RnoINT0076398 @ rn6
Intron Retention
Gene
ENSRNOG00000005580 | Itgb4
Description
integrin subunit beta 4 [Source:RGD Symbol;Acc:2928]
Coordinates
chr10:104558777-104559239:+
Coord C1 exon
chr10:104558777-104558965
Coord A exon
chr10:104558966-104559083
Coord C2 exon
chr10:104559084-104559239
Length
118 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCTCCCTCTGCTGTCTCCAGGCT
3' ss Score
9.81
Exon sequences
Seq C1 exon
GCGAGATGCATCGGCTCAACATCCCTAACCCTGGCCAAACCTCTGTGGTGGTAGAGGATCTCCTGCCTAACCACTCCTATGTGTTCCGGGTGCGGGCACAAAGCCAGGAGGGCTGGGGCCGGGAGCGAGAGGGTGTCATCACCATCGAGTCCCAGGTGCACCCGCAGAGCCCTCTCTGCCCCCTGCCAG
Seq A exon
GTGAGCTGTCTGCCCCTGCTGCTGCCCCTGGTGCTATCTCACCACCCACACCAGACCCACCGAATGCTGAGCACATCTTCTACCCTTACCCGTGACGCTCTCCCTCTGCTGTCTCCAG
Seq C2 exon
GCTCCGCCTTCACCTTGAGCACCCCCAGCGCCCCAGGCCCCCTGGTGTTCACTGCCCTAAGCCCAGACTCTCTGCAGCTGAGCTGGGAGCGCCCAAGAAGGCCCAACGGAGATATCCTTGGCTACCTGGTGACCTGTGAGATGGCCCAAGGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005580:ENSRNOT00000065339:38
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.312 A=NA C2=0.226
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(50.0=65.6)
A:
NA
C2:
PF0004116=fn3=PU(49.4=81.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCCCTAACCCTGGCCAAAC
R:
TGCAGAGAGTCTGGGCTTAGG
Band lengths:
246-364
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]