RnoINT0040319 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117698935-117699291:+
Coord C1 exon
chr8:117698935-117699078
Coord A exon
chr8:117699079-117699165
Coord C2 exon
chr8:117699166-117699291
Length
87 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CCTCTGTCTTTAATCCCCAGATC
3' ss Score
11.26
Exon sequences
Seq C1 exon
GGGTCGAGCGGACTTTGTTGCTTCCTGGGAGTCAGACAACCTTTGACTTAGATGATGTTCGAGCCGGGATTAGCTACACAGTGCGAGTGTCTGCTCGAGTGGGCACTCATGAGGGTGATGCCAGCACCCTCACCATCCACAGAG
Seq A exon
GTGAGCAATTTAGGAGACTTACGGGAGATGGCGACTGACTTGCTCCTGTCCTCATGTTGACCCTTGACCTCTGTCTTTAATCCCCAG
Seq C2 exon
ATCAAGAAGCCCCACTTATTATCCCAGGACTGCAGGTTGTGGCATCAGATGCAACAAGAATTAGAGTGGCCTGGGGACTTGTCCCTGGAGCCAGTGGATTTCGGATTAGCTGGAGGACAGGCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.184 A=NA C2=0.116
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(51.9=83.7)
A:
NA
C2:
PF0004116=fn3=PU(45.5=81.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTTCCTGGGAGTCAGACAA
R:
ATCTGATGCCACAACCTGCAG
Band lengths:
176-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]