RnoINT0076336 @ rn6
Intron Retention
Gene
ENSRNOG00000001224 | Itgb2
Description
integrin subunit beta 2 [Source:RGD Symbol;Acc:1305581]
Coordinates
chr20:11783344-11784862:-
Coord C1 exon
chr20:11784675-11784862
Coord A exon
chr20:11783589-11784674
Coord C2 exon
chr20:11783344-11783588
Length
1086 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
ACCCTTCCTCATCACACCAGGTG
3' ss Score
8.91
Exon sequences
Seq C1 exon
GTCACCTTCCAGGTAAAGGTCACGGCTTCGGAGTGTATCCAGGAGCAGTCCTTTGTCATCCGGGCGCTGGGCTTCACCGACACAGTGACGGTACAGGTCCATCCCCAGTGCGAGTGCCAGTGCCGGGACCAGAGTCGGATGAGGAATCTCTGTGGAGGCAAGGGAGTCATGGAGTGTGGCATCTGCAG
Seq A exon
GTGAGGAGGGTGCATGGGGCCTGTGGGATATCAGTCCATGGAAAAGGTGTCTGTAGATGAGGCTAGCCCAGAGCACGGCATGAGGAATATACATGAATAGCCTGTGGCACGCCTTGTCTATGAGGCAAGTGCCTTCAAGCGAAGTAGGTATGGCCAGCTCACCCAGGAAGTCGATGCTCTGCAGATACTCCTAACTCCTAGCTCTCTCTGACCTCAGAGACCCTGAGCAATCGCAACATGCATCTAGAGCTCCTTTGGGACATATGACCACTCCTGGCAGCCTGGGCCCTAAAGCCATCCTGTGGACATGTATACAATGGCCTCAGTTCAGAATGCTCTACCTCAAGGAGGAGAAAGGATGTGGTGGGCCCAGCAGAGAGTATGTAGTTGTTAGTCTGGGTACCAACCATCTCCATCTGACTGCTTTTCCAGTTTCTGATCTTTGAGGTATCCCACCCCTCAGACCTGCACTGGCTACATACCTCCTCCCAGAAACTCTTAACAGTGGTGTTTTTTTTTTTTTTTTTTTTGTGGTTGCCCTCTGGCCGGTAGCACCTTGTCCTGGTCCTGAGTGTGAAGCCCTAAGTGGCCTCTCTACAAGGCTGAGCTAACTTGCCTGGAGGATTGGGCTGTTGGTCAGTGAATTCTGCGGCTTCTTCCTGCAGGAGGACACTGCAGGATGAGTCGCGGTTGGCTACTGCCGTTCTTGTCTTCCTAAGCTATGTATGGTGTCCATGCATTCTTCTGTCTACCTAGTTCAGTGATAAGGCAGGGATCCTAGATCCCCACTGGATCCTTCTTCCAAATCTAGGTCAGCGGGGACAGATACTGGCTTCTTGGGACAATCCACTCACACAAGCCTCAGGCAGCTTCCAGGCGAGCCTGCCAGAGGTGCTATGCTCATAGGACGGTCGCTGTATGACCCGAGATATCCTTGCCTCACACATGACGCATGCTCAGGAGACCTTTGGAGAGCGGGTGTGATATAGCACACTCGACAGGTGGTTGGGTGATTGCTGGGCCGGGAAGGATGGGTGTCCCCATCCCAGGGGCAGACCTAAGTGCAACCCTTCCTCATCACACCAG
Seq C2 exon
GTGTGAGTCTGGCTACATTGGGAAAAACTGTGAGTGTCAGACGCAGGGCCGGAGCAGCCAGGAGCTGGAGGGGAACTGCCGGAAGGACAATAGTTCCATTGTGTGCTCGGGGCTGGGGGACTGCATCTGCGGGCAGTGCGTGTGCCACACGAGTGACATCCCCAACAAAGTGATCTTTGGGCAATACTGCGAGTGTGACAACTTCAACTGTGAGAGATATGATGGCCAAGTCTGCGGTGGCCTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001224:ENSRNOT00000001639:13
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:
PF0036213=Integrin_beta=PD(9.1=60.3),PF126612=hEGF=PU(15.4=3.2)
A:
NA
C2:
PF126612=hEGF=PD(76.9=12.0),PF079748=EGF_2=PU(36.4=14.5)
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:
GTAAAGGTCACGGCTTCGGAG
R:
GTTGGGGATGTCACTCGTGTG
Band lengths:
342-1428
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]