RnoINT0076054 @ rn6
Intron Retention
Gene
ENSRNOG00000001518 | Itga6
Description
integrin subunit alpha 6 [Source:RGD Symbol;Acc:621633]
Coordinates
chr3:58499587-58499893:+
Coord C1 exon
chr3:58499587-58499666
Coord A exon
chr3:58499667-58499815
Coord C2 exon
chr3:58499816-58499893
Length
149 bp
Sequences
Splice sites
5' ss Seq
AACGTAAGA
5' ss Score
7.69
3' ss Seq
GTTTCCCCTTTCATTTTCAGAAC
3' ss Score
11.86
Exon sequences
Seq C1 exon
GTTACTTTTTATCTGATTTTAAGTACCACCGAGGTCACCTTTGACACCACAGATCTGGATATTAATCTGAAGTTGGAAAC
Seq A exon
GTAAGAGTTACTTCAACCCTTCCATTCTTACTTTGGGAGAACCCTAGAGCTGCTGAATTAGCGCTGATCTAACTCATAAAAGAAATGTAATTGTAATGAGAAAGCTGACTGTTCAAATAAAACCCCATTGTTTCCCCTTTCATTTTCAG
Seq C2 exon
AACAAGCAATCAGGATAATTTGGCTCCAATTACAGCGAAAGCAAAAGTGGTTATTGAATTGCTTTTATCGGTCTCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001518:ENSRNOT00000002075:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF084417=Integrin_alpha2=FE(5.5=100)
A:
NA
C2:
PF084417=Integrin_alpha2=FE(5.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGATTTTAAGTACCACCGAGG
R:
CCAGAGACCGATAAAAGCAATTCA
Band lengths:
147-296
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]