RnoINT0040402 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117717804-117718050:+
Coord C1 exon
chr8:117717804-117717845
Coord A exon
chr8:117717846-117718005
Coord C2 exon
chr8:117718006-117718050
Length
160 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TGTGACCCTTATGTCTATAGGGA
3' ss Score
8.47
Exon sequences
Seq C1 exon
GGAGCCCCAGGAGACCTTGCTGGAGCCCTGCTGGGTGAGCCG
Seq A exon
GTGAGTGTGACACCCTGACAGGAGGGGTCCCTTAACCCACAGTTTATCTATTTCCCTGACTCTTAGCTTTCACAAGATCCCTCCACATTTGACCCTGGCCTCCTTAAGATTTGTTTGTGACTGACACATGTGTGATCATATGTGACCCTTATGTCTATAG
Seq C2 exon
GGAGCCAAGGGTGACCGAGGACTGCCTGGACCACGGGGTGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:89
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=PD(12.3=57.1),PF0139113=Collagen=PU(10.9=42.9)
A:
NA
C2:
PF0139113=Collagen=FE(25.5=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:
GGAGCCCCAGGAGACCTTG
R:
CTTTTCACCCCGTGGTCCAG
Band lengths:
87-247
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]