RnoINT0076050 @ rn6
Intron Retention
Gene
ENSRNOG00000001518 | Itga6
Description
integrin subunit alpha 6 [Source:RGD Symbol;Acc:621633]
Coordinates
chr3:58496884-58499028:+
Coord C1 exon
chr3:58496884-58497027
Coord A exon
chr3:58497028-58498912
Coord C2 exon
chr3:58498913-58499028
Length
1885 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGC
5' ss Score
4.72
3' ss Seq
TTGTGTTTGCTTCCCTCCAGGTC
3' ss Score
12.38
Exon sequences
Seq C1 exon
GAAAACATCAGAGACAAGCTGCGCCCCATCCCCATCACGGCTTCTGTGGAGATCCAGGAGCCCAGCTCTCGACGGCGGGTGAATTCACTTCCAGAAGTTCTTCCCATCTTGAATTCAAATGAAGCCAAAACAGTGCAGACAGAT
Seq A exon
GTGAGCTTCTTGGCTTTCTCTTTTGCCAGTGTTGGGTTTGTTTTGCAGGCCACTTCCTGTGGCAGGTATGTATGGCCAGGTGTGGTGGCCGTGTGTGTGCTTTTAATCCCAGCACTCGGAGGCAGAGGCTGGAGGATCTCTGTGAGGTCAAGGTCAGTGTGATTTACACAGCAAATTTCAGACCAACCAGGGTGCAAGGTGAGACCTTAAGAAAAAATAATCAACAAAAACACTTCTTCTTATTTCTATGCACATAATTGGCCTCTGAGAAGTTGTCTCTCAAATTGGCAGTGAAGATTAAAAACCTAAGATGGGTTTTGGGGATCAGATTTCTTTTTCTTCATTGTTTTCTTCATTGTTTTTGGTCCCTGGTACTTACCGAGACTATAATTAACCAAACTTCATTCTCCTGTAGTTGACATACTTTATTCTACTGAGAACAACACAGTATGATACGTGTCTATTATTAAAATTAAGGAATAGAGTAAAACTTAGCAAAGCAAAAAAACCCAATCACAACGAAATACTTCAGTGTCTAATGCAGCTTAGTCATTATAGGAACGTGTATTCCGTGGCCTGCTGGATATGTCGTATGATATGGGATGTGTGCGCTAGGACAGAGTAGAAATGAGCCTAGTGAAGTATGACATCTTGATCCGGCATTGTTGTTGTTATTACTGCTGTTGTTGTTGTCATCGTCGTCATCATCTTTTTATTTTGTTTTGAGACAGGATTTCTCTGTGTAGCCCTGGCTGTCCTAGAACTTGCTCTGTAGACCAGGCTGGCCTCGAACTCAGACCCACCTTCCTCTTCCTCCTCCTGAGTACTGGGATTAAAGGCGTGTGCCTCCACAGCCTGGCTATTACTAGCATCATCTTGGTCACTGTCTTGGTGCTGGGAATTATACCCAGGGCCTCCCAAATGCTTAGCACGTTTGCTGTGACACCACGTGCTAGCTGTCAAGATCCAGTTGGTGAATGCAGATGTGGCTGAGTGGGTAGAGTGCTTGCCTGGCACAAAGCCTTGACTTCATCCCCAGCACCACATAAAAATGGCAAGGTGGTCCATGCCTGTAATGCCCACACTTGGGAGGTAGAGACAGGAGGACCAGAAATTCAGGGCCATCTTTGACTATATAGCAACTTTAAGGCCTGCCTAGGCTACCTGACACACTGTCTTCATAAAAACCAAAACCAAACCGAAACAACAACAACAACAACAAAAATCCAGCTACTGCTGAAATGGTAACTGAGGCCCCGGTACAGTTCCTTACCCTTAGCTTTGAAAAAGAACTCACTGCTTTCAATCTAACGCTACCCTTTGTTGGTTGTTTGGTCACCAGTTAGGATTAGTCATGTTTTTCTACCCTTCGTGTCTTGTGATGTGAAACACTGTTACTGTGTTACTAGTTCTTGTGCACAATTCCAGCTCCTGAGCCAAGTTAAACATAACAGGAAGAGGAGAACTTGTTCCTAATTAGGTTTTCCTCATCTGTACAATGGGCTCAGAAGGATAGGGTCTCTGTAGAATGTTGTGACGGTTAAATGAGTTAAAATATATAGCTCACTTCAGGGAGCATAGGGCCGTGATACTGAAACAGCTCCCCTTCAAGGGCTCCCCTACGTGAGACCATGATCTGATCAAGCCAGAATGAAAAGTGTCTAAAGCCACACAGCCCAGCAGGTGTCAGAGGTGGGTTTGGAACTCAGATTCCCCGAGGCTTGGTGGGGGCTTGTGCTCTGCTGCACCCCACCGCCTTGACCTGGTCAATGTCACTTTGATAGAGTAGGACCCAGGCTGTTTGACAAAGGAGGGTAAAAGACCACAGGGATGCAGACTGTGAAGACCTTTAGGAACTTACATCTTTGTGTTTGCTTCCCTCCAG
Seq C2 exon
GTCCACTTCTTAAAGGAAGGATGTGGAGACGACAATGTCTGTAACAGCAACCTTAAGCTAGAGTATAAATTTGGTACCCGAGAAGGAAATCAAGACAAATTCTCTTACCTTCCAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001518:ENSRNOT00000002075:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=NA C2=0.051
Domain overlap (PFAM):
C1:
PF084417=Integrin_alpha2=FE(9.9=100)
A:
NA
C2:
PF084417=Integrin_alpha2=FE(8.0=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:
AACATCAGAGACAAGCTGCGC
R:
TGGAAGGTAAGAGAATTTGTCTTGA
Band lengths:
255-2140
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]