RnoINT0040359 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117696500-117696926:+
Coord C1 exon
chr8:117696500-117696661
Coord A exon
chr8:117696662-117696762
Coord C2 exon
chr8:117696763-117696926
Length
101 bp
Sequences
Splice sites
5' ss Seq
CTTGTAAGC
5' ss Score
4.33
3' ss Seq
TCCCCCAACCCCCTTCGCAGCCG
3' ss Score
7.07
Exon sequences
Seq C1 exon
GAATCAAGAACGCCGATCCTGAGGAACTGAAGCGCATCGCCTCACAGCCAACCAGCGATTTCTTCTTCTTTGTCAATGACTTCAGCATCTTGAGGACCCTGTTGCCCCTCATTTCCCGGAGGGTGTGCACCACGGCTGGTGGTGTGCCTGTGACCCTGCCTT
Seq A exon
GTAAGCTCCTGCCCATTCTGAGTACCCTGATCCCAGCCTGGGAGTGCTGACCTGTGCACTCCTCACCCCTGACCTATACTGTCCCCCAACCCCCTTCGCAG
Seq C2 exon
CCGATGACACTCCGTCTGGGCCCCGGGACCTGGTGCTGTCTGAGCCAAGTAGCCAATCCTTACGAGTACAGTGGACAGCAGCCAGTGGCCCTGTGACTGGCTACAAAATTCAGTACACGCCCCTGACGGGGCTAGGACAGCCACTGCCAAGTGAGCGAAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.182 A=NA C2=0.418
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.3=67.3)
A:
NA
C2:
PF0004116=fn3=PU(57.0=89.1)
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:
GATCCTGAGGAACTGAAGCGC
R:
TTTTGTAGCCAGTCACAGGGC
Band lengths:
256-357
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]