DreEX6014340 @ danRer10
Exon Skipping
Gene
ENSDARG00000052094 | notch1b
Description
notch 1b [Source:ZFIN;Acc:ZDB-GENE-990415-183]
Coordinates
chr5:65012318-65017197:-
Coord C1 exon
chr5:65017049-65017197
Coord A exon
chr5:65015994-65016207
Coord C2 exon
chr5:65012318-65012408
Length
214 bp
Sequences
Splice sites
3' ss Seq
AACGGTTGTTCCTGTGGCAGGTG
3' ss Score
7.38
5' ss Seq
GAGGTCAGT
5' ss Score
7.7
Exon sequences
Seq C1 exon
CTCCGTGGTTTATCTGGAGATTGACAACCGGCAGTGCTACCAGCAAACCTCCGAATGCTTCCAGAGCGCCAACGACGCGGCGGCGTTCCTCGGAGCGCTGGCTTCCAGCGGCAGTCTGAAAATGCCTTACGTCATCGAGGCCGTCACAA
Seq A exon
GTGAGATCGATGGACCGTCGCCTGTAGAGCTCTATCCAGTCTACGTGGTTCTGGCAGGATTGGCGCTGCTGGCCTTTGTCGCCATTGGGATGGTGGCGTCCCGTAAACGGCGCCGGGAACACGGACAACTTTGGTTTCCGGAGGGTTTTAAGACCAGCGAGCCCAGCAAGAAGAAGAGGAGAGAGCCGGTCGGAGAAGATTCAGTCGGTTTGAG
Seq C2 exon
GCCACTTAAGAACTGTTCAGACATTTCGTTAATGGACGACAACCAGAATGAATGGGGAGAGGAGGAACAGTCCGACAGCAAACGCTTCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052094-'30-32,'30-31,31-32=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.361 C2=0.677
Domain overlap (PFAM):
C1:
PF076847=NODP=FE(79.4=100)
A:
PF076847=NODP=PD(14.3=12.5)
C2:
NO
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGTGGTTTATCTGGAGATTGACA
R:
GTTTGCTGTCGGACTGTTCCT
Band lengths:
230-444
Functional annotations
There are 2 annotated functions for this event
PMID: 16530045
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: inferred by author. ELM ID: ELMI002957; ELM sequence: LWFP; Overlap: FULL
PMID: 20028974
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: coimmunoprecipitation, inferred by author, isothermal titration calorimetry, x-ray crystallography. ELM ID: ELMI002957; ELM sequence: LWFP; Overlap: FULL
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]