RnoINT0076396 @ rn6
Intron Retention
Gene
ENSRNOG00000005580 | Itgb4
Description
integrin subunit beta 4 [Source:RGD Symbol;Acc:2928]
Coordinates
chr10:104557614-104558333:+
Coord C1 exon
chr10:104557614-104557772
Coord A exon
chr10:104557773-104558183
Coord C2 exon
chr10:104558184-104558333
Length
411 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGTA
5' ss Score
5.89
3' ss Seq
GGCCACCCTCCATAATCCAGATT
3' ss Score
3.58
Exon sequences
Seq C1 exon
GCCTCCCTCCTATCTGGGAAGATGGGAGGAGCAGGCTTCCGCTGTCCTGGACCCTTGGGTCCTGGAGCCGGGCTCAGATGAAGGGTGTGCCCGCATCCAGGGGCTCACCAGACTCTATAATCCTGGCCGGGCAGTCAGCAGCGCCCTCCTGGGGTACAG
Seq A exon
GTAGTACAGGGGTGGTCACCATGTATCCACGGCTGTCTTGCTCCATTTGTCACCCAGCTACCATCACAGCCTGTGCTCGTGCACTCACTGCTTCATTGCATTCAGAACCTCAGTCCACCCACAGGAGCTAACCACTGCCCTGCCTGCCCCCATCAGTGCTGAAGCCTAACACATCTGCCCTCCTTGTGGGTATAAAGCAAGAGTTGAACAAGGTGTGGGGCAGATTGTAGAGGGGGTGGGTTGAGGAGTCTAGCAGACTCAAGGGGGCTCCAAGGCCATATGGGAAGGCAGCCTGGTTAGGTCAGCATGAAGCTGTAACATGGCTGCAGAAGCAAGCAAGGGATAGACTGTATCTCATCTCAGACCCCGAACCCTGTCTTGGACTGACCATGGCCACCCTCCATAATCCAG
Seq C2 exon
ATTCCCGTGGGGCTATGGGTGTGCCCGACACACCCACTCGGCTGGTGTTCTCCGCCCTGGGGCCCACATCTCTGAAGGTGAGCTGGCAGGAGCCACAGTGTGATCGAGCACTGCTGGGCTACAGCGTGGAATACCAGCTACTCAACGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005580:ENSRNOT00000065339:36
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.383 A=NA C2=0.196
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004116=fn3=PU(48.8=80.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTCCTATCTGGGAAGATGGG
R:
CGCCGTTGAGTAGCTGGTATT
Band lengths:
305-716
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]