RnoINT0040325 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117700978-117701462:+
Coord C1 exon
chr8:117700978-117701124
Coord A exon
chr8:117701125-117701339
Coord C2 exon
chr8:117701340-117701462
Length
215 bp
Sequences
Splice sites
5' ss Seq
CACGTAGGA
5' ss Score
3.74
3' ss Seq
TTGTAATGCTCTCTCTTAAGCGC
3' ss Score
6.31
Exon sequences
Seq C1 exon
GTGGACCTATGAGACACCAGATAGTCCCAGGAAACAAAGACTCTGCAGAGATAACAGGTCTGGAAGGCGGAGTCAGCTACTCCGTGAGAGTGACGGCGCTTGTTGGAGACCGAGAGGGTGCACCCGTGTCCATTGTCGTCACCACAC
Seq A exon
GTAGGAGGATGCTTGGGTTGAAAGGAGTCTTGAACTGGGGCTTGTGTTCAAGGGATGGGGCTTATGGGGAAACGGTTTGTGCCGGGGTTGGAGAGGGATCGAGGATTTATAGTAAGCCTGTGTGTGTGGGTAAAGTCTGGGGGAGGAAACGTATTCAGTGCGGTCAGTCCAGCCTAGCGGGCAGAGCCTCCCTGATTGTAATGCTCTCTCTTAAG
Seq C2 exon
CGCCTGAGGTCCCAGCACCTCTGGAGACCCTTCAGGTAGTGCAGAGTGGGGAGCACTCCTTGAGGCTGCACTGGAACCGAGTCCCCGGAGCACAGGGCTTCCGTCTGCATTGGCAACCTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.440 A=NA C2=0.286
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(51.9=82.0)
A:
NA
C2:
PF0004116=fn3=PU(46.8=88.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGACCTATGAGACACCAGA
R:
TGCCAATGCAGACGGAAGC
Band lengths:
262-477
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]