau6)

chr2:103941937-103942095

HIGH PSI

BtaEX6011326

(FN1)

Chicken

(galGal4)

chr7:4376687-4376845

HIGH PSI

GgaEX1066072

(fn1)

Chicken

(galGal3)

chr7:4405092-4405250

HIGH PSI

GgaEX1066072

(FN1)

Fruitfly

(dm6)

No conservation detected

Primers PCR

Suggestions for RT-PCR validation

F:

GCTGGATGATTGTGGACTGCA

R:

TTCACAGCTGACACCGTTTCC

Band lengths:

257-416

Functional annotations

(Submit an annotation)

There are 6 annotated functions for this event

PMID: 1532572

HsaEX6018351

Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: affinity chromatography technology, coimmunoprecipitation, polyclonal antibody, western blot. ELM ID: ELMI002206; ELM sequence: NGR; Overlap: FULL

PMID: 1694173

HsaEX6018351

Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: affinity chromatography technology, coimmunoprecipitation, polyclonal antibody, western blot. ELM ID: ELMI002206; ELM sequence: NGR; Overlap: FULL

PMID: 17015452

HsaEX6018351

Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: affinity chromatography technology, coimmunoprecipitation, nuclear magnetic resonance, peptide binding to perpetrator, polyclonal antibody, western blot. ELM ID: ELMI002206; ELM sequence: NGR; Overlap: FULL

PMID: 18480047

HsaEX6018351

Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: nuclear magnetic resonance. ELM ID: ELMI002206; ELM sequence: NGR; Overlap: FULL

PMID: 17591922

MmuEX6025145

Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: nuclear magnetic resonance, sequence based prediction. ELM ID: ELMI002210; ELM sequence: NGR; Overlap: FULL

PMID: 18480047

MmuEX6025145

Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: nuclear magnetic resonance. ELM ID: ELMI002210; ELM sequence: NGR; Overlap: FULL

GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]

Special

DreEX0033144 @ danRer10

GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]