RnoINT0076376 @ rn6
Intron Retention
Gene
ENSRNOG00000005580 | Itgb4
Description
integrin subunit beta 4 [Source:RGD Symbol;Acc:2928]
Coordinates
chr10:104538866-104539227:+
Coord C1 exon
chr10:104538866-104538967
Coord A exon
chr10:104538968-104539097
Coord C2 exon
chr10:104539098-104539227
Length
130 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGG
5' ss Score
9.63
3' ss Seq
TTCTCCTCTCCTCTCCCCAGATA
3' ss Score
12.23
Exon sequences
Seq C1 exon
GGCATCTGCAATGGACTAGGCTTCTGTGAGTGTGGCCGTTGTCACTGCAACCAGCGGTCTTCGCTCTACACGGACACCACCTGTGAGATCAACTACTCGGCG
Seq A exon
GTAAGGCAAGGGTTCCTGGGTTGTGGGCATGAGAACCCCAGAGGCTGGGAAGGAGAAGCTGGCTGGGGGCACTAGGGAAAGGGAGTTGGGTTCAAACAGCATGGTGTCTATTCTCCTCTCCTCTCCCCAG
Seq C2 exon
ATACGCCTGGGCCTCTGTGAGGACCTCCGCTCCTGTGTACAGTGCCAGGCCTGGGGCACTGGGGAGAAGAAAGGGCGCACGTGTGAGGAATGCAACTTTAAGGTCAAGATGGTAGACGAGCTTAAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005580:ENSRNOT00000065339:15
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:
NO
A:
NA
C2:
PF079657=Integrin_B_tail=PU(44.2=86.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCATCTGCAATGGACTAGGC
R:
TAAGCTCGTCTACCATCTTGACCT
Band lengths:
226-356
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]