RnoINT0040400 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117717202-117717431:+
Coord C1 exon
chr8:117717202-117717270
Coord A exon
chr8:117717271-117717395
Coord C2 exon
chr8:117717396-117717431
Length
125 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTCT
5' ss Score
2.68
3' ss Seq
TCACTGGGCATTCCCCACAGGTG
3' ss Score
10.45
Exon sequences
Seq C1 exon
GGGTTACCAGGTCTGCCCGGCCCTGTTGGACCTAAAGGAGAACCTGGACCTGTGGGGGCCCCTGGACAG
Seq A exon
GTGTCTCTTGGCTCTGCTCCCTACTCCCGGCCCACCCTGAAGCCTCAGTTTCTATCTACCCTCTGGGATGCAGGATGGGGTGGGAAGCCAGGGTGACTGAACCACTCACTGGGCATTCCCCACAG
Seq C2 exon
GTGGTGGTCGGGCCCCCTGGAGCAAAAGGCGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:87
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(33.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(16.9=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:
GGTTACCAGGTCTGCCCGG
R:
CTTCTCGCCTTTTGCTCCAGG
Band lengths:
104-229
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]