RnoINT0040351 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117707270-117707422:+
Coord C1 exon
chr8:117707270-117707314
Coord A exon
chr8:117707315-117707386
Coord C2 exon
chr8:117707387-117707422
Length
72 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
GACCTCGTCTTTTCTCCCAGGGT
3' ss Score
9.1
Exon sequences
Seq C1 exon
GGTGATCGGGGACTGACAGGGACCCCGGGTGAGCCTGGAGAGAAG
Seq A exon
GTATGTAGAACATGGGGGGAGCTTGGGAGGATCTGGGACCATTCTCAGCTCTGACCTCGTCTTTTCTCCCAG
Seq C2 exon
GGTGAACGGGGACCACCTGGTCCCGTGGGACCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:42
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(16.3=100),PF0139113=Collagen=PU(13.1=53.3)
A:
NA
C2:
PF0139113=Collagen=PD(9.3=66.7),PF0139113=Collagen=FE(18.0=100)
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:
GGGACTGACAGGGACCCC
R:
CCAGGTGGTCCCCGTTCA
Band lengths:
57-129
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]