RnoINT0040332 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117703719-117704074:+
Coord C1 exon
chr8:117703719-117703845
Coord A exon
chr8:117703846-117703927
Coord C2 exon
chr8:117703928-117704074
Length
82 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGG
5' ss Score
9.31
3' ss Seq
CGAGATGCCCTCTTCCCCAGGCA
3' ss Score
6.53
Exon sequences
Seq C1 exon
GTTGGCCTGCTGTCCTACAGCCACCGGCCCTCCCCACTGTTCCCGCTGAATAGTTCTCACGATCTTGGTGTCATCTTGCAAAAGATCCGTGACATCCCCTATGTGGACCCAAGTGGTAACAACCTAG
Seq A exon
GTAAGGACCGCAGTCAGCATGGACTCCTGGGGATTTTCCATCAGGTTCAGTGTCTCAGGTTCCGAGATGCCCTCTTCCCCAG
Seq C2 exon
GCACAGCCGTGACCACAGCTCACAGATACCTCTTAGCACCCAATGCTCCCGGTCGCCGTCGGCAAGTGCCAGGCGTGATGGTACTGTTAGTGGATGAACCTCTGAGAGAAGACATATTGAGCCCCATTCGTGAGGCCCAGGCTTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.023 A=NA C2=0.040
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(23.9=100)
A:
NA
C2:
PF0009223=VWA=FE(27.8=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:
TCCCCTATGTGGACCCAAGTG
R:
CCTCACGAATGGGGCTCAATA
Band lengths:
168-250
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]