RnoINT0040324 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117700762-117701124:+
Coord C1 exon
chr8:117700762-117700887
Coord A exon
chr8:117700888-117700977
Coord C2 exon
chr8:117700978-117701124
Length
90 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGG
5' ss Score
10.26
3' ss Seq
CTCTCCACTGGCCTGGCTAGGTG
3' ss Score
6.78
Exon sequences
Seq C1 exon
CTCCTGAGCCTGTAGGCAGTGTGTCAAAACTGCAAATCCTTAATGCTTCCAGTGATGTTCTCCGCGTCACTTGGGTGGGAGTCCCTGGAGCCACATCCTATAGACTGGCTTGGGGACGTAGTGAAG
Seq A exon
GTACGGCTCCATGACTCCATCCTGGTCCTTCCTGGCTACACGTGCCCTCTCTGGTTACCCCTAACTCTTACTCTCCACTGGCCTGGCTAG
Seq C2 exon
GTGGACCTATGAGACACCAGATAGTCCCAGGAAACAAAGACTCTGCAGAGATAACAGGTCTGGAAGGCGGAGTCAGCTACTCCGTGAGAGTGACGGCGCTTGTTGGAGACCGAGAGGGTGCACCCGTGTCCATTGTCGTCACCACAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.093 A=NA C2=0.440
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(46.8=86.0)
A:
NA
C2:
PF0004116=fn3=PD(51.9=82.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAGACTGGCTTGGGGACGTAG
R:
TGTGGTGACGACAATGGACAC
Band lengths:
172-262
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]