DreINT0083304 @ danRer10
Intron Retention
Gene
ENSDARG00000028507 | itgb4
Description
integrin, beta 4 [Source:ZFIN;Acc:ZDB-GENE-030131-7209]
Coordinates
chr8:13099177-13099587:+
Coord C1 exon
chr8:13099177-13099314
Coord A exon
chr8:13099315-13099404
Coord C2 exon
chr8:13099405-13099587
Length
90 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGA
5' ss Score
5.73
3' ss Seq
ATTTTTTTTTTTTTGTTCAGAGC
3' ss Score
8.85
Exon sequences
Seq C1 exon
TACCTGGTGAACCTGGTCGTCTGGCTTTCAACGTCATCAGCCCTACTGTTACTCAGGTTAGTTGGGCGGAGCCAGCAGAAGCCAATGGTATCATCACTGGCTATGAGGTCATCTACATGCCCATTAACGAGGACAAGA
Seq A exon
GTAAGAGCCTTAAAATATATATTCTGTGCATCAGTTTTGGGAGTGAAAGCTTCTCTGATTGTATATGTCTATTTTTTTTTTTTTGTTCAG
Seq C2 exon
AGCCTACAGGACCTCCTAAGAAGGTGATGATTGACAACCCTAAAAAGCGCATGTTGCTCATTGAGAACCTGCAACCTTCTCAGACCTACTGTTATAAAGTGCGTGCCAGCAATAAGGTGGGCTGGGGCCCATACAGAGAAGCCACAATCAACCTGGCATCACAGCCTACCAGACCCATGTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000028507:ENSDART00000029308:31
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.161
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(48.9=93.6)
A:
NA
C2:
PF0004116=fn3=PD(50.0=72.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACTCAGGTTAGTTGGGCGGA
R:
AGGTCTGAGAAGGTTGCAGGT
Band lengths:
176-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]